Crystal structures of Thermotoga maritima reverse gyrase: inferences for the mechanism of positive DNA supercoiling

Reverse gyrase is an ATP-dependent topoisomerase that is unique to hyperthermophilic archaea and eubacteria. The only reverse gyrase structure determined to date has revealed the arrangement of the N-terminal helicase domain and the C-terminal topoisomerase domain that intimately cooperate to generate the unique function of positive DNA supercoiling. Although the structure has elicited hypotheses as to how supercoiling may be achieved, it lacks structural elements important for supercoiling and the molecular mechanism of positive supercoiling is still not clear. We present five structures of authentic Thermotoga maritima reverse gyrase that reveal a first view of two interacting zinc fingers that are crucial for positive DNA supercoiling. The so-called latch domain, which connects the helicase and the topoisomerase domains is required for their functional cooperation and presents a novel fold. Structural comparison defines mobile regions in parts of the helicase domain, including a helical insert and the latch that are likely important for DNA binding during catalysis. We show that the latch, the helical insert and the zinc fingers contribute to the binding of DNA to reverse gyrase and are uniquely placed within the reverse gyrase structure to bind and guide DNA during strand passage. A possible mechanism for positive supercoiling by reverse gyrases is presente

The reverse gyrase helicase-like domain is a nucleotide-dependent switch that is attenuated by the topoisomerase domain

Reverse gyrase is a topoisomerase that introduces positive supercoils into DNA in an ATP-dependent manner. It is unique to hyperthermophilic archaea and eubacteria, and has been proposed to protect their DNA from damage at high temperatures. Cooperation between its N-terminal helicase-like and the C-terminal topoisomerase domain is required for positive supercoiling, but the precise role of the helicase-like domain is currently unknown. Here, the characterization of the isolated helicase-like domain from Thermotoga maritima reverse gyrase is presented. We show that the helicase-like domain contains all determinants for nucleotide binding and ATP hydrolysis. Its intrinsic ATP hydrolysis is significantly stimulated by ssDNA, dsDNA and plasmid DNA. During the nucleotide cycle, the helicase-like domain switches between high- and low-affinity states for dsDNA, while its affinity for ssDNA in the ATP and ADP states is similar. In the context of reverse gyrase, the differences in DNA affinities of the nucleotide states are smaller, and the DNA-stimulated ATPase activity is strongly reduced. This inhibitory effect of the topoisomerase domain decelerates the progression of reverse gyrase through the nucleotide cycle, possibly providing optimal coordination of ATP hydrolysis with the complex reaction of DNA supercoiling

New urbanism, crime and the suburbs: a review of the evidence

Sustainability now influences government policy in the UK, Australia and USA and planning policy currently advocates high density, mixed-use residential developments in 'walkable', permeable neighbourhoods, close to public transport, employment and amenities. This clearly demonstrates the growing popularity, influence and application of New Urbanist ideas.This paper reviews the criminological research relating to New Urbanism associated with the three key issues of permeability, rear laneway car parking and mixed-use development. These key issues are discussed from an environmental criminology perspective and challenge New Urbanist assumptions concerning crime. The paper proposes that crime prevention through environmental design (CPTED) and its crime risk assessment model represents a valuable tool for New Urbanists to utilise to reduce opportunities for crime and tackle fear of crime in the community. Recommendations for future research and collaboration are discussed

Whose Sense of Place? A Political Ecology of Amenity Development

Using a political ecology framework, this chapter examines the ways in which sense of place and amenity migration contribute to alternative residential development, which relies on uneven use of conservation subdivision features in the American West. Using case studies from Central Oregon, this chapter demonstrates how senses of place and developer decision-making are tied to wider political economic changes. It highlights the roles that amenity migrants and developers, two groups that are sometimes identical, play in landscape transformations that simultaneously draw on a particular sense of place and commodify landscapes in new ways

Obesity, physical activity, and the urban environment: public health research needs

Persistent trends in overweight and obesity have resulted in a rapid research effort focused on built environment, physical activity, and overweight. Much of the focus of this research has been on the design and form of suburbs. It suggests that several features of the suburban built environment such as low densities, poor street connectivity and the lack of sidewalks are associated with decreased physical activity and an increased risk of being overweight. But compared to suburban residents, inner city populations have higher rates of obesity and inactivity despite living in neighborhoods that are dense, have excellent street connectivity and who's streets are almost universally lined with sidewalks. We suggest that the reasons for this apparent paradox are rooted in the complex interaction of land use, infrastructure and social factors affecting inner city populations. Sometimes seemingly similar features are the result of very different processes, necessitating different policy responses to meet these challenges. For example, in suburbs, lower densities can result from government decision making that leads to restrictive zoning and land use issues. In the inner city, densities may be lowered because of abandonment and disinvestment. In the suburbs, changes in land use regulations could result in a healthier built environment. In inner cities, increasing densities will depend on reversing economic trends and investment decisions that have systematically resulted in distressed housing, abandoned buildings and vacant lots. These varying issues need to be further studied in the context of the totality of urban environments, incorporating what has been learned from other disciplines, such as economics and sociology, as well as highlighting some of the more successful inner city policy interventions, which may provide examples for communities working to improve their health. Certain disparities among urban and suburban populations in obesity and overweight, physical activity and research focus have emerged that are timely to address. Comparable research on the relationship of built environment and health is needed for urban, especially inner city, neighborhoods

African Americans, Gentrification, and Neoliberal Urbanization: the Case of Fort Greene, Brooklyn

This article examines the gentrification of Fort Greene, which is located in the western part of black Brooklyn, one of the largest contiguous black urban areas in the USA. Between the late 1960s and 2003, gentrification in Fort Greene followed the patterns discovered by scholars of black neighborhoods; the gentrifying agents were almost exclusively black and gentrification as a process was largely bottom-up because entities interested in the production of space were mostly not involved. Since 2003, this has changed. Whites have been moving to Fort Greene in large numbers and will soon represent the numerical majority. Public and private interventions in and around Fort Greene have created a new top-down version of gentrification, which is facilitating this white influx. Existing black residential and commercial tenants are replaced and displaced in the name of urban economic development