BackgroundThe design and construction of novel biological systems by combining basic building blocks represents a dominant paradigm in synthetic biology. Creating and maintaining a database of these building blocks is a way to streamline the fabrication of complex constructs. The Registry of Standard Biological Parts (Registry) is the most advanced implementation of this idea.Methods/Principal FindingsBy analyzing inclusion relationships between the sequences of the Registry entries, we build a network that can be related to the Registry abstraction hierarchy. The distribution of entry reuse and complexity was extracted from this network. The collection of clones associated with the database entries was also analyzed. The plasmid inserts were amplified and sequenced. The sequences of 162 inserts could be confirmed experimentally but unexpected discrepancies have also been identified.Conclusions/SignificanceOrganizational guidelines are proposed to help design and manage this new type of scientific resources. In particular, it appears necessary to compare the cost of ensuring the integrity of database entries and associated biological samples with their value to the users. The initial strategy that permits including any combination of parts irrespective of its potential value leads to an exponential and economically unsustainable growth that may be detrimental to the quality and long-term value of the resource to its users.

Agroecosystem nitrogen (N) loss produces greenhouse gases, induces eutrophication, and is costly for farmers; therefore, conservation agricultural management practices aimed at reducing N loss are increasingly adopted. However, the ecosystem consequences of these practices have not been well-studied. We quantified N loss via leaching, NH3 volatilization, N2O emissions, and N retention in plant and soil pools of corn conservation agroecosystems in Kentucky, USA. Three systems were evaluated: (1) an unfertilized, organic system with cover crops hairy vetch (Vicia villosa), winter wheat (Triticum aestivum), or a mix of the two (bi-culture); (2) an organic system with a hairy vetch cover crop employing three fertilization schemes (0 N, organic N, or a fertilizer N-credit approach); and (3) a conventional system with a winter wheat cover crop and three fertilization schemes (0 N, urea N, or organic N). In the unfertilized organic system, cover crop species affected NO3-N leaching (vetch > bi-culture > wheat) and N2O-N emissions and yield during corn growth (vetch, bi-culture > wheat). Fertilization increased soil inorganic N, gaseous N loss, N leaching, and yield in the organic vetch and conventional wheat systems. Fertilizer scheme affected the magnitude of growing season N2O-N loss in the organic vetch system (organic N > fertilizer N-credit) and the timing of loss (organic N delayed N2O-N loss vs. urea) and NO3-N leaching (urea >> organic N) in the conventional wheat system, but had no effect on yield. Cover crop selection and N fertilization techniques can reduce N leaching and greenhouse gas emissions without sacrificing yield, thereby enhancing N conservation in both organic and conventional conservation agriculture systems.

ABSTRACT. Experiments to create spaces for social-ecological transformation are multiplying. These experiments aim at transcending traditional spaces for rational deliberation, planning, and participatory decision-making. We present a methodological approach for triggering the emergence of "transformation laboratories" (T-labs), which are participatory spaces where new agency is activated in relation to a stagnant sustainability challenge to generate intentional bottom-up transformations. We applied a set of participatory research tools to elicit current perceptions and foster personal involvement in transforming the ongoing urbanization of a culturally and ecologically significant historical wetland in Mexico City. Given that the emergence of T-labs as genuine bottom-up transformative spaces involves changes at multiple levels (individual, collective, and social-ecological), our approach was designed to promote a safe space that stimulates openness and personal interaction. We posit that through enabling participants to reformulate their connections to the system, to others in the system, and to themselves, the system may be transformed from the inside out. We argue that transformation, in this sense, is essentially about how changes in perception about one's own role in the system's dynamics translate into changes in agency. Our T-lab brought in 19 agents involved in the use and management of the Xochimilco urban wetland. Through a set of research tools, we elicited and presented information that helped agents to see their social-ecological position and role and to identify the practices they share with others within specific social networks and spaces of action. We argue that the process of collaboration initiated by our application of these tools and communication of their results are key for advancing initiatives that seek to create conditions for endogenous transformations.

We explore how loss of livelihood, loss of ecological function, and loss of group identity are linked in the process of social-ecological change through the narratives of stakeholders associated with the wetland of Xochimilco in Mexico City. Drawing from interviews, focus groups, and participatory workshops with a variety of residents and city administrators, we analyze narratives about what is valued, what is problematized, and what social and ecological relationships appear as critical from the perspective of contemporary residents and officials. Loss is prominent in these narratives, capturing the interdependence of ecology, identity, meaning, and livelihood for the inhabitants. We trace these narratives to the historical roots of center-periphery politics of land and water use, situating the current dynamic context within the social-ecological system's long pathway of change. Diffuse blame for social-ecological change expressed in the narratives appears to inhibit collective action, as does a conflicted history of local response to the city's control of resources. We posit that finding a sustainable pathway forward may depend in part on how residents are able to cognitively or emotionally accommodate landscape change while still enabling the values they have come to associate with the landscape. Such accommodation may entail accepting some degree of loss in system function and structure, but this loss may also provide opportunities for new social-ecological relations that enable the persistence of local identity.

Cities are far more than the people who reside within them, the activities that drive urban dynamism, and hard and soft infrastructure that create urban structure and form. Cities are also composed of stories-narratives-that emerge from the experiences, ideas, knowledge and agendas of urban residents, administrators, and individuals with stakes in the city's future. These narratives collectively not only reflect how the material landscape is perceived and socially and culturally appropriated, but also, by motivating and rationalizing human actions, contribute to shaping that material world, including the behavior and attitudes of humans within it. Here, we explore the narratives and associated solution pathways that have emerged and consolidated around the issue of water scarcity and flooding in the megalopolis of Mexico City. Effective and sustainable management of water resources has long been considered essential to the city's future, yet many scholars consider the city "stuck" in path-dependent development trajectories that seems unable to address pervasive social inequity, infrastructure fragility, and the city's precarious supplies. Through mental model data elicited from qualitative interviews and workshops with a cross section of urban stakeholders, we identify dominant narratives that articulate distinct causal premises and consequences associated with water related risk in the city. We juxtapose these narratives with the current and proposed solution pathways proposed by the interviewees. Our analysis demonstrates how, on the one hand, dominant narratives may quell innovation, and on the other, narratives collectively can foster the seeds of urban sustainability transformation.