Plasma oxidation as key mechanism for stoichiometry in Pulsed Laser Deposition grown oxide films

We present a unique overview on the influence of growth parameters on the characteristics of the PLD plasma plume using Optical Self-Emission (OSE) imaging and spectroscopy, supported with Laser Induced Fluorescence (LIF) measurements. It is shown that in a relatively small background gas pressure regime, from 10-2 mbar to 10-1 mbar oxygen pressure, a transition from nonstoichiometric to stoichiometric growth of SrTiO3 films occurs as measured with X-ray Diffraction (XRD). In this pressure regime, OSE spectroscopy and LIF measurements also show a transition from incomplete to full oxidation of species in the plasma plume. This suggests that the oxidation of species in the plasma is a crucial mechanism for the stoichiometric reconstruction of the synthesized oxide thin films

Arabidopsis Roots and Shoots Show Distinct Temporal Adaptation Patterns toward Nitrogen Starvation

Nitrogen (N) is an essential macronutrient for plants. N levels in soil vary widely, and plants have developed strategies to cope with N deficiency. However, the regulation of these adaptive responses and the coordinating signals that underlie them are still poorly understood. The aim of this study was to characterize N starvation in adult Arabidopsis (Arabidopsis thaliana) plants in a spatiotemporal manner by an integrative, multilevel global approach analyzing growth, metabolites, enzyme activities, and transcript levels. We determined that the remobilization of N and carbon compounds to the growing roots occurred long before the internal N stores became depleted. A global metabolite analysis by gas chromatography-mass spectrometry revealed organ-specific differences in the metabolic adaptation to complete N starvation, for example, for several tricarboxylic acid cycle intermediates, but also for carbohydrates, secondary products, and phosphate. The activities of central N metabolism enzymes and the capacity for nitrate uptake adapted to N starvation by favoring N remobilization and by increasing the high-affinity nitrate uptake capacity after long-term starvation. Changes in the transcriptome confirmed earlier studies and added a new dimension by revealing specific spatiotemporal patterns and several unknown N starvation-regulated genes, including new predicted small RNA genes. No global correlation between metabolites, enzyme activities, and transcripts was evident. However, this multilevel spatiotemporal global study revealed numerous new patterns of adaptation mechanisms to N starvation. In the context of a sustainable agriculture, this work will give new insight for the production of crops with increased N use efficiency

Quantitative Assessment of the Risk of Release of Foot-and-Mouth Disease Virus via Export of Bull Semen from Israel

Various foot-and-mouth disease (FMD) virus strains circulate in the Middle East, causing frequent episodes of FMD outbreaks among Israeli livestock. Since the virus is highly resistant in semen, artificial insemination with contaminated bull semen may lead to the infection of the receiver cow. As a non-FMD-free country with vaccination, Israel is currently engaged in trading bull semen only with countries of the same status. The purpose of this study was to assess the risk of release of FMD virus through export of bull semen in order to estimate the risk for FMD-free countries considering purchasing Israeli bull semen. A stochastic risk assessment model was used to estimate this risk, defined as the annual likelihood of exporting at least one ejaculate of bull semen contaminated with viable FMD virus. A total of 45 scenarios were assessed to account for uncertainty and variability around specific parameter estimates and to evaluate the effect of various mitigation measures, such as performing a preexport test on semen ejaculates. Under the most plausible scenario, the annual likelihood of exporting bull semen contaminated with FMD virus had a median of 1.3 * 10(-7) for an export of 100 ejaculates per year. This corresponds to one infected ejaculate exported every 7 million years. Under the worst-case scenario, the median of the risk rose to 7.9 * 10(-5), which is equivalent to the export of one infected ejaculate every 12,000 years. Sensitivity analysis indicated that the most influential parameter is the probability of viral excretion in infected bulls

Dichotomy in the NRT Gene Families of Dicots and Grass Species

A large proportion of the nitrate (NO3−) acquired by plants from soil is actively transported via members of the NRT families of NO3− transporters. In Arabidopsis, the NRT1 family has eight functionally characterised members and predominantly comprises low-affinity transporters; the NRT2 family contains seven members which appear to be high-affinity transporters; and there are two NRT3 (NAR2) family members which are known to participate in high-affinity transport. A modified reciprocal best hit (RBH) approach was used to identify putative orthologues of the Arabidopsis NRT genes in the four fully sequenced grass genomes (maize, rice, sorghum, Brachypodium). We also included the poplar genome in our analysis to establish whether differences between Arabidopsis and the grasses may be generally applicable to monocots and dicots. Our analysis reveals fundamental differences between Arabidopsis and the grass species in the gene number and family structure of all three families of NRT transporters. All grass species possessed additional NRT1.1 orthologues and appear to lack NRT1.6/NRT1.7 orthologues. There is significant separation in the NRT2 phylogenetic tree between NRT2 genes from dicots and grass species. This indicates that determination of function of NRT2 genes in grass species will not be possible in cereals based simply on sequence homology to functionally characterised Arabidopsis NRT2 genes and that proper functional analysis will be required. Arabidopsis has a unique NRT3.2 gene which may be a fusion of the NRT3.1 and NRT3.2 genes present in all other species examined here. This work provides a framework for future analysis of NO3− transporters and NO3− transport in grass crop species

A Differential Innate Immune Response in Active and Chronic Stages of Bovine Infectious Digital Dermatitis

Digital dermatitis (DD) commonly associated with Treponema spp. infection is a prevalent infectious bovine foot disease characterized by ulcerative and necrotic lesions. Lesions associated with DD are often classified using the M-stage scoring system, with M0 indicating healthy heel skin and M4 indicating chronic lesions. Current treatments utilizing antimicrobials or chemical footbaths are often ineffective and rarely cure DD lesions. Understanding the function of the innate immune response in the pathogenesis of DD will help to identify novel therapeutic approaches. In this study, the expression of the local innate host defense peptides cathelicidins and β-defensins was investigated in cows with DD and associated with the presence of treponemes and inflammatory reactions. Samples from active ulcerative DD lesions (M2) had considerable epidermal neutrophilic infiltration and increased gene expression of β-defensin tracheal antimicrobial peptides compared to control skin. Samples from acute lesions also had elevated local Cxcl-8 and TLR4 gene expression and abundant treponemes as identified by direct visualization, immunohistochemistry, and culture. Conversely, the anti-inflammatory peptide IL-10 was elevated in skin from chronic (M4) lesions, whereas bovine cathelicidin myeloid antimicrobial peptide 28 (Bmap-28) was increased in skin from oxytetracycline-treated M2 lesions. Experiments using cultured human keratinocytes challenged with Treponema spp. isolated from clinical cases of bovine DD showed that structural products from treponemes are able to initiate the innate immune response, in part through TLR2 signaling. These findings indicate that neutrophil influx, Cxcl-8, and β-defensin are key markers of active DD. Cathelicidins and IL-10 seem important in response to treatment or during the chronic proliferative stages of the disease

Redefining the "carrier" state for foot-and-mouth disease from the dynamics of virus persistence in endemically affected cattle populations

The foot-and-mouth disease virus (FMDV) “carrier” state was defined by van Bekkum in 1959. It was based on the recovery of infectious virus 28 days or more post infection and has been a useful construct for experimental studies. Using historic data from 1,107 cattle, collected as part of a population based study of endemic FMD in 2000, we developed a mixed effects logistic regression model to predict the probability of recovering viable FMDV by probang and culture, conditional on the animal’s age and time since last reported outbreak. We constructed a second set of models to predict the probability of an animal being probang positive given its antibody response in three common non-structural protein (NSP) ELISAs and its age. We argue that, in natural ecological settings, the current definition of a ”carrier” fails to capture the dynamics of either persistence of the virus (as measured by recovery using probangs) or the uncertainty in transmission from such animals that the term implies. In these respects it is not particularly useful. We therefore propose the first predictive statistical models for identifying persistently infected cattle in an endemic setting that captures some of the dynamics of the probability of persistence. Furthermore, we provide a set of predictive tools to use alongside NSP ELISAs to help target persistently infected cattle