Solving One Dimensional Scalar Conservation Laws by Particle Management

We present a meshfree numerical solver for scalar conservation laws in one space dimension. Points representing the solution are moved according to their characteristic velocities. Particle interaction is resolved by purely local particle management. Since no global remeshing is required, shocks stay sharp and propagate at the correct speed, while rarefaction waves are created where appropriate. The method is TVD, entropy decreasing, exactly conservative, and has no numerical dissipation. Difficulties involving transonic points do not occur, however inflection points of the flux function pose a slight challenge, which can be overcome by a special treatment. Away from shocks the method is second order accurate, while shocks are resolved with first order accuracy. A postprocessing step can recover the second order accuracy. The method is compared to CLAWPACK in test cases and is found to yield an increase in accuracy for comparable resolutions.Comment: 15 pages, 6 figures. Submitted to proceedings of the Fourth International Workshop Meshfree Methods for Partial Differential Equation

The challenge of modelling nitrogen management at the field scale : simulation and sensitivity analysis of N2O fluxes across nine experimental sites using DailyDayCent

Peer reviewedPublisher PD

Impact of droughts on the carbon cycle in European vegetation : a probabilistic risk analysis using six vegetation models

Peer reviewedPublisher PD

Fine-suspended sediment and water budgets for a large, seasonally dry tropical catchment: Burdekin River catchment, Queensland, Australia

The Burdekin River catchment (~130,400 km2) is a seasonally dry tropical catchment located in north-east Queensland, Australia. It is the single largest source of suspended sediment to the Great Barrier Reef (GBR). Fine sediments are a threat to ecosystems on the GBR where they contribute to elevated turbidity (reduced light), sedimentation stress, and potential impacts from the associated nutrients. Suspended sediment data collected over a 5 year period were used to construct a catchment-wide sediment source and transport budget. The Bowen River tributary was identified as the major source of end-of-river suspended sediment export, yielding an average of 530 t km−2 yr−1 during the study period. Sediment trapping within a large reservoir (1.86 million ML) and the preferential transport of clays and fine silts downstream of the structure were also examined. The data reveal that the highest clay and fine silt loads—which are of most interest to environmental managers of the GBR—are not always sourced from areas that yield the largest total suspended sediment load (i.e., all size fractions). Our results demonstrate the importance of incorporating particle size into catchment sediment budget studies undertaken to inform management decisions to reduce downstream turbidity and sedimentation. Our data on sediment source, reservoir influence, and subcatchment and catchment yields will improve understandings of sediment dynamics in other tropical catchments, particularly those located in seasonally wet-dry tropical savannah/semiarid climates. The influence of climatic variability (e.g., drought/wetter periods) on annual sediment loads within large seasonally dry tropical catchments is also demonstrated by our data

Evolution of the leukotoxin promoter in genus Mannheimia

<b>Background</b>: The <i>Mannheimia</i> species encompass a wide variety of bacterial lifestyles, including opportunistic pathogens and commensals of the ruminant respiratory tract, commensals of the ovine rumen, and pathogens of the ruminant integument. Here we present a scenario for the evolution of the leukotoxin promoter among representatives of the five species within genus <i>Mannheimia</i>. We also consider how the evolution of the leukotoxin operon fits with the evolution and maintenance of virulence. <b>Results</b>: The alignment of the intergenic regions upstream of the leukotoxin genes showed significant sequence and positional conservation over a 225-bp stretch immediately proximal to the transcriptional start site of the <i>lktC</i> gene among all <i>Mannheimia</i> strains. However, in the course of the <i>Mannheimia</i> genome evolution, the acquisition of individual noncoding regions upstream of the conserved promoter region has occurred. The rate of evolution estimated branch by branch suggests that the conserved promoter may be affected to different extents by the types of natural selection that potentially operate in regulatory regions. Tandem repeats upstream of the core promoter were confined to <i>M. haemolytica</i> with a strong association between the sequence of the repeat units, the number of repeat units per promoter, and the phylogenetic history of this species. <b>Conclusion</b>: The mode of evolution of the intergenic regions upstream of the leukotoxin genes appears to be highly dependent on the lifestyle of the bacterium. Transition from avirulence to virulence has occurred at least once in <i>M. haemolytica</i> with some evolutionary success of bovine serotype A1/A6 strains. Our analysis suggests that changes in <i>cis</i>-regulatory systems have contributed to the derived virulence phenotype by allowing phase-variable expression of the leukotoxin protein. We propose models for how phase shifting and the associated virulence could facilitate transmission to the nasopharynx of new hosts

Manipulation and removal of defects in spontaneous optical patterns

Defects play an important role in a number of fields dealing with ordered structures. They are often described in terms of their topology, mutual interaction and their statistical characteristics. We demonstrate theoretically and experimentally the possibility of an active manipulation and removal of defects. We focus on the spontaneous formation of two-dimensional spatial structures in a nonlinear optical system, a liquid crystal light valve under single optical feedback. With increasing distance from threshold, the spontaneously formed hexagonal pattern becomes disordered and contains several defects. A scheme based on Fourier filtering allows us to remove defects and to restore spatial order. Starting without control, the controlled area is progressively expanded, such that defects are swept out of the active area.Comment: 4 pages, 4 figure

Recovery of temperature records from slow-growing corals by fine scale sampling of skeletons

Author Posting. © American Geophysical Union, 2007. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 34 (2007): L17706, doi:10.1029/2007GL030967.We used laser ablation inductively coupled plasma mass spectrometry (LA ICP-MS) to analyze Sr/Ca ratios in 5 colonies of the Atlantic corals, Diploria labyrinthiformis and Montastrea franski, each growing less than 5 mm yr−1. By targeting the centers of septa we avoided thickening deposits to achieve an analytical sampling resolution of 5-10 days. The sensitivity of Sr/Ca to temperature (−0.096 mmol/mol/°C) is ∼3 times higher than previously reported for these species and equivalent to that exhibited by fast-growing Porites corals from the Indo-Pacific. The Sr/Ca-sea surface temperature (SST) calibrations derived from these corals were not statistically different and were independent of colony growth rate over the period studied. Data from 4 D. labyrinthiformis colonies were pooled to produce a single Sr/Ca-SST calibration with a calculated standard error on the predicted ocean temperature of ±0.51°C. Applying our calibration to Sr/Ca analyses of D. labyrinthiformis skeleton deposited in the late 18th century indicated that average annual sea surface temperatures around Bermuda were ∼1°C cooler than today.This study was supported by a WHOI Ocean Life Institute fellowship to ALC, by OLI grant 25051316 to ALC and SRT, by NSF OCE-0402728 and NSF OCE- 0215905

Minimalistic mycoplasmas harbor different functional toxin-antitoxin systems

Mycoplasmas are minute bacteria controlled by very small genomes ranging from 0.6 to 1.4 Mbp. They encompass several important medical and veterinary pathogens that are often associated with a wide range of chronic diseases. The long persistence of mycoplasma cells in their hosts can exacerbate the spread of antimicrobial resistance observed for many species. However, the nature of the virulence factors driving this phenomenon in mycoplasmas is still unclear. Toxin-antitoxin systems (TA systems) are genetic elements widespread in many bacteria that were historically associated with bacterial persistence. Their presence on mycoplasma genomes has never been carefully assessed, especially for pathogenic species. Here we investigated three candidate TA systems in M. mycoides subsp. capri encoding a (i) novel AAA-ATPase/subtilisin-like serine protease module, (ii) a putative AbiEii/AbiEi pair and (iii) a putative Fic/RelB pair. We sequence analyzed fourteen genomes of M. mycoides subsp. capri and confirmed the presence of at least one TA module in each of them. Interestingly, horizontal gene transfer signatures were also found in several genomic loci containing TA systems for several mycoplasma species. Transcriptomic and proteomic data confirmed differential expression profiles of these TA systems during mycoplasma growth in vitro. While the use of heterologous expression systems based on E. coli and B. subtilis showed clear limitations, the functionality and neutralization capacities of all three candidate TA systems were successfully confirmed using M. capricolum subsp. capricolum as a host. Additionally, M. capricolum subsp. capricolum was used to confirm the presence of functional TA system homologs in mycoplasmas of the Hominis and Pneumoniae phylogenetic groups. Finally, we showed that several of these M. mycoides subsp. capri toxins tested in this study, and particularly the subtilisin-like serine protease, could be used to establish a kill switch in mycoplasmas for industrial applications

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