Who’s in Charge? The Role of Power in Collaborative Governance and Forest Management.

Collaborative processes for working toward common management goals between individuals and organizations, despite their differences, emerged as one enduring legacy resulting from the Timber Wars in the American West during the late-1980s and the early 1990s. Power imbalances are often cited as a common problem in collaborative processes and can have a lasting, deleterious impact on the collaborative process and its outcomes. For all its importance, however, there is a yet unfulfilled need to understand the extent to which power and power imbalances affect collaborative relationships. Our research uses a case study approach to qualitatively analyze power dynamics within three collaborative efforts comprised of the United States Forest Service and community stakeholders. We identified four sources of power in play within the three case studies examined to include authority, resources, discursive legitimacy, and trust. We also discuss the application of these power sources and the ensuing outcomes. These powers, and the imbalance that sometimes result from their application, are representative of some of the underlying tensions that can be present in collaborative processes

Burning without borders : cooperatively managing wildfire risk in northern Colorado

2 pagesBecause wildfires don’t stop at ownership boundaries, managers from governmental and nongovernmental organizations in Northern Colorado are taking steps to pro-actively “co-manage” wildfire risk through the Northern Colorado Fireshed Collaborative (NCFC). For this research project, co-management refers to the collective actions taken by organizations to share the resources, costs, and burdens associated with managing fire risk across a large landscape. We examine factors that facilitated and limited wildfire risk co-management in a case study of the NCFC.FUNDER: Joint Fire Science Program

Who's in place, who's out of place : examining the politics of natural resource collaboration

A qualitative research approach composed of three strategies was employed to systematically examine the politics of natural resource collaboration. First, using the Oregon Plan for Salmon and Watersheds as a case study, the behavioral assumptions of natural resource policy instruments enabling collaboration were uncovered and analyzed. Three key assumptions emerge: 1) stakeholders are internally motivated by strong social values to work with others to save salmon and restore their watersheds; 2) stakeholders are willing to take action in their watershed but lack the capacity to do so, such as financial, technical, and information resources; 3) stakeholders are capable of learning about, testing, and processing feedback from alternative restoration approaches. Second, theoretical perspectives focusing on the social influence of place were integrated with Elinor Ostrom's behavioral theory of collective action. The resulting theoretical framework proposes that place is a variable that influences choice of behavioral strategies in natural resource collaboration by: 1) providing a means for stakeholders to identify and, therefore, understand how to relate to one another; and 2) influencing the probabilities that stakeholders can expect to interact with one another in the future. Third, a qualitative, comparative case study of two watershed councils in western Oregon applied the framework and identified three key dimensions of group identification related to place: 1) group identities related to stakeholders' interest and values in the watershed; 2) group identities related to stakeholders' ways of knowing the watershed; and 3) group identities related to social ties within the watershed. The qualitative research approach sheds light on the diverse behaviors stakeholders exhibit in natural resource collaboration. It challenges the notion that stakeholders are strictly motivated to maximize material self-interest in natural resource politics. Stakeholders vary in their interactions depending on the geographic scale of the landscape in question. The study also provides compelling evidence that stakeholders' collective identification to a shared place generates a higher likelihood of sustaining collaborative relationships and trust in one another

Genome-wide discovery and characterization of maize long non-coding RNAs

BACKGROUND Long non-coding RNAs (lncRNAs) are transcripts that are 200 bp or longer, do not encode proteins, and potentially play important roles in eukaryotic gene regulation. However, the number, characteristics and expression inheritance pattern of lncRNAs in maize are still largely unknown. RESULTS By exploiting available public EST databases, maize whole genome sequence annotation and RNA-seq datasets from 30 different experiments, we identified 20,163 putative lncRNAs. Of these lncRNAs, more than 90% are predicted to be the precursors of small RNAs, while 1,704 are considered to be high-confidence lncRNAs. High confidence lncRNAs have an average transcript length of 463 bp and genes encoding them contain fewer exons than annotated genes. By analyzing the expression pattern of these lncRNAs in 13 distinct tissues and 105 maize recombinant inbred lines, we show that more than 50% of the high confidence lncRNAs are expressed in a tissue-specific manner, a result that is supported by epigenetic marks. Intriguingly, the inheritance of lncRNA expression patterns in 105 recombinant inbred lines reveals apparent transgressive segregation, and maize lncRNAs are less affected by cis- than by trans-genetic factors. CONCLUSIONS We integrate all available transcriptomic datasets to identify a comprehensive set of maize lncRNAs, provide a unique annotation resource of the maize genome and a genome-wide characterization of maize lncRNAs, and explore the genetic control of their expression using expression quantitative trait locus mapping

Secondary Structure, a Missing Component of Sequence-Based Minimotif Definitions

Minimotifs are short contiguous segments of proteins that have a known biological function. The hundreds of thousands of minimotifs discovered thus far are an important part of the theoretical understanding of the specificity of protein-protein interactions, posttranslational modifications, and signal transduction that occur in cells. However, a longstanding problem is that the different abstractions of the sequence definitions do not accurately capture the specificity, despite decades of effort by many labs. We present evidence that structure is an essential component of minimotif specificity, yet is not used in minimotif definitions. Our analysis of several known minimotifs as case studies, analysis of occurrences of minimotifs in structured and disordered regions of proteins, and review of the literature support a new model for minimotif definitions that includes sequence, structure, and function. © 2012 Sargeant et al

UroMark-a urinary biomarker assay for the detection of bladder cancer.

BACKGROUND: Bladder cancer (BC) is one of the most common cancers in the western world and ranks as the most expensive to manage, due to the need for cystoscopic examination. BC shows frequent changes in DNA methylation, and several studies have shown the potential utility of urinary biomarkers by detecting epigenetic alterations in voided urine. The aim of this study is to develop a targeted bisulfite next-generation sequencing assay to diagnose BC from urine with high sensitivity and specificity. RESULTS: We defined a 150 CpG loci biomarker panel from a cohort of 86 muscle-invasive bladder cancers and 30 normal urothelium. Based on this panel, we developed the UroMark assay, a next-generation bisulphite sequencing assay and analysis pipeline for the detection of bladder cancer from urinary sediment DNA. The 150 loci UroMark assay was validated in an independent cohort (n = 274, non-cancer (n = 167) and bladder cancer (n = 107)) voided urine samples with an AUC of 97%. The UroMark classifier sensitivity of 98%, specificity of 97% and NPV of 97% for the detection of primary BC was compared to non-BC urine. CONCLUSIONS: Epigenetic urinary biomarkers for detection of BC have the potential to revolutionise the management of this disease. In this proof of concept study, we show the development and utility of a novel high-throughput, next-generation sequencing-based biomarker for the detection of BC-specific epigenetic alterations in urine

The expanding functional roles and signaling mechanisms of adhesion G protein–coupled receptors

The adhesion class of G protein–coupled receptors (GPCRs) is the second largest family of GPCRs (33 members in humans). Adhesion GPCRs (aGPCRs) are defined by a large extracellular N‐terminal region that is linked to a C‐terminal seven transmembrane (7TM) domain via a GPCR‐autoproteolysis inducing (GAIN) domain containing a GPCR proteolytic site (GPS). Most aGPCRs undergo autoproteolysis at the GPS motif, but the cleaved fragments stay closely associated, with the N‐terminal fragment (NTF) bound to the 7TM of the C‐terminal fragment (CTF). The NTFs of most aGPCRs contain domains known to be involved in cell–cell adhesion, while the CTFs are involved in classical G protein signaling, as well as other intracellular signaling. In this workshop report, we review the most recent findings on the biology, signaling mechanisms, and physiological functions of aGPCRs