Kinetic modelling of competition and depletion of shared miRNAs by competing endogenous RNAs

Non-conding RNAs play a key role in the post-transcriptional regulation of mRNA translation and turnover in eukaryotes. miRNAs, in particular, interact with their target RNAs through protein-mediated, sequence-specific binding, giving rise to extended and highly heterogeneous miRNA-RNA interaction networks. Within such networks, competition to bind miRNAs can generate an effective positive coupling between their targets. Competing endogenous RNAs (ceRNAs) can in turn regulate each other through miRNA-mediated crosstalk. Albeit potentially weak, ceRNA interactions can occur both dynamically, affecting e.g. the regulatory clock, and at stationarity, in which case ceRNA networks as a whole can be implicated in the composition of the cell's proteome. Many features of ceRNA interactions, including the conditions under which they become significant, can be unraveled by mathematical and in silico models. We review the understanding of the ceRNA effect obtained within such frameworks, focusing on the methods employed to quantify it, its role in the processing of gene expression noise, and how network topology can determine its reach.Comment: review article, 29 pages, 7 figure

Infectious Disease Ontology

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain

Ecosystem services from smallholder forestry and agroforestry in the tropics

Smallholder forestry and agroforestry systems in the tropics provide essential products and services for millions of producers, their surrounding communities, national and international consumers, and global society. The diversity of products provided by these systems meet the needs of smallholder producers for fuelwood, food, animal fodder, and other household and farm needs; they provide additional income to supplement major commodity crops; and they offer flexibility in production and income to buffer against falling commodity prices, crop failure, or other sources of financial or economic difficulty. The sustainability of these systems is increasingly dependent upon sources of income beyond the sale of conventional products, such as price premiums from sustainability certification and agro- and ecotourism. Payments for ecosystem services (PES) programs have been developed at multiple levels to provide incentives for smallholders to conserve and enhance tree cover and management practices to provide ecosystem services such as watershed protection and carbon sequestration. Ecotourism provides an enterprise-based strategy to engage producers in conservation and enhancement of these services. This review evaluates the ability of smallholder systems to support the provision of ecosystem services (ES) and the capacity of smallholders to participate in support programs and take advantage of other emerging opportunities to support smallholder enterprises