In silico prediction of Gallibacterium anatis pan-immunogens

The Gram-negative bacterium Gallibacterium anatis is a major cause of salpingitis and peritonitis in commercial egg-layers, leading to reduced egg production and increased mortality. Unfortunately, widespread multidrug resistance and antigenic diversity makes it difficult to control infections and novel prevention strategies are urgently needed. In this study, a pan-genomic reverse vaccinology (RV) approach was used to identify potential vaccine candidates. Firstly, the genomes of 10 selected Gallibacterium strains were analyzed and proteins selected on the following criteria; predicted surface-exposure or secretion, none or one transmembrane helix (TMH), and presence in six or more of the 10 genomes. In total, 42 proteins were selected. The genes encoding 27 of these proteins were successfully cloned in Escherichia coli and the proteins expressed and purified. To reduce the number of vaccine candidates for in vivo testing, each of the purified recombinant proteins was screened by ELISA for their ability to elicit a significant serological response with serum from chickens that had been infected with G. anatis. Additionally, an in silico prediction of the protective potential was carried out based on a protein property prediction method. Of the 27 proteins, two novel putative immunogens were identified; Gab_1309 and Gab_2312. Moreover, three previously characterized virulence factors; GtxA, FlfA and Gab_2156, were identified. Thus, by combining the pan-genomic RV approach with subsequent in vitro and in silico screening, we have narrowed down the pan-proteome of G. anatis to five vaccine candidates. Importantly, preliminary immunization trials indicated an in vivo protective potential of GtxA-N, FlfA and Gab_1309.

Electronic supplementary material

The online version of this article (doi:10.1186/s13567-014-0080-0) contains supplementary material, which is available to authorized users.     

Landscape-scale variation in the structure and biomass of the hill dipterocarp forest of Sumatra: Implications for carbon stock assessments

One of the first steps in estimating the potential for reducing emissions from deforestation and forest degradation (REDD) initiatives is the proper estimation of the carbon components. There are still considerable uncertainties about carbon stocks in tropical rain forest, coming essentially from poor knowledge of the quantity and spatial distribution of forest biomass at the landscape level.     

Transformation of organic rhizodepositions by rhizosphere bacteria and its influence on the availability of tertiary calcium phosphate

This study assesses the influence of saccharides in the rhizodeposition on the phosphate solubilizing ability of rhizosphere bacteria. Water‐soluble rhizodeposits were analyzed of ¹⁴C‐labeled pea plants (Pisum sativum, cv. ‘Grapis’) which were grown at two different levels of P‐nutrition. The sugars produced were fed in vitro either as single compounds or as synthetic mixtures to three bacterial strains and the ability of the bacteria to mobilize Ca₃(PO₄)₂ was measured. The relative glucose proportion of pea exudates decreased under P deficiency while the content of galactose, ribose, xylose and fucose increased. In vitro feeding of single sugars and sugar mixtures showed that the ability of Pseudomonas fluorescens (PsIA12) to dissolve tertiary calcium phosphate was lower with pentoses and the mixed sugars of the P‐deficient plants than with glucose. On the other hand, the shifted sugar pattern observed under P deficiency increased the phosphate mobilization ability of Pantoea agglomerans (D5/23) and Azospirillum sp. (CC 322) considerably. This observation can only partly be explained by the acidification of the nutrient medium. Bacteria also produced different carboxylic anions depending on sugar supply. In addition to low‐molecular mono‐, di‐, and tricarboxylic acids which are known as P‐solubilizing substances, sugar acids also played an important role in cultures D 5/23 and CC 322.     

Detection of near-atmospheric concentrations of CO2 by an olfactory subsystem in the mouse

Carbon dioxide (CO2) is an important environmental cue for many organisms but is odorless to humans. It remains unclear whether the mammalian olfactory system can detect CO2 at concentrations around the average atmospheric level (0.038%). We demonstrated the expression of carbonic anhydrase type II (CAII), an enzyme that catabolizes CO2, in a subset of mouse olfactory neurons that express guanylyl cyclase D (GC-D+ neurons) and project axons to necklace glomeruli in the olfactory bulb. Exposure to CO2 activated these GC-D+ neurons, and exposure of a mouse to CO2 activated bulbar neurons associated with necklace glomeruli. Behavioral tests revealed CO2 detection thresholds of approximately 0.066%, and this sensitive CO2 detection required CAII activity. We conclude that mice detect CO2 at near-atmospheric concentrations through the olfactory subsystem of GC-D+ neurons.     

The use of the first industrial X-ray CT scanner increases the lumber recovery value: case study on visually strength-graded Douglas-fir timber

Key message

Industrial computed tomography scanning of logs provides detailed information on timber quality prior to sawing. A sawing simulation—considering log rotation angle and knot size accuracy—revealed an average value increase of up to 20% for the best angle compared to the conventional horns-up position.

Context

Computed tomography (CT) scanning has the potential to improve the value of products sawn from logs and meets the increasing demands of the wood industry for detailed information on log quality prior to processing.

Aims

In a validation step, automated measurements of knot cluster variable DAB (DIN 4074-1:2012-06) using CT were compared with manual measurements. In a second optimization step, the hypothesis that the value of the sawn products is increased by sawing at the best rotation angle as opposed to the horns-up position was tested.

Methods

A sample of 36 Douglas-fir logs were scanned in an industrial CT scanner, and sawn into boards. Knots on the boards were manually measured, and compared with the corresponding knots on virtual boards created from the CT data. The error of the DAB was measured by comparing CT data to manual measurements. An optimized sawing simulation was performed, using the measured DAB error to account for CT measurement errors, as well as a rotational error to account for errors in the log turning equipment. Using the results of the sawing simulation, Monte Carlo simulations were performed to show the potential and benefit of an industrial CT scanner.

Results

The three largest DABs measured by the CT showed good correlation to the measurements on the manual boards. The simulation revealed an average increase of value from 4 to 20% compared to the conventional horns-up position depending on the relative price differences between the strength grades.

Conclusion

By using a CT scanner to optimize sawing, sawmill owners can process logs in a better way to produce final products with increased added value.

     

NH3 Volatilization,N2O Emission and Microbial Biomass Turnover from 15N-Labeled Manure Under Laboratory Conditions

On irrigated agricultural soils from semi-arid and arid regions, ammonia (NH₃) volatilization and nitrous oxide (N₂O) emission can be a considerable source of N losses. This study was designed to test the capture of ¹⁵N loss as NH₃ and N₂O from previous and recent manure application using a sandy, calcareous soil from Oman amended one or two times with ¹⁵N labeled manure to elucidate microbial turnover processes under laboratory conditions. The system allowed to detect ¹⁵N enrichments in evolved N₂O-N and NH₃-N of up to 17% and 9%, respectively, and total N, K₂SO₄ extractable N and microbial N pools from previous and recent ¹⁵N labeled manure applications of up to 7%, 8%, and 15%. One time manured soil had higher cumulative N₂O-N emissions (141 µg kg^?1) than repeatedly manured soil with 43 µg kg^?1 of which only 22% derived from recent manure application indicating a priming effect.     

Fate of heavy metals in a strongly acidic shooting‐range soil: small‐scale metal distribution and its relation to preferential water flow

To assess the mobility of Pb and associated metals in a highly contaminated shooting range soil (Losone, Ticino, Switzerland), we investigated the spatial distribution of the metals and their relation to preferential water flow paths. A 2.2 m² plot located 40 m behind the stop butt was irrigated with a solution containing bromide and Brilliant Blue, a slightly sorbing dye. A soil profile 50 cm in width was sampled down to 80 cm with a spatial resolution of 2.5 cm, resulting in 626 samples. Concentrations of elements (12 ≤ Z ≤ 92) were determined by energy‐dispersive Xray fluorescence spectrometry, and Brilliant Blue concentrations were determined with a chromameter. In the acidic (pH 3), organic matter‐rich, well drained Dystric Cambisol, maximum concentrations of 80.9 g kg^‐1 Pb, 4.0 g kg^‐1 Sb, and 0.55 g kg^‐1 Cu were measured in the topsoil. Within 40 cm soil depth, however, Pb, Sb, and Cu approached background concentrations of 23 mg kg^‐1, 0.4 mg kg^‐1, and 9.4 mg kg^‐1, respectively. The even horizontal distribution and the steep gradient along soil depth indicate tight metal binding in the topsoil, and a fairly homogeneous transport front. In contrast, water flow through the profile was highly heterogeneous. In the uppermost 20 cm, preferential flow was initiated by heterogeneous infiltration at the soil surface, but had no influence on metal distribution. Below 20 cm, however, preferential flow originated from larger tree roots, and metal concentrations were significantly elevated along these macropores. Spatial distributions of Pb, Sb, and Cu were similar, suggesting that all three metals are strongly retained in the topsoil and transported along preferential water flow paths in the subsoil.     

Phosphorus availability,root exudates,and microbial activity in the rhizosphere

Field and pot experiments showed that the P demand of wheat is highest in early stages of growth (up to 1.67 μg P per cm² root surface and day). The needed orthophosphate ions H₂PO₄? and HPO₄²-move from soil to the root by diffusion. This process is controlled by the concentration gradient of the diffusible phosphate and the effective diffusion coefficient according to Pick's first law. Root excretions (rhizodeposition) are able to affect both characteristics. The water soluble portion of rhizodeposition contains more than 50% of up to 8 different sugars, 10–40% carboxylic acids and 10–15 amino acids and amides. The composition varies in dependence on the age of the root parts and on nutrition (Zea mays L., Brassica napus L., Pisum sativum L.). Diffusion experiments using small soil blocks showed that 50–75% of the root exudates were decomposed by respiration within 3 days. The rest was largely chemically converted. Originally present sugars disappeared. Due to the biosynthesis of different organic acids from the individual sugars the mobilisation of Ca₃(PO₄)₂ by Pantoea agglomerans increased when the sugar mixture was derived from the rhizodeposition of P deficient plants with more pentoses instead of glucose and fructose (mainly effect of anions). In the rhizosphere therefore a mixture of rhizodeposition and its conversion products exists which affects the binding of phosphorus in soil and the P transport to the root. This should be considered both for the development of new soil extractants and for modelling the P supply to plants.     

Phosphorus and iron erosion from non-vegetated sites in a post-mining landscape,Lusatia, Germany: Impact on aborning mining lakes

Particulate phosphorus (P) can be transported via soil erosion in overland flow to waters, where it provides a long-term source of P for aquatic biota, and can accelerate freshwater eutrophication. Hence, knowledge of P sources is important for good environmental management. However, data on P, and related Fe, losses from various structures of a post-mining landscape are lacking. A year-long monitoring, and ten short rainfall simulations on plot scale, at ridges and rills and a combination of them, revealed high erosion from bare lignite mining dumps at Schlabendorf-North, Lusatia, Germany. The mean annual soil erosion rate from the year-long monitoring site was 18 × 10⁶ kg km^− 2 yr^− 1, corresponding to 0.034 g m^− 2 min^− 1. The erosion rates were lowest at rill plots (1.9–4.4 g m^− 2 min^− 1), intermediate at ridge plots (14.3–37.1 g m^− 2 min^− 1), and highest at a combined rill and ridge plot (48.7–63.4 g m^− 2 min^− 1). These differences in extent were due to small scale differences in morphology and extreme water repellency. The hydrophobicity leads to very low infiltration, thus generating surface runoff even at low rainfall intensities. Loss rates of P and Fe, as deduced from the year-long erosion rate, were 470–650 kg km^− 2 yr^− 1, and 37.9 × 10³–71 × 10³ kg km^− 2 yr^− 1 respectively. However, these P inputs from lignite mining dump erosion, consisting of P-poor (17–90 μg g^− 1) tertiary spoil materials, into aborning mining lakes, are negligible since they are accompanied by high Fe inputs, which favour an efficient P co-precipitation in the water column.     

Quantum spin hall insulator state in HgTe quantum wells

Recent theory predicted that the quantum spin Hall effect, a fundamentally new quantum state of matter that exists at zero external magnetic field, may be realized in HgTe/(Hg,Cd)Te quantum wells. We fabricated such sample structures with low density and high mobility in which we could tune, through an external gate voltage, the carrier conduction from n-type to p-type, passing through an insulating regime. For thin quantum wells with well width d < 6.3 nanometers, the insulating regime showed the conventional behavior of vanishingly small conductance at low temperature. However, for thicker quantum wells (d > 6.3 nanometers), the nominally insulating regime showed a plateau of residual conductance close to 2e(2)/h, where e is the electron charge and h is Planck's constant. The residual conductance was independent of the sample width, indicating that it is caused by edge states. Furthermore, the residual conductance was destroyed by a small external magnetic field. The quantum phase transition at the critical thickness, d = 6.3 nanometers, was also independently determined from the magnetic field-induced insulator-to-metal transition. These observations provide experimental evidence of the quantum spin Hall effect.