Toward Large-Eddy Simulations of Dust Devils of Observed Intensity: Effects of Grid Spacing, Background Wind, and Surface Heterogeneities

Dust devils are convective vortices with a vertical axis of rotation made visible by lifted soil particles. Currently, there is great uncertainty about the extent to which dust devils contribute to the atmospheric aerosol input and thereby influence Earth's radiation budget. Past efforts to quantify the aerosol transport and study their formation, maintenance, and statistics using large-eddy simulation (LES) have been of limited success. Therefore, some important features of dust devil-like vortices simulated with LES still do not compare well with those of observed ones. One major difference is the simulated value of the core pressure drop, which is almost 1 order of magnitude smaller compared to the observed range of 250 to 450 Pa. However, most of the existing numerical simulations are based on highly idealized setups and coarse grid spacings. In this study, we investigate the effects of various factors on the simulated vortex strength with high-resolution LES. For the fist time, we are able to reproduce observed core pressures by using a high spatial resolution of 2 m, a model setup with moderate background wind and a spatially heterogeneous surface heat flux. It is found that vortices mainly appear at the lines of horizontal flow convergence above the centers of the strongly heated patches, which is in contrast to some older observations in which vortices seemed to be created along the patch edges

Integrated Nuclear Knowledge Management System – NUTEMA

Knowledge Management has become one of the most important issues for the nuclear industry. On the one hand, the amount of codifiable knowledge in the nuclear technology area saw a steep increase in the last years; on the other hand, due to the “generation gap” in the nuclear industry it became very challenging to organize the seamless transfer of the noncodifiable knowledge from one generation of engineers to the other. Computer aided systems so far where aiming at to preserve the codifiable knowledge. The present paper introduces a system that should support knowledge management not only dealing with the codifiable part of it, but also address broader aspects (which includes the management of non-codifiable knowledge).- NUTEMA. The integrated nuclear knowledge management system NUTEMA should provide interactive combination of information and methods, but also identifying competences which more adequately fit to a given task, keeping track of keeping skills of the experts within an organization. Application is foreseen in nuclear engineering fields as system design, operation and maintenance plant and process modifications, standardization, certification and even for licensing-related tasks. The system combines an extensively diverse and modular database with computer based simulations including a scientific software platform. NUTEMA is conceived to operate in different modes, for example collecting and retrieving database knowledge, training applications, NPP operations support, computer code applications, and as plant analyzer. This paper will present two examples; one acting as at a supporting tool for typical NPP plant modification: In a second case, application on review and optimization of operational process is described. Despite the provided examples deal with different objectives and methods associated with different stages of an NPP lifetime, (design and operation) both are supported by the integrated nuclear knowledge management system

A re-investigation of the path of carbon in photosynthesis utilizing GC/MS methodology. Unequivocal verification of the participation of octulose phosphates in the pathway

A GC/EIMS/SIM methodology has been developed to re-examine the path of carbon in photosynthesis. Exposing isolated spinach chloroplasts to (13)CO(2 )on a solid support for a defined period followed by quenching and work-up provided a mixture of labelled sugar phosphates. After enzymatic dephosphorylation and derivatization, the Mox-TMS sugars were analysed using the above method. The purpose of the study was to try to calculate the atom% enrichment of (13)C in as many of the individual carbons in each of the derivatized sugars as was practical using diagnostic fragment ions. In the event, only one 45 s experiment provided sufficient data to enable a range of enrichment values to be calculated. This confirmed that D-glycero-D-altro-octulose phosphate was present in the chloroplasts and was heavily labelled in the C4, C5 and C6 positions, in keeping with the hypothesis that it had an inclusive role and a labelling pattern consistent with a new modified pathway of carbon in photosynthesis

CRISPR-UnLOCK: Multipurpose Cas9-Based Strategies for Conversion of Yeast Libraries and Strains

Citation: Roggenkamp E, Giersch RM, Wedeman E, Eaton M, Turnquist E, Schrock MN, Alkotami L, Jirakittisonthon T, Schluter-Pascua SE, Bayne GH, Wasko C, Halloran M and Finnigan GC (2017) CRISPR-UnLOCK: Multipurpose Cas9-Based Strategies for Conversion of Yeast Libraries and Strains. Front. Microbiol. 8:1773. doi: 10.3389/fmicb.2017.01773Saccharomyces cerevisiae continues to serve as a powerful model system for both basic biological research and industrial application. The development of genome-wide collections of individually manipulated strains (libraries) has allowed for high-throughput genetic screens and an emerging global view of this single-celled Eukaryote. The success of strain construction has relied on the innate ability of budding yeast to accept foreign DNA and perform homologous recombination, allowing for efficient plasmid construction (in vivo) and integration of desired sequences into the genome. The development of molecular toolkits and “integration cassettes” have provided fungal systems with a collection of strategies for tagging, deleting, or over-expressing target genes; typically, these consist of a C-terminal tag (epitope or fluorescent protein), a universal terminator sequence, and a selectable marker cassette to allow for convenient screening. However, there are logistical and technical obstacles to using these traditional genetic modules for complex strain construction (manipulation of many genomic targets in a single cell) or for the generation of entire genome-wide libraries. The recent introduction of the CRISPR/Cas gene editing technology has provided a powerful methodology for multiplexed editing in many biological systems including yeast. We have developed four distinct uses of the CRISPR biotechnology to generate yeast strains that utilizes the conversion of existing, commonly-used yeast libraries or strains. We present Cas9-based, marker-less methodologies for (i) N-terminal tagging, (ii) C-terminally tagging yeast genes with 18 unique fusions, (iii) conversion of fluorescently-tagged strains into newly engineered (or codon optimized) variants, and finally, (iv) use of a Cas9 “gene drive” system to rapidly achieve a homozygous state for a hypomorphic query allele in a diploid strain. These CRISPR-based methods demonstrate use of targeting universal sequences previously introduced into a genome

A method for estimation of elasticities in metabolic networks using steady state and dynamic metabolomics data and linlog kinetics

BACKGROUND: Dynamic modeling of metabolic reaction networks under in vivo conditions is a crucial step in order to obtain a better understanding of the (dis)functioning of living cells. So far dynamic metabolic models generally have been based on mechanistic rate equations which often contain so many parameters that their identifiability from experimental data forms a serious problem. Recently, approximative rate equations, based on the linear logarithmic (linlog) format have been proposed as a suitable alternative with fewer parameters. RESULTS: In this paper we present a method for estimation of the kinetic model parameters, which are equal to the elasticities defined in Metabolic Control Analysis, from metabolite data obtained from dynamic as well as steady state perturbations, using the linlog kinetic format. Additionally, we address the question of parameter identifiability from dynamic perturbation data in the presence of noise. The method is illustrated using metabolite data generated with a dynamic model of the glycolytic pathway of Saccharomyces cerevisiae based on mechanistic rate equations. Elasticities are estimated from the generated data, which define the complete linlog kinetic model of the glycolysis. The effect of data noise on the accuracy of the estimated elasticities is presented. Finally, identifiable subset of parameters is determined using information on the standard deviations of the estimated elasticities through Monte Carlo (MC) simulations. CONCLUSION: The parameter estimation within the linlog kinetic framework as presented here allows the determination of the elasticities directly from experimental data from typical dynamic and/or steady state experiments. These elasticities allow the reconstruction of the full kinetic model of Saccharomyces cerevisiae, and the determination of the control coefficients. MC simulations revealed that certain elasticities are potentially unidentifiable from dynamic data only. Addition of steady state perturbation of enzyme activities solved this problem

Overview of the PALM model system 6.0

In this paper, we describe the PALM model system 6.0. PALM (formerly an abbreviation for Parallelized Largeeddy Simulation Model and now an independent name) is a Fortran-based code and has been applied for studying a variety of atmospheric and oceanic boundary layers for about 20 years. The model is optimized for use on massively parallel computer architectures. This is a follow-up paper to the PALM 4.0 model description in Maronga et al. (2015). During the last years, PALM has been significantly improved and now offers a variety of new components. In particular, much effort was made to enhance the model with components needed for applications in urban environments, like fully interactive land surface and radiation schemes, chemistry, and an indoor model. This paper serves as an overview paper of the PALM 6.0 model system and we describe its current model core. The individual components for urban applications, case studies, validation runs, and issues with suitable input data are presented and discussed in a series of companion papers in this special issue

Diversity of Melissococcus plutonius from Honeybee Larvae in Japan and Experimental Reproduction of European Foulbrood with Cultured Atypical Isolates

European foulbrood (EFB) is an important infectious disease of honeybee larvae, but its pathogenic mechanisms are still poorly understood. The causative agent, Melissococcus plutonius, is a fastidious organism, and microaerophilic to anaerobic conditions and the addition of potassium phosphate to culture media are required for growth. Although M. plutonius is believed to be remarkably homologous, in addition to M. plutonius isolates with typical cultural characteristics, M. plutonius-like organisms, with characteristics seemingly different from those of typical M. plutonius, have often been isolated from diseased larvae with clinical signs of EFB in Japan. Cultural and biochemical characterization of 14 M. plutonius and 19 M. plutonius-like strain/isolates revealed that, unlike typical M. plutonius strain/isolates, M. plutonius-like isolates were not fastidious, and the addition of potassium phosphate was not required for normal growth. Moreover, only M. plutonius-like isolates, but not typical M. plutonius strain/isolates, grew anaerobically on sodium phosphate-supplemented medium and aerobically on some potassium salt-supplemented media, were positive for β-glucosidase activity, hydrolyzed esculin, and produced acid from L-arabinose, D-cellobiose, and salicin. Despite the phenotypic differences, 16S rRNA gene sequence analysis and DNA-DNA hybridization demonstrated that M. plutonius-like organisms were taxonomically identical to M. plutonius. However, by pulsed-field gel electrophoresis analysis, these typical and atypical (M. plutonius-like) isolates were separately grouped into two genetically distinct clusters. Although M. plutonius is known to lose virulence quickly when cultured artificially, experimental infection of representative isolates showed that atypical M. plutonius maintained the ability to cause EFB in honeybee larvae even after cultured in vitro in laboratory media. Because the rapid decrease of virulence in cultured M. plutonius was a major impediment to elucidation of the pathogenesis of EFB, atypical M. plutonius discovered in this study will be a breakthrough in EFB research