Geography, News Media Discourse, and Water Management: A Case Study of the Devils Lake Outlet

This thesis explores the print news media discourse surrounding the dispute between Manitoba and North Dakota over a flood mitigation plan in Devils Lake North Dakota. In order to do so, critical discourse analysis was applied to news media from a seventeen year period during the dispute. Findings were compared between media sources as well as to pertinent policy documents. The thesis finds that the political arena provided by local newspapers as well as the discourses of scale, confrontation, history, and economics had the largest effect on the dispute’s public face. A total of nine findings within these areas are discussed for their relationship to the dispute. Existing concepts from within geography are acknowledged to place these insights into the broader set of geographical and water management discussions. It is concluded that research on environmental conflicts needs to pay special attention to news media and other forms of discourse creation, or promotion, in the public sphere in order to better understand these conflicts, broaden the scope of values involved and promote the potential for efficient conflict resolution and water management

The Governance of Climate Change Adaptation in Canada: Two Multilevel Case Studies

Anthropogenic climate change is affecting, and will continue to affect, communities across Canada. From increased average temperatures and alterations of seasonal precipitation patterns, to extreme rainfall and heat events, Canadians face a 21st century environment significantly different from that of the past. With risks to people and services identified via the global scientific and social science literature, the need to adapt to climate change is pressing. Climate change adaptation includes the identification of climate impacts in order to develop interventions into systems and services so to avoid negative effects and recognize opportunities. The emerging consensus is that climate change adaptation is challenged by the complexity of the cross-sector and cross-scale nature of climate impacts and the systems and services which are vulnerable to them. Due to jurisdictional divisions and public-private divides in many climate-impacted systems, adaptation scholarship has increasingly turned to the study of governance to conceptualize and overcome challenges. To contribute to this field, this study engages in an in-depth characterization of the current governance of climate change adaptation in Canada. Using an established theoretical framework of competing governance modes, the study characterizes adaptation governance in two Canadian sites as well as identifies the preferred visions of governing processes according to expert practitioners. Through analysis of key documents, eighty-one in-depth interviews, and two expert workshops, the thesis provides a number of novel insights for Canadian and international scholarship. In the thesis it is argued that the study of adaptation governance benefits from the application of a typology of competing governance modes. Further, the study identifies that current adaptation efforts in the Canadian sites are dominated by network processes and that the concept of network failure is consistent with the observed adaptation implementation deficit. Finally, it is revealed that practitioners at different scales of government in Canada’s federal structure idealize the governance of adaptation in drastically different ways, with local respondents providing critiques of network processes and increased interest in hierarchical governance. As climate impacts are projected to worsen in the coming decades, the findings of the study offer crucial insights for intervention into the governance of climate change adaptation

Applying a Typology of Governance Modes to Climate Change Adaptation

Climate change adaptation is a complex field of public policy that requires action by multiple levels of government, the private sector, and civil society. In recent years, increasing scholarly attention has been focused on the governance of adaptation, which has included exploring alternatives to state-centric models of decision-making and identifying appropriate roles and responsibilities of multiple actors to achieve desired outcomes. Scholars have called for greater clarity in distinguishing between different approaches to adaptation governance. Drawing on the rich scholarship about public governance, this article articulates and applies a typology of four modes of governance by which adaptation takes place (hierarchy, market, network, and community). Using examples of initiatives from across Canada, the article offers a framework for describing, comparing, and evaluating the governance of adaptation initiatives

Engineering the protein dynamics of an ancestral luciferase.

Protein dynamics are often invoked in explanations of enzyme catalysis, but their design has proven elusive. Here we track the role of dynamics in evolution, starting from the evolvable and thermostable ancestral protein AncHLD-RLuc which catalyses both dehalogenase and luciferase reactions. Insertion-deletion (InDel) backbone mutagenesis of AncHLD-RLuc challenged the scaffold dynamics. Screening for both activities reveals InDel mutations localized in three distinct regions that lead to altered protein dynamics (based on crystallographic B-factors, hydrogen exchange, and molecular dynamics simulations). An anisotropic network model highlights the importance of the conformational flexibility of a loop-helix fragment of Renilla luciferases for ligand binding. Transplantation of this dynamic fragment leads to lower product inhibition and highly stable glow-type bioluminescence. The success of our approach suggests that a strategy comprising (i) constructing a stable and evolvable template, (ii) mapping functional regions by backbone mutagenesis, and (iii) transplantation of dynamic features, can lead to functionally innovative proteins

Fluorescent substrates for haloalkane dehalogenases: Novel probes for mechanistic studies and protein labeling

Haloalkane dehalogenases are enzymes that catalyze the cleavage of carbon-halogen bonds in halogenated compounds. They serve as model enzymes for studying structure-function relationships of >100.000 members of the alpha/beta-hydrolase superfamily. Detailed kinetic analysis of their reaction is crucial for understanding the reaction mechanism and developing novel concepts in protein engineering. Fluorescent substrates, which change their fluorescence properties during a catalytic cycle, may serve as attractive molecular probes for studying the mechanism of enzyme catalysis. In this work, we present the development of the first fluorescent substrates for this enzyme family based on coumarin and BODIPY chromophores. Steady-state and pre-steady-state kinetics with two of the most active haloalkane dehalogenases, DmmA and LinB, revealed that both fluorescent substrates provided specificity constant two orders of magnitude higher (0.14-12.6 mu M(-1)s(-1)) than previously reported representative substrates for the haloalkane dehalogenase family (0.00005-0.014 mu M(-1)s(-1)). Stopped-flow fluorescence/FRET analysis enabled for the first time monitoring of all individual reaction steps within a single experiment: (i) substrate binding, (ii-iii) two subsequent chemical steps and (iv) product release. The newly introduced fluorescent molecules are potent probes for fast steady-state kinetic profiling. In combination with rapid mixing techniques, they provide highly valuable information about individual kinetic steps and mechanism of haloalkane dehalogenases. Additionally, these molecules offer high specificity and efficiency for protein labeling and can serve as probes for studying protein hydration and dynamics as well as potential markers for cell imaging. (C) 2020 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology

The effect of anthropogenic arsenic contamination on the earthworm microbiome

Earthworms are globally distributed and perform essential roles for soil health and microbial structure. We have investigated the effect of an anthropogenic contamination gradient on the bacterial community of the keystone ecological species Lumbricus rubellus through utilising 16S rRNA pyrosequencing to establish the microbiome of the host and surrounding soil. The earthworm-associated microbiome differs from the surrounding environment which appears to be a result of both filtering and stimulation likely linked to the altered environment associated with the gut micro-habitat (neutral pH, anoxia and increased carbon substrates). We identified a core earthworm community comprising Proteobacteria (~50%) and Actinobacteria (~30%), with lower abundances of Bacteroidetes (~6%) and Acidobacteria (~3%). In addition to the known earthworm symbiont (Verminephrobacter sp.) we identified a potential host-associated Gammaproteobacteria species (Serratia sp.) which was absent from soil yet observed in most earthworms. Although a distinct bacterial community defines these earthworms, clear family- and species-level modification were observed along an arsenic and iron contamination gradient. Several taxa observed in uncontaminated control microbiomes are suppressed by metal/metalloid field exposure, including eradication of the hereto ubiquitously associated Verminephrobacter symbiont, which raises implications to its functional role in the earthworm microbiome

Engineering the protein dynamics of an ancestral luciferase

Abstract: Protein dynamics are often invoked in explanations of enzyme catalysis, but their design has proven elusive. Here we track the role of dynamics in evolution, starting from the evolvable and thermostable ancestral protein AncHLD-RLuc which catalyses both dehalogenase and luciferase reactions. Insertion-deletion (InDel) backbone mutagenesis of AncHLD-RLuc challenged the scaffold dynamics. Screening for both activities reveals InDel mutations localized in three distinct regions that lead to altered protein dynamics (based on crystallographic B-factors, hydrogen exchange, and molecular dynamics simulations). An anisotropic network model highlights the importance of the conformational flexibility of a loop-helix fragment of Renilla luciferases for ligand binding. Transplantation of this dynamic fragment leads to lower product inhibition and highly stable glow-type bioluminescence. The success of our approach suggests that a strategy comprising (i) constructing a stable and evolvable template, (ii) mapping functional regions by backbone mutagenesis, and (iii) transplantation of dynamic features, can lead to functionally innovative proteins

CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures

ABSTRACT Summary: The transport of ligands, ions or solvent molecules into proteins with buried binding sites or through the membrane is enabled by protein tunnels and channels. CAVER Analyst is a software tool for calculation, analysis and real-time visualization of access tunnels and channels in static and dynamic protein structures. It provides an intuitive graphic user interface for setting up the calculation and interactive exploration of identified tunnels/channels and their characteristics. Availability and Implementation: CAVER Analyst is a multi-platform software written in JAVA. Binaries and documentation are freely available for non-commercial use at http://www.caver.cz