Cloning, sequencing, and characterization of the hexahydro-1,3,5-trinitro-1,3,5-triazine degradation gene cluster from Rhodococcus rhodochrous

Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a high explosive which presents an environmental hazard as a major land and groundwater contaminant. Rhodococcus rhodochrous strain 11Y was isolated from explosive contaminated land and is capable of degrading RDX when provided as the sole source of nitrogen for growth. Products of RDX degradation in resting-cell incubations were analyzed and found to include nitrite, formaldehyde, and formate. No ammonium was excreted into the medium, and no dead-end metabolites were observed. The gene responsible for the degradation of RDX in strain 11Y is a constitutively expressed cytochrome P450-like gene, xpLA, which is found in a gene cluster with an adrenodoxin reductase homologue, xplB. The cytochrome P450 also has a flavodoxin domain at the N terminus. This study is the first to present a gene which has been identified as being responsible for RDX biodegradation. The mechanism of action of XplA on RDX is thought to involve initial denitration followed by spontaneous ring cleavage and mineralization

Inspired by chance: valuing patients' informal contributions to research

Serendipitous contributions from patients that influence the research agenda should be better recognised and acknowledged, argue Sebastian Crutch and colleagues

Using unsupervised learning to partition 3D city scenes for distributed building energy microsimulation

Microsimulation is a class of Urban Building Energy Modeling techniques in which energetic interactions between buildings are explicitly resolved. Examples include SUNtool and CitySim+, both of which employ a sophisticated radiosity-based algorithm to solve for radiation exchange. The computational cost of this algorithm increases in proportion to the square of the number of surfaces of which an urban scene is comprised. To simulate large scenes, of the order of 10,000 to 1,000,000 surfaces, it is desirable to divide the scene to distribute the simulation task. However, this partitioning is not trivial as the energy-related interactions create uneven inter-dependencies between computing nodes. To this end, we describe in this paper two approaches (K-means and Greedy Community Detection algorithms) for partitioning urban scenes, and subsequently performing building energy microsimulation using CitySim+ on a distributed memory High-Performance Computing Cluster. To compare the performance of these partitioning techniques, we propose two measures evaluating the extent to which the obtained clusters exploit data locality. We show that our approach using Greedy Community Detection performs well in terms of exploiting data locality and reducing inter-dependencies among sub-scenes, but at the expense of a higher data preparation cost and algorithm run-time

Quantitative Chevalley-Weil theorem for curves

The classical Chevalley-Weil theorem asserts that for an \'etale covering of projective varieties over a number field K, the discriminant of the field of definition of the fiber over a K-rational point is uniformly bounded. We obtain a fully explicit version of this theorem in dimension 1.Comment: version 4: minor inaccuracies in Lemma 3.4 and Proposition 5.2 correcte

Gated rotation mechanism of site-specific recombination by ϕC31 integrase

Integrases, such as that of the Streptomyces temperate bacteriophage ϕC31, promote site-specific recombination between DNA sequences in the bacteriophage and bacterial genomes to integrate or excise the phage DNA. ϕC31 integrase belongs to the serine recombinase family, a large group of structurally related enzymes with diverse biological functions. It has been proposed that serine integrases use a “subunit rotation” mechanism to exchange DNA strands after double-strand DNA cleavage at the two recombining att sites, and that many rounds of subunit rotation can occur before the strands are religated. We have analyzed the mechanism of ϕC31 integrase-mediated recombination in a topologically constrained experimental system using hybrid “phes” recombination sites, each of which comprises a ϕC31 att site positioned adjacent to a regulatory sequence recognized by Tn3 resolvase. The topologies of reaction products from circular substrates containing two phes sites support a right-handed subunit rotation mechanism for catalysis of both integrative and excisive recombination. Strand exchange usually terminates after a single round of 180° rotation. However, multiple processive “360° rotation” rounds of strand exchange can be observed, if the recombining sites have nonidentical base pairs at their centers. We propose that a regulatory “gating” mechanism normally blocks multiple rounds of strand exchange and triggers product release after a single round

Identification of floodwater source areas in Nepal using SCIMAP‐Flood

Practical approaches for managing flooding from fluvial sources are moving away from mitigation solely at the point of impact and towards integrated catchment management. This considers the source areas, flow pathways of floodwaters and the locations and exposure to the risk of communities. For a field site in southern Nepal, we analyse catchment response to a range of simulated rainfall events, which when evaluated collectively can help guide potential flood management solutions. This is achieved through the adoption of SCIMAP-Flood, a decision support framework that works at the catchment-scale to identify critical source areas for floodwaters. The SCIMAP-Flood Fitted inverse modelling approach has been applied to the East Rapti catchment, Nepal. For multiple flood impact locations throughout the catchment, SCIMAP-Flood effectively identifies locations where flood management measures would have the most positive effects on risk reduction. The results show that the spatial targeting of mitigation measures in areas of irrigated and rainfed agriculture and the prevention of deforestation or removal of shrubland would be the most effective approaches. If these actions were in the upper catchment above Hetauda or upstream of Manahari they would have the most effective reduction in the flood peak

Fredkin Gates for Finite-valued Reversible and Conservative Logics

The basic principles and results of Conservative Logic introduced by Fredkin and Toffoli on the basis of a seminal paper of Landauer are extended to d-valued logics, with a special attention to three-valued logics. Different approaches to d-valued logics are examined in order to determine some possible universal sets of logic primitives. In particular, we consider the typical connectives of Lukasiewicz and Godel logics, as well as Chang's MV-algebras. As a result, some possible three-valued and d-valued universal gates are described which realize a functionally complete set of fundamental connectives.Comment: 57 pages, 10 figures, 16 tables, 2 diagram

Colloquium: Statistical mechanics of money, wealth, and income

This Colloquium reviews statistical models for money, wealth, and income distributions developed in the econophysics literature since the late 1990s. By analogy with the Boltzmann-Gibbs distribution of energy in physics, it is shown that the probability distribution of money is exponential for certain classes of models with interacting economic agents. Alternative scenarios are also reviewed. Data analysis of the empirical distributions of wealth and income reveals a two-class distribution. The majority of the population belongs to the lower class, characterized by the exponential ("thermal") distribution, whereas a small fraction of the population in the upper class is characterized by the power-law ("superthermal") distribution. The lower part is very stable, stationary in time, whereas the upper part is highly dynamical and out of equilibrium.Comment: 24 pages, 13 figures; v.2 - minor stylistic changes and updates of references corresponding to the published versio