Population Dynamics and Community Composition of Ammonia Oxidizers in Salt Marshes after the Deepwater Horizon Oil Spill

The recent oil spill in the Gulf of Mexico had significant effects on microbial communities in the Gulf, but impacts on nitrifying communities in adjacent salt marshes have not been investigated. We studied persistent effects of oil on ammonia-oxidizing archaeal (AOA) and bacterial (AOB) communities and their relationship to nitrification rates and soil properties in Louisiana marshes impacted by the Deepwater Horizon oil spill. Soils were collected at oiled and unoiled sites from Louisiana coastal marshes in July 2012, 2 years after the spill, and analyzed for community differences based on ammonia monooxygenase genes (amoA). Terminal Restriction Fragment Polymorphism and DNA sequence analyses revealed significantly different AOA and AOB communities between the three regions, but few differences were found between oiled and unoiled sites. Community composition of nitrifiers was best explained by differences in soil moisture and nitrogen content. Despite the lack of significant oil effects on overall community composition, we identified differences in correlations of individual populations with potential nitrification rates between oiled and unoiled sites that help explain previously published correlation patterns. Our results suggest that exposure to oil, even 2 years post-spill, led to subtle changes in population dynamics. How, or if, these changes may impact ecosystem function in the marshes, however, remains uncertain

Justifications-on-demand as a device to promote shifts of attention associated with relational thinking in elementary arithmetic

Student responses to arithmetical questions that can be solved by using arithmetical structure can serve to reveal the extent and nature of relational, as opposed to computational thinking. Here, student responses to probes which require them to justify-on-demand are analysed using a conceptual framework which highlights distinctions between different forms of attention. We analyse a number of actions observed in students in terms of forms of attention and shifts between them: in the short-term (in the moment), medium-term (over several tasks), and long-term (over a year). The main factors conditioning students´ attention and its movement are identified and some didactical consequences are proposed

Conceptual learning : the priority for higher education

The common sense notion of learning as the all-pervasive acquisition of new behaviour and knowledge, made vivid by experience, is an incomplete characterisation, because it assumes that the learning of behaviour and the learning of knowledge are indistinguishable, and that acquisition constitutes learning without reference to transfer. A psychological level of analysis is used to argue that conceptual learning should have priority in higher education

Educational action research as the quest for virtue in teaching

Curriculum aims often remain unrealised aspirations. This is because the values and principles implicit in them fail to get articulated in forms that can effectively inform and guide the practice of teaching. Ideas such as ‘learner-centred education’, ‘independent/autonomous learning’, ‘self-directed learning', ‘enquiry/discovery learning’, ‘collaborative learning’, ‘active learning’ and ‘learning with understanding’ refer to critical aspects of the learning process rather than its outcomes. While often enthusiastically embraced by teachers, they rarely get realised in appropriate forms of virtuous action. Such is the power of an outcomes-based model of teaching and learning to shape the practice of teaching. This paper cites examples of curriculum design that specify the pedagogical values and principles implicit in various educational aims, and shows how they can provide a basis for practical experiments by teachers in their classrooms and schools, in a quest to transform their teaching into concrete forms of virtuous action. Indeed, the paper depicts a number of actual action research projects in which teachers generated some common insights into how to transform their teaching into the practice of virtue in education. It also explores the role of theory-informed action research in developing teaching as a virtuous form of action

Real-time large-scale dense RGB-D SLAM with volumetric fusion

We present a new simultaneous localization and mapping (SLAM) system capable of producing high-quality globally consistent surface reconstructions over hundreds of meters in real time with only a low-cost commodity RGB-D sensor. By using a fused volumetric surface reconstruction we achieve a much higher quality map over what would be achieved using raw RGB-D point clouds. In this paper we highlight three key techniques associated with applying a volumetric fusion-based mapping system to the SLAM problem in real time. First, the use of a GPU-based 3D cyclical buffer trick to efficiently extend dense every-frame volumetric fusion of depth maps to function over an unbounded spatial region. Second, overcoming camera pose estimation limitations in a wide variety of environments by combining both dense geometric and photometric camera pose constraints. Third, efficiently updating the dense map according to place recognition and subsequent loop closure constraints by the use of an ‘as-rigid-as-possible’ space deformation. We present results on a wide variety of aspects of the system and show through evaluation on de facto standard RGB-D benchmarks that our system performs strongly in terms of trajectory estimation, map quality and computational performance in comparison to other state-of-the-art systems.Science Foundation Ireland (Strategic Research Cluster Grant 07/SRC/I1168)Irish Research Council (Embark Initiative)United States. Office of Naval Research (Grant N00014-10-1-0936)United States. Office of Naval Research (Grant N00014-11-1-0688)United States. Office of Naval Research (Grant N00014-12-1-0093)United States. Office of Naval Research (Grant N00014-12-10020)National Science Foundation (U.S.) (Grant IIS-1318392

A Genetic Screen Reveals Arabidopsis Stomatal and/or Apoplastic Defenses against Pseudomonas syringae pv. tomato DC3000

Bacterial infection of plants often begins with colonization of the plant surface, followed by entry into the plant through wounds and natural openings (such as stomata), multiplication in the intercellular space (apoplast) of the infected tissues, and dissemination of bacteria to other plants. Historically, most studies assess bacterial infection based on final outcomes of disease and/or pathogen growth using whole infected tissues; few studies have genetically distinguished the contribution of different host cell types in response to an infection. The phytotoxin coronatine (COR) is produced by several pathovars of Pseudomonas syringae. COR-deficient mutants of P. s. tomato (Pst) DC3000 are severely compromised in virulence, especially when inoculated onto the plant surface. We report here a genetic screen to identify Arabidopsis mutants that could rescue the virulence of COR-deficient mutant bacteria. Among the susceptible to coronatine-deficient Pst DC3000 (scord) mutants were two that were defective in stomatal closure response, two that were defective in apoplast defense, and four that were defective in both stomatal and apoplast defense. Isolation of these three classes of mutants suggests that stomatal and apoplastic defenses are integrated in plants, but are genetically separable, and that COR is important for Pst DC3000 to overcome both stomatal guard cell- and apoplastic mesophyll cell-based defenses. Of the six mutants defective in bacterium-triggered stomatal closure, three are defective in salicylic acid (SA)-induced stomatal closure, but exhibit normal stomatal closure in response to abscisic acid (ABA), and scord7 is compromised in both SA- and ABA-induced stomatal closure. We have cloned SCORD3, which is required for salicylic acid (SA) biosynthesis, and SCORD5, which encodes an ATP-binding cassette (ABC) protein, AtGCN20/AtABCF3, predicted to be involved in stress-associated protein translation control. Identification of SCORD5 begins to implicate an important role of stress-associated protein translation in stomatal guard cell signaling in response to microbe-associated molecular patterns and bacterial infection

Taxonomy of the order Mononegavirales : update 2016

In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV)

Creative destruction in science

Drawing on the concept of a gale of creative destruction in a capitalistic economy, we argue that initiatives to assess the robustness of findings in the organizational literature should aim to simultaneously test competing ideas operating in the same theoretical space. In other words, replication efforts should seek not just to support or question the original findings, but also to replace them with revised, stronger theories with greater explanatory power. Achieving this will typically require adding new measures, conditions, and subject populations to research designs, in order to carry out conceptual tests of multiple theories in addition to directly replicating the original findings. To illustrate the value of the creative destruction approach for theory pruning in organizational scholarship, we describe recent replication initiatives re-examining culture and work morality, working parents\u2019 reasoning about day care options, and gender discrimination in hiring decisions. Significance statement It is becoming increasingly clear that many, if not most, published research findings across scientific fields are not readily replicable when the same method is repeated. Although extremely valuable, failed replications risk leaving a theoretical void\u2014 reducing confidence the original theoretical prediction is true, but not replacing it with positive evidence in favor of an alternative theory. We introduce the creative destruction approach to replication, which combines theory pruning methods from the field of management with emerging best practices from the open science movement, with the aim of making replications as generative as possible. In effect, we advocate for a Replication 2.0 movement in which the goal shifts from checking on the reliability of past findings to actively engaging in competitive theory testing and theory building. Scientific transparency statement The materials, code, and data for this article are posted publicly on the Open Science Framework, with links provided in the article