High-resolution protein structure determination by serial femtosecond crystallography

Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.     

Mobilities of organic compounds in reconstituted cuticular wax of barley leaves: Determination of diffusion coefficients

Isolated cuticular wax, obtained from barley leaves, was mixed with ¹⁴Clabelled organic chemicals including aromatic pesticides and long-chain linear alkanes, alcohols and acids. These mixtures were reconstituted from the melt and labelled chemicals were desorbed from the wax by immersing the wax samples in aqueous phospholipid suspensions. Diffusion coefficients (D) of radiolabelled test compounds in the wax were derived from desorption kinetics. Diffusion coefficients ranged from 10^?17 to 10^?22 m² s^?1 and decreased rapidly with increasing molar volumes of solutes. However, size selectivity of D was much more pronounced with the linear, long-chain molecules than with the aromatic compounds. It is argued that the two different groups of chemicals (compounds occurring naturally in cuticular waxes vs pesticide molecules) were trapped in different fractions of wax during crystallization from the melt. The normal long-chain aliphatic compounds appear to be incorporated into the crystalline fraction of the wax, while the cyclic pesticide molecules are confined to the solid amorphous regions. Our data indicate that constituents of cuticular waxes are not immobile. In fact, relatively small linear aliphatic molecules have mobilities that do not differ too much from those of cyclic pesticides. However, the pronounced size selectivity of diffusivities of long-chain aliphatic compounds causes a rapid decrease in D with increasing chain length. The value of D of hexadecanoic acid was 3.81 × 10^?18 m² s^?1 while that of dotriacontane was only 4.07 × 10^?22 m² s^?1. Thus, increasing the carbon number by a factor of two resulted in a decrease in mobility by almost four orders of magnitude. Diffusivities of selected pesticide molecules in reconstituted wax were compared with permeances measured using intact barley leaves and were found to be in satisfactory agreement.     

Natural variation in baseline data: when do we call a new sample 'resistant'?

Mortality of pear psylla to amitraz was studied by means of bioassays. Variation between samples, temporal variation within the season in one orchard and spatial variation between Swiss regions were considered. Variation between samples was large enough to produce different Probit functions and LC50 values. Temporal and spatial variations were too small to indicate resistance. Prediction intervals of the pooled functions using bootstrapping were calculated to determine if future samples come from a population with decreased sensitivity. Probabilistic criteria on the population level were proposed for resistance.     

Mobilities of Organic Compounds in Reconstituted Cuticular Wax of Barley Leaves: Effects of Monodisperse Alcohol Ethoxylates on Diffusion of Pentachlorophenol and Tetracosanoic Acid

Effects of monodisperse alcohol ethoxylates on mobilities of ¹⁴C-labelled pentachlorophenol (PCP) and tetracosanoic acid (C₂₄AC) in reconstituted cuticular wax of barley leaves were measured. Depending on the respective alcohol ethoxylate investigated, the diffusion coefficient (D) of PCP in barley wax was increased by factors ranging from 3·3 to 19·6, whereas D of C₂₄AC, was increased by factors varying between 22 and 315. In order to analyse the relationship between the concentration of surfactants in the wax and their effects on D, the amounts of alcohol ethoxylates dissolved in the wax at equilibrium with external concentrations well above the critical micelle concentration (CMC) were determined. Wax/water partition coefficients (K_ww) of the alcohol ethoxylates were about one order of magnitude lower than cuticle/water partition coefficients (K_cw), which is a consequence of the semi-crystalline structure of the wax compared with amorphous cutin. Correlations between effects on D and maximum amounts of alcohol ethoxylates dissolved in the wax were obtained indicating an unspecific wax/surfactant interaction. This was solely dependent on the amount of surfactant sorbed to the wax, leading to increased mobilities of pesticides in the wax. Applying ESR-spectroscopy, which gave an insight into the molecular structure of the wax, supported this interpretation of an unspecific plasticising effect of the alcohol ethoxylates on the molecular structure of the wax. The results obtained in this study are in good accordance with the results obtained in a recent study investigating the effects of the same group of alcohol ethoxylates on mobilities of pesticides in isolated, but intact, cuticular membranes of Citrus. This demonstrates that the investigation of isolated and subsequently reconstituted cuticular wax is a useful model system analysing the mechanisms of the surfactant interaction with the transport-limiting barrier of plant cuticles.     

Plant growth responses to biochar addition: an Australian soils perspective

The use of biochar as an agricultural amendment has attracted much attention owing to its potential to improve soil condition and plant growth; however, production outcomes are often uncertain. Although soil type is a major driver of plant productivity, there are relatively few biochar studies that directly compare plant growth responses across a range of soil types. We tested the wheat growth response to biochar derived from poultry litter and from wheat straw applied at 1, 5 and 10 t ha^?1 (approximately 0.13, 0.67 and 1.33 % w/w) in four soils representing major agricultural regions in Australia: an acidic arenosol (Western Australian cereal belt), an acidic rhodic ferralsol (Northern New South Wales), a neutral vertisol (Queensland cropping) and an alkaline haplic calcisol (Eyre Peninsula in South Australia). In the neutral vertisol, where plant growth was vigorous in the control treatments, biochar had little impact, whereas in the alkaline calcisol, there was a small significant increase in shoot biomass at high (10 t ha^?1) application rates. Plant growth responses in the acidic soils were most evident but demonstrated a strong contrast to one another. In the acidic arenosol, negative growth impact correlated with increasing electrical conductivity, while in the acidic ferralsol a small rate-dependent increase in pH correlated with relatively large gains in biomass, possibly due to improved phosphorus nutrition and alleviated Al toxicity. Moving towards effective integration of biochar as a management tool will not only require stratification based on soil types, but wider consideration of the main plant production constraints, such as pH, pertinent to a particular system.     

Sorption in reconstituted waxes of homologous series of alcohol ethoxylates and n-alkyl esters and their effects on the mobility of 2,4-dichlorophenoxybutyric acid

Equilibrium sorption of n-alkyl esters (dimethyl suberate, diethyl suberate, diethyl sebacate, dibutyl suberate and dibutyl sebacate) and monodisperse alcohol ethoxylates (diethylene glycol, tetraethylene glycol, pentaethylene glycol, hexaethylene glycol and octaethylene glycol monododecyl ether) between the reconstituted cuticular waxes of Stephanotis floribunda Brongn (Madagascar jasmine) or Hordeum vulgare L (barley) leaves and an external aqueous receptor solution was determined. Logarithms of the wax/receptor partition coefficient (K(wax/rec)) of the n-alkyl esters increased linearly with the number of C-atoms. With alcohol ethoxylates, log K(wax/rec) decreased linearly with the number of ethylene oxide units. For both groups of compounds, K(wax/rec) increased with increasing lipophilicity. The values of K(wax/rec) in Stephanotis wax were between 5 and 16 times higher than in barley wax. It is argued that this difference was due to different chemical composition and crystallinity of the waxes. Mobility of [14C]2,4-dichlorophenoxybutyric acid (2,4-DB) in reconstituted Stephanotis and barley wax was increased by a factor of 2-8 by both n-alkyl esters and alcohol ethoxylates. Effects on the mobility of 2,4-DB were linearly related to the internal concentrations of n-alkyl esters and alcohol ethoxylates in reconstituted Stephanotis or barley wax. At the same internal concentrations the effect of n-alkyl esters on the mobility of 2,4-DB in wax exceeded that of alcohol ethoxylates by between 1 and 2 orders of magnitude. Results are discussed in relation to formulating systemic pesticides.     

Spatial interpretation of plant parameters in winter wheat

A methodology is described for the spatial interpretation of plant parameters (SIOPP), which was used to diagnose the nutritional status of winter wheat. The data used in this study were collected in 2010 throughout the monitoring of two fields (52 and 38 ha) with uniform and conventional agricultural management, located in the Czech Republic. The survey was carried out at BBCH 30 phenological stage in a regular sampling grid with 150 m of distance between grid points (27 and 18 samples). The plant height and the chlorophyll concentration (Yara N-Tester) were recorded. Plant and soil samples were taken to analyse the nutrient concentrations (N, P, K, Mg, Ca, and S). A crop development index (CDI) was developed combining plant height and N-Tester values to quantify the growth of the plant (biomass and vigour). The relationship between this index and the concentration of nutrients were studied and confirmed by cross-validation and spatial analysis; the aim was to determine the factors that limit plant growth. The method revealed the limiting factors in field #1 were potassium, calcium (pH problems) and nitrogen (in descending order of relevance). In field #2, CDI was only related to the soil moisture. In all cases, it was found that the spatial variability of the indices and the limiting factors followed a pattern result of the combination of the gradients in climate, topography and soils of each field. This allowed the interpolation of the maps for variable-rate application using only 0.5 samples per hectare arranged in regular mesh, which was insufficient for the use of geostatistics. All diagnoses were consistent with the crop yield, the soil sampling and the DRIS diagnoses. The results showed that if leaf analyses are complemented with a few additional measures, instantaneous and with a minimal cost, it is possible to deduce the diagnosis using statistical and spatial analysis.     

Evaluation of the benefit of emergency vaccination in a foot-and-mouth disease free country with low livestock density

Foot-and-mouth disease (FMD) is highly contagious and one of the most economically devastating diseases of cloven-hoofed animals. Scientific-based preparedness about how to best control the disease in a previously FMD-free country is therefore essential for veterinary services. The present study used a spatial, stochastic epidemic simulation model to compare the effectiveness of emergency vaccination with conventional (non-vaccination) control measures in Switzerland, a low-livestock density country. Model results revealed that emergency vaccination with a radius of 3 km or 10 km around infected premises (IP) did not significantly reduce either the cumulative herd incidence or epidemic duration if started in a small epidemic situation where the number of IPs is still low. However, in a situation where the epidemic has become extensive, both the cumulative herd incidence and epidemic duration are reduced significantly if vaccination were implemented with a radius of 10 km around IPs. The effect of different levels of conventional strategy measures was also explored for the non-vaccination strategy. It was found that a lower compliance level of farmers for movement restrictions and delayed culling of IPs significantly increased both the cumulative IP incidence and epidemic duration. Contingency management should therefore focus mainly on improving conventional strategies, by increasing disease awareness and communication with stakeholders and preparedness of culling teams in countries with a livestock structure similar to Switzerland; however, emergency vaccination should be considered if there are reasons to believe that the epidemic may become extensive, such as when disease detection has been delayed and many IPs are discovered at the beginning of the epidemic.     

Endoscopic Assessment of the Duodenum in Dogs with Inflammatory Bowel Disease

Background

Endoscopy is performed for direct inspection of the mucosa and acquisition of biopsies in dogs with inflammatory bowel disease (IBD).

Aim

To evaluate the interobserver agreement in the endoscopic assessment of duodenal mucosa in dogs with IBD.

Methods

Thirty‐five archived endoscopic images of grossly normal (n = 6) and inflamed (n = 29) duodenal mucosa were displayed to 3 expert and 5 trainee endoscopists. Each image was assessed independently by endoscopists for mucosal abnormalities using established indices (of hyperemia, granularity, friability, lymphatic dilatation, and erosions) or interpreted as normal mucosa (trial 1). A repeated trial (trial 2) was performed with the same images presented in random order 1 month later, and accompanied by a visual template.

Results

There was slight interobserver agreement in initial mucosal assessment for expert and trainee endoscopists in trial 1 (kappa ≤ 0.02, P > .05). Interobserver agreement improved in trial 2 for both expert and trainee endoscopists (kappa = 0.2, P > .05) for experts and (P < .05) for trainees. There was a significant (P < .01) improvement in trainee endoscopy scores of lesions from trial 1 to trial 2. Regression analysis showed a significant (P < .01) difference between expert versus trainee endoscopy scores in trial 1. Repeat lesion assessment aided by use of a visual template (trial 2) improved the overall scores of trainee endoscopists to near that of expert endoscopists (P = .06).

Conclusions and Clinical Importance

Interobserver agreement of IBD mucosal appearance from endoscopic findings benefitted from operator experience.     

Rapid destruction of human Cdc25A in response to DNA damage

To protect genome integrity and ensure survival, eukaryotic cells exposed to genotoxic stress cease proliferating to provide time for DNA repair. Human cells responded to ultraviolet light or ionizing radiation by rapid, ubiquitin- and proteasome-dependent protein degradation of Cdc25A, a phosphatase that is required for progression from G1 to S phase of the cell cycle. This response involved activated Chk1 protein kinase but not the p53 pathway, and the persisting inhibitory tyrosine phosphorylation of Cdk2 blocked entry into S phase and DNA replication. Overexpression of Cdc25A bypassed this mechanism, leading to enhanced DNA damage and decreased cell survival. These results identify specific degradation of Cdc25A as part of the DNA damage checkpoint mechanism and suggest how Cdc25A overexpression in human cancers might contribute to tumorigenesis.