Social science to improve fuels management: A synthesis of research on collaboration

This document is part of the Fuels Planning: Science Synthesis and Integration Project, a pilot project initiated by the USDA Forest Service to respond to the need for tools and information useful for planning site-specific fuel (vegetation) treatment projects. The information addresses fuel and forest conditions of the dry inland forests of the Western United States: those dominated by ponderosa pine, Douglas-fir, dry grand fir/white fir, and dry lodgepole pine potential vegetation types. Information was developed primarily for application at the stand level and is intended to be useful within this forest type regardless of ownership. Portions of the information also will be directly applicable to the pinyon pine/juniper potential vegetation types. Many of the concepts and tools developed by the project may be useful for planning fuel projects in other forest types. In particular, many of the social science findings would have direct applicability to fuel planning activities for forests throughout the United States

Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator

The rapid accumulation of whole-genome data has renewed interest in the study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research all require models and algorithms to elucidate the mechanisms, history, and consequences of these rearrangements. However, even simple models lead to NP-hard problems, particularly in the area of phylogenetic analysis. Current approaches are limited to small collections of genomes and low-resolution data (typically a few hundred syntenic blocks). Moreover, whereas phylogenetic analyses from sequence data are deemed incomplete unless bootstrapping scores (a measure of confidence) are given for each tree edge, no equivalent to bootstrapping exists for rearrangement-based phylogenetic analysis. We describe a fast and accurate algorithm for rearrangement analysis that scales up, in both time and accuracy, to modern high-resolution genomic data. We also describe a novel approach to estimate the robustness of results-an equivalent to the bootstrapping analysis used in sequence-based phylogenetic reconstruction. We present the results of extensive testing on both simulated and real data showing that our algorithm returns very accurate results, while scaling linearly with the size of the genomes and cubically with their number. We also present extensive experimental results showing that our approach to robustness testing provides excellent estimates of confidence, which, moreover, can be tuned to trade off thresholds between false positives and false negatives. Together, these two novel approaches enable us to attack heretofore intractable problems, such as phylogenetic inference for high-resolution vertebrate genomes, as we demonstrate on a set of six vertebrate genomes with 8,380 syntenic blocks. A copy of the software is available on demand

SCJ: A Variant of Breakpoint Distance for Which Sorting, Genome Median and Genome Halving Problems Are Easy

Feijão P, Meidanis J. SCJ: A Variant of Breakpoint Distance for Which Sorting, Genome Median and Genome Halving Problems Are Easy. In: Salzberg SL, Warnow T, eds. Algorithms in Bioinformatics. Lecture Notes in Computer Science. Vol 5724. Berlin, Heidelberg: Springer Berlin Heidelberg; 2009: 85-96

Deregulation of the Egfr/Ras Signaling Pathway Induces Age-related Brain Degeneration in the Drosophila Mutant vap

Ras signaling has been shown to play an important role in promoting cell survival in many different tissues. Here we show that upregulation of Ras activity in adult Drosophila neurons induces neuronal cell death, as evident from the phenotype of vacuolar peduncle (vap) mutants defective in the Drosophila RasGAP gene, which encodes a Ras GTPase-activating protein. These mutants show age-related brain degeneration that is dependent on activation of the EGF receptor signaling pathway in adult neurons, leading to autophagic cell death (cell death type 2). These results provide the first evidence for a requirement of Egf receptor activity in differentiated adult Drosophila neurons and show that a delicate balance of Ras activity is essential for the survival of adult neurons