Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane

Abstract Background MicroRNAs (miRNAs) are small regulatory RNAs, some of which are conserved in diverse plant genomes. Therefore, computational identification and further experimental validation of miRNAs from non-model organisms is both feasible and instrumental for addressing miRNA-based gene regulation and evolution. Sugarcane (Saccharum spp.) is an important biofuel crop with publicly available expressed sequence tag and genomic survey sequence databases, but little is known about miRNAs and their targets in this highly polyploid species. Results In this study, we have computationally identified 19 distinct sugarcane miRNA precursors, of which several are highly similar with their sorghum homologs at both nucleotide and secondary structure levels. The accumulation pattern of mature miRNAs varies in organs/tissues from the commercial sugarcane hybrid as well as in its corresponding founder species S. officinarum and S. spontaneum. Using sugarcane MIR827 as a query, we found a novel MIR827 precursor in the sorghum genome. Based on our computational tool, a total of 46 potential targets were identified for the 19 sugarcane miRNAs. Several targets for highly conserved miRNAs are transcription factors that play important roles in plant development. Conversely, target genes of lineage-specific miRNAs seem to play roles in diverse physiological processes, such as SsCBP1. SsCBP1 was experimentally confirmed to be a target for the monocot-specific miR528. Our findings support the notion that the regulation of SsCBP1 by miR528 is shared at least within graminaceous monocots, and this miRNA-based post-transcriptional regulation evolved exclusively within the monocots lineage after the divergence from eudicots. Conclusions Using publicly available nucleotide databases, 19 sugarcane miRNA precursors and one new sorghum miRNA precursor were identified and classified into 14 families. Comparative analyses between sugarcane and sorghum suggest that these two species retain homologous miRNAs and targets in their genomes. Such conservation may help to clarify specific aspects of miRNA regulation and evolution in the polyploid sugarcane. Finally, our dataset provides a framework for future studies on sugarcane RNAi-dependent regulatory mechanisms.

Risk analysis of light-frame wood construction due to multiple hazards

Light-frame wood buildings are widely built in the United States (U.S.). Natural hazards cause huge losses to light-frame wood construction. This study proposes methodologies and a framework to evaluate the performance and risk of light-frame wood construction. Performance-based engineering (PBE) aims to ensure that a building achieves the desired performance objectives when subjected to hazard loads. In this study, the collapse risk of a typical one-story light-frame wood building is determined using the Incremental Dynamic Analysis method. The collapse risks of buildings at four sites in the Eastern, Western, and Central regions of U.S. are evaluated. Various sources of uncertainties are considered in the collapse risk assessment so that the influence of uncertainties on the collapse risk of lightframe wood construction is evaluated. The collapse risks of the same building subjected to maximum considered earthquakes at different seismic zones are found to be non-uniform. In certain areas in the U.S., the snow accumulation is significant and causes huge economic losses and threatens life safety. Limited study has been performed to investigate the snow hazard when combined with a seismic hazard. A Filtered Poisson Process (FPP) model is developed in this study, overcoming the shortcomings of the typically used Bernoulli model. The FPP model is validated by comparing the simulation results to weather records obtained from the National Climatic Data Center. The FPP model is applied in the proposed framework to assess the risk of a light-frame wood building subjected to combined snow and earthquake loads. The snow accumulation has a significant influence on the seismic losses of the building. The Bernoulli snow model underestimates the seismic loss of buildings in areas with snow accumulation. An object-oriented framework is proposed in this study to performrisk assessment for lightframe wood construction. For home owners and stake holders, risks in terms of economic losses is much easier to understand than engineering parameters (e.g., inter story drift). The proposed framework is used in two applications. One is to assess the loss of the building subjected to mainshock-aftershock sequences. Aftershock and downtime costs are found to be important factors in the assessment of seismic losses. The framework is also applied to a wood building in the state of Washington to assess the loss of the building subjected to combined earthquake and snow loads. The proposed framework is proven to be an appropriate tool for risk assessment of buildings subjected to multiple hazards. Limitations and future works are also identified.