A Gene-Centered Method For Mapping 3’UTR-RBP Interactions: A Dissertation

Interactions between 3´ untranslated regions (UTRs) and RNA-binding proteins (RBPs) play critical roles in post-transcriptional gene regulation. Metazoan genomes encode hundreds of RBPs and thousands of 3’ UTRs have been experimentally identified, yet the spectrum of interactions between 3´UTRs and RBPs remains largely unknown. Several methods are available to map these interactions, including protein-centered methods such as RBP immunoprecipitation (RIP) and cross-link immunoprecipitation (CLIP), yeast three-hybrid assays and RNAcompete. However, there is a paucity of RNA-centered approaches for assaying an RNA element of interest against multiple RBPs in a parallel, scalable manner. Here, I present a strategy for delineating protein-RNA interaction networks using a gene centered approach. This approach includes annotating RBPs and identifying physical interactions between an RNA of interest and these RBPs using the Protein-RNA Interaction Mapping Assay (PRIMA). Few RBPs have been experimentally determined in most eukaryotic organisms. Therefore I show that existing RBP annotations can be supplemented using computational predictions of RNA binding domains (RBD) from protein sequences. A single RNA of interest can be tested using PRIMA against a library of RBPs constructed from these annotations. PRIMA utilizes the green fluorescent protein (GFP) in yeast as a reporter. PRIMA is based on reconstitution of the interaction between the 5´ and 3´ ends of an mRNA, which increases mRNA stability and enhances translation. PRIMA recapitulates known and uncovers new interactions involving RBPs from human, Caenorhabditis elegans and bacteriophage with short RNA fragments and full-length 3´UTRs. The development of RBP prey libraries will enable the testing of 3´UTRs against the hundreds of RBPs, which is essential to gain broad insights into post-transcriptional gene regulation at a systems level

Transcatheter treatment of severe mitral regurgitation in Brazil: a new kid on the block

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Water management for irrigation, crop yield and social attitudes: a socio-agricultural agent-based model to explore a collective action problem

When rainfall does not meet crop water requirements, supplemental irrigation is needed to maintain productivity. On-farm ponds can prevent excessive groundwater exploitation - to the benefit of the whole community - but they reduce the cultivated area and require investments by each farmer. Thus, choosing the source of water for irrigation (groundwatervson-farm pond) is a problem of collective action. An agent-based model is developed to simulate a smallholder farming system; the farmers' long-/short-view orientation determines the choice of the water source. We identify the most beneficial water source for economic gain and its stability, and how it can change across communities and under future climate scenarios. By using on-farm ponds, long-view-oriented farmers provide collective advantages but have individual advantages only under extreme climates; a tragedy of the commons is always possible. Changes in farmers' attitudes (and hence sources of water) based on previous experiences can worsen the economic outcome

Tratamento transcateter da insuficiência mitral grave no Brasil: uma novidade na área

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Three-Dimensional Angle Assessment and Plaque Distribution Classification in Left Main Disease: Impact of Geometry on Outcome.

Bifurcation geometry and plaque distribution in a diseased left main artery (LM) have the potential to drive operators' decisions regarding treatment strategies, techniques, and material selection. The three-dimensional (3D) geometry of the LM bifurcation typically results in specific patterns of plaque distribution. Plaque distribution may, in turn, significantly affect the procedural and long-term clinical and angiographic outcomes of LM percutaneous coronary intervention. Each LM bifurcation must be treated according to its unique anatomic and pathologic characteristics. Novel classification schemes of plaque distribution and 3D assessment may be valuable aids to obtaining a working picture of the bifurcation geometry

A dissipative algorithm for wave-like equations in the characteristic formulation

We present a dissipative algorithm for solving nonlinear wave-like equations when the initial data is specified on characteristic surfaces. The dissipative properties built in this algorithm make it particularly useful when studying the highly nonlinear regime where previous methods have failed to give a stable evolution in three dimensions. The algorithm presented in this work is directly applicable to hyperbolic systems proper of Electromagnetism, Yang-Mills and General Relativity theories. We carry out an analysis of the stability of the algorithm and test its properties with linear waves propagating on a Minkowski background and the scattering off a Scwharszchild black hole in General Relativity.Comment: 23 pages, 7 figure