Integration of Expressed Sequence Tag Data Flanking Predicted RNA Secondary Structures Facilitates Novel Non-Coding RNA Discovery

Many computational methods have been used to predict novel non-coding RNAs (ncRNAs), but none, to our knowledge, have explicitly investigated the impact of integrating existing cDNA-based Expressed Sequence Tag (EST) data that flank structural RNA predictions. To determine whether flanking EST data can assist in microRNA (miRNA) prediction, we identified genomic sites encoding putative miRNAs by combining functional RNA predictions with flanking ESTs data in a model consistent with miRNAs undergoing cleavage during maturation. In both human and mouse genomes, we observed that the inclusion of flanking ESTs adjacent to and not overlapping predicted miRNAs significantly improved the performance of various methods of miRNA prediction, including direct high-throughput sequencing of small RNA libraries. We analyzed the expression of hundreds of miRNAs predicted to be expressed during myogenic differentiation using a customized microarray and identified several known and predicted myogenic miRNA hairpins. Our results indicate that integrating ESTs flanking structural RNA predictions improves the quality of cleaved miRNA predictions and suggest that this strategy can be used to predict other non-coding RNAs undergoing cleavage during maturation

Smooth Muscle Strips for Intestinal Tissue Engineering

Functionally contracting smooth muscle is an essential part of the engineered intestine that has not been replicated in vitro. The purpose of this study is to produce contracting smooth muscle in culture by maintaining the native smooth muscle organization. We employed intact smooth muscle strips and compared them to dissociated smooth muscle cells in culture for 14 days. Cells isolated by enzymatic digestion quickly lost maturity markers for smooth muscle cells and contained few enteric neural and glial cells. Cultured smooth muscle strips exhibited periodic contraction and maintained neural and glial markers. Smooth muscle strips cultured for 14 days also exhibited regular fluctuation of intracellular calcium, whereas cultured smooth muscle cells did not. After implantation in omentum for 14 days on polycaprolactone scaffolds, smooth muscle strip constructs expressed high levels of smooth muscle maturity markers as well as enteric neural and glial cells. Intact smooth muscle strips may be a useful component for engineered intestinal smooth muscle

Adjusting wastewater treatment effluent standards to protect the receiving waters: the case of low flow rivers in central Spain

[EN] Freshwater quality is deteriorating worldwide. In populated areas, urban pollution is the main pressure on surface continental waters, but intensive wastewater treatment is costly. Setting standards for treatment of wastewater before discharge is a major policy instrument for water authorities, balancing environmental gains and operational costs. Discharge permits usually define concentration limits at the discharge point of the plant effluent. This approach, however, may not guarantee the good status of the receiving waters. Discharge permits should be directly linked to pollutant concentration in the river. Our paper develops an approach to adaptively adjust discharge permits and applies it to Madrid and the Manzanares river, a city of more than 3 million inhabitants discharging its treated wastewater to a stream having less than 2 m(3) s(-1) average flow. Stricter limits to 5-day biological oxygen demand (11 mg O-2 L-1), ammonium (0.5 mg N-NH4 L-1), nitrate (5.9 mg N-NO3 L-1), and phosphate (0.17 mg P-PO4 L-1) at plant effluent are required to meet the river environmental objectives. The results can be generalized to assess wastewater management decisions in other geographical areas.The authors wish to thank the Tagus River Basin Authority (Confederacion Hidrografica del Tajo) for their availability and readiness to share information, and the anonymous reviewers for their valuable and constructive comments. This research was funded by the Botin Foundation, Spain.Bolinches, A.; De Stefano, L.; Paredes Arquiola, J. (2020). Adjusting wastewater treatment effluent standards to protect the receiving waters: the case of low flow rivers in central Spain. 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