Incorporating limited field operability and legacy soil samples in a hypercube sampling design for digital soil mapping

Most calibration sampling designs for Digital Soil Mapping (DSM) demarcate spatially distinct sample sites. In practical applications major challenges are often limited field accessibility and the question on how to integrate legacy soil samples to cope with usually scarce resources for field sampling and laboratory analysis. The study focuses on the development and application of an efficiency improved DSM sampling design that (1) applies an optimized sample set size, (2) compensates for limited field accessibility, and (3) enables the integration of legacy soil samples. The proposed sampling design represents a modification of conditioned Latin Hypercube Sampling (cLHS), which originally returns distinct sample sites to optimally cover a soil related covariate space and to preserve the correlation of the covariates in the sample set. The sample set size was determined by comparing multiple sample set sizes of original cLHS sets according to their representation of the covariate space. Limited field accessibility and the integration of legacy samples were incorporated by providing alternative sample sites to replace the original cLHS sites. We applied the modified cLHS design (cLHS_adapt) in a small catchment (4.2 km²) in Central China to model topsoil sand fractions using Random Forest regression (RF). For evaluating the proposed approach, we compared cLHS_adapt with the original cLHS design (cLHS_orig). With an optimized sample set size n = 30, the results show a similar representation of the cLHS covariate space between cLHS_adapt and cLHS_orig, while the correlation between the covariates is preserved (r = 0.40 vs. r = 0.39). Furthermore, we doubled the sample set size of cLHS_adapt by adding available legacy samples (cLHS_adapt+) and compared the prediction accuracies. Based on an external validation set cLHS_val (n = 20), the coefficient of determination (R²) of the cLHS_adapt predictions range between 0.59 and 0.71 for topsoil sand fractions. The R²‐values of the RF predictions based on cLHS_adapt+, using additional legacy samples, are marginally increased on average by 5%.     

Aspen Populus tremula is a key habitat for tree-dwelling bats in boreonemoral and south boreal woodlands in Norway

This study aims to identify which tree species bats use as maternity roosts in woodland in southern Norway and, to assess the effectiveness of bat boxes as potential mitigating measures if roosts are lost to forestry or other factors. Radio telemetry was used to find roosts in summer during late pregnancy and through the lactation period by tagging two common species; Daubenton's bats Myotis daubentonii (Kuhl 1817) and soprano pipistrelles Pipistrellus pygmaeus (Leach 1825). In addition, tree roosts were searched using ultrasound detectors at three sites. A total of 35 roosts in natural crevices were found using radio telemetry and through searches with ultrasound detectors and 31 of these roosts were in hollow trees, the majority in aspens Populus tremula L. (n?=?30). Some tree roosts were even used by the northern bat Eptesicus nilssonii (Keyserling &; Blasius 1839) which is considered a house-dwelling species in Norway. Aspens have some qualities preferred by bats and were both warmer and safer than other hollow tree species in this study area. Bat boxes are used as maternity roosts mainly by soprano pipistrelles at these latitudes, thus at present, there is no suitable alternative to hollow trees that would satisfy all tree-dwelling bat species.     

Modelling natural drying of European beech (Fagus sylvatica L.) logs for energy based on meteorological data

A key factor for improving the whole fuel wood supply chain is moisture management. Moisture affects material quality, transport costs and revenue. The aim of this study was to develop a drying model for piled European beech (Fagus sylvatica L.) logs based on meteorological data, employing the continuous weighing approach. Two drying cycles with three piles altogether were conducted. In the first one (February to October 2013) the moisture content of the pile dropped from 43.5% to 22.5%, whereas in the second one (December 2013 to March 2015), the moisture content of the 2 piles dropped from 42.1% and 40.5% to 20.6% and 19.8%, respectively. Model performance (R² adj?=?0.41) was validated by applying the model developed from the second cycle's data on the first cycle's data. Model's mean deviation in moisture content from the observed curve was ?0.41%?±?0.72%. Economic benefits and environmental impact were highlighted. Calorific value increased from 2.65 to 3.57?kWh?kg^–1 from February to October 2013. Truckload volume utilization increased by 25.1% and transported calorific value by 48.0%. The number of truck trips for transportation was reduced from nine to seven.     

Epidemiologically non-feasible singleton reactors at the final stage of BoHV1 eradication: Serological evidence of BoHV2 cross-reactivity

A voluntary marker-independent Bovine Herpesvirus 1 (BoHV1) eradication program started in 1986; in 1998 it changed to a compulsory one. Certification of free regions in European member states is based on Article 10 of directive 64/432/EEC. According to this rule Bavaria is listed as free of BoHV1 since October 2011. Surveillance of BoHV1-free dairy cattle farms is currently performed with quarterly bulk-milk testing. Non-negative bulk-milk results must be confirmed by blood tests in cattle older than nine months. An increased regional rate of non-negative bulk-milk samples and the subsequent detection of epidemiologically non-feasible singleton BoHV1-reactors by analysis of blood were observed at the final stage of eradication in southwest Bavaria. Nineteen case farms (734 animals) defined by singleton reactors born at least two years after certification of the farms as BoHV1-free, 23 negative control (NC) farms (NC I: 321 animals) from the same region, 11 NC-farms (NC II: 423 animals) from an already-certified Article 10 region in northeast Bavaria and two BoHV1-infected farms (264 animals) were analysed using BoHV1-, BoHV2- and Feline Herpesvirus 1 (FeHV1)-neutralisation tests (NTs), and three commercially available ELISAs supplied by Idexx Laboratories, B.V., The Netherlands: the CHEKIT? Trachitest 2nd Gen. test for milk or serum (Trachitest), Herdchek? gB- (gB-ELISA) and Herdchek? gE-ELISA (gE-ELISA). Significantly increased levels of BoHV2 antibodies were observed on case farms compared to NC I or II farms. Additionally, reactivity by gB-ELISA and the Trachitest was significantly increased for animals with BoHV2 neutralising antibodies. Singleton BoHV1-reactors tested negative by gE-ELISA even if an elevated cut-off of 0.95±0.05 was applied. At this cut-off, the gE-ELISA was as sensitive and specific as the gB-ELISA. Comparative titration of milk samples from seropositive animals from a BoHV1-infected dairy cattle farm and from singleton BoHV1-reactors performed in CHEKIT? Trachitest 2nd Gen. Milk revealed that the slopes of both groups were distinct; therefore, optimised cut-offs for bulk-milk testing to exclude singleton BoHV1-reactors are proposed.     

A case of a canine pigmented plaque associated with the presence of a Chi-papillomavirus

The seven fully described canine papillomaviruses (CPVs) have been allocated by sequence comparison and other genetic features into three phylogenetic clades. This largely reflects clinical findings, so each sequence of a newly discovered CPV in combination with clinical and pathological details is a valuable piece of evidence. We hypothesize that the genomic sequence of a new CPV can help to predict clinical features and progression, and that this can be tested in subsequent cases. In this case, a 2-year-old female dachshund-mix presented with papillomatosis clinically and histologically characterized as pigmented viral plaques. PCRs using primers evaluated for CPVs successfully amplified papillomavirus (PV) DNA. Sequencing of the products revealed an unknown PV putatively belonging to the PV genus Chi. Rolling circle amplification was used to amplify the entire viral genome. Sequencing revealed a novel PV, designated as CPV8, which was most closely related (63% homology) to the recently discovered CPV4. CPV4 is associated with benign pigmented plaques in pugs. Phylogenetic analysis based on the nucleotide sequences of four viral genes showed that the novel virus was closest to CPV3, CPV4 and CPV5. The presence of viral DNA was confirmed in the lesions by in situ hybridization using specific probes. CPV8 may consequently be regarded as the fourth member of the Chi-papillomavirus genus. All viruses belonging to this genus induce pigmented plaques in dogs. These findings support the hypothesis that genomic sequences can be useful in predicting the clinical features of CPV infection.     

Proteomic analyses of Ehrlichia ruminantium highlight differential expression of MAP1-family proteins

The Rickettsiales Ehrlichia ruminantium (ER) is the causative agent of heartwater, a fatal tick-borne disease of livestock in sub-Saharan Africa and in the Caribbean, posing strong economical constraints to livestock production. In an attempt to identify the most prominent proteins expressed by this bacterium, especially those encoded by the major antigenic protein 1 (map1) multigene family, a proteome map of ER cultivated in endothelial cells was constructed by using two dimensional gel electrophoresis combined with mass spectrometry. Among the sixty-four spots detected, we could identify only four proteins from the MAP1-family; the other proteins detected were mainly related to energy, amino acid and general metabolism (26%), to protein turnover, chaperones and survival (21%) and to information processes (14%) or classified as hypothetical proteins (23%). Additional studies on MAP1-family protein using immunochemical labeling also revealed that these proteins are differentially expressed along the bacterium life cycle, presenting different structural organization. Interestingly, when infectious elementary bodies (EBs) are released from host cells, MAP1 appears to be organized in SDS and heat-resistant dimers and trimers stabilized by disulfide bridges. Overall, the results presented herein not only reveal the first partial proteome map of ER but provide new insights on the expression ER MAP1-family proteins in host endothelial cells.     

Natural Bagaza virus infection in game birds in southern Spain

ABSTRACT: In late summer 2010 a mosquito born flavivirus not previously reported in Europe called Bagaza virus (BAGV) caused high mortality in red-legged partridges (Alectoris rufa) and ring-necked pheasants (Phasianus colchicus). We studied clinical findings, lesions and viral antigen distribution in naturally BAGV infected game birds in order to understand the apparently higher impact on red-legged partridges. The disease induced neurologic signs in the two galliform species and, to a lesser extent, in common wood pigeons (Columba palumbus). In red-legged partridges infection by BAGV caused severe haemosiderosis in the liver and spleen that was absent in pheasants and less evident in common wood pigeons. Also, BAGV antigen was present in vascular endothelium in multiple organs in red-legged partridges, and in the spleen in common wood pigeons, while in ring-necked pheasants it was only detected in neurons and glial cells in the brain. These findings indicate tropism of BAGV for endothelial cells and a severe haemolytic process in red-legged partridges in addition to the central nervous lesions that were found in all three species.     

Pathogenicity and immunogenicity of different recombinant Newcastle disease virus clone 30 variants after in ovo vaccination

Even though Newcastle disease virus (NDV) live vaccine strains can be applied to 1-day-old chickens, they are pathogenic to chicken embryos when given in ovo 3 days before hatch. Based on the reverse genetics system, we modified recombinant NDV (rNDV) established from lentogenic vaccine strain Clone 30 by introducing specific mutations within the fusion (F) and hemagglutinin-neuraminidase (HN) proteins, which have recently been suggested as being responsible for attenuation of selected vaccine variants (Mast et al. Vaccine 24:1756-1765, 2006) resulting in rNDV49. Another recombinant (rNDVGu) was generated to correct sequence differences between rNDV and vaccine strain NDV Clone 30. Recombinant viruses rNDV, rNDV49, and rNDVGu have reduced virulence compared with NDV Clone 30, represented by lower intracerebral pathogenicity indices and elevated mean death time. After in ovo inoculation, hatchability was comparable for all infected groups. However, only one chicken from the NDV Clone 30 group survived a 21-day observation period; whereas, the survival rate of hatched chicks from groups receiving recombinant NDV was between 40% and 80%, with rNDVGu being the most pathogenic virus. Furthermore, recombinant viruses induced protection against challenge infection with virulent NDV 21 days post hatch. Differences in antibody response of recombinant viruses indicate that immunogenicity is correlated to virulence. In summary, our data show that point mutations can reduce virulence of NDV. However, alteration of specific amino acids in F and HN proteins of rNDV did not lead to further attenuation as indicated by their pathogenicity for chicken after in ovo inoculation.     

Efficacy of two vaccine formulations against contagious bovine pleuropneumonia (CBPP) in Kenyan indigenous cattle

A live, attenuated vaccine is currently the only viable option to control of CBPP in Africa. It has been suggested that simple modifications to current vaccines and protocols might improve efficacy in the field. In this report we compared the current vaccine formulation with a buffered preparation that maintains Mycoplasma viability at ambient temperature for a longer time. Groups of animals were vaccinated with the two formulations and compared with non vaccinated groups. Half of the animals in each group were challenged 3 months post vaccination, the other half after 16 months. Protection levels were measured using the pathology index, calculated from post mortem scores of lesions from animals killed during the course of clinical disease. In the challenge at 3 months post vaccination, the protection levels were 52% and 77% for the modified and current vaccine preparations, respectively. At 16 months post vaccination, the protection levels were 56% and 62% for the modified and current vaccine preparations, respectively. These findings indicate that there are no differences in protection levels between the two vaccines. Because of its longer half life after reconstitution, the modified vaccine might be preferred in field situations where the reconstituted vaccine is likely not to be administered immediately.     

Application of principal component and discriminant analyses to morpho-structural indices of indigenous and exotic chickens raised under intensive management system

The objectives of this study were to investigate the relationships between body weight and morpho-structural indices to predict body weight from their orthogonal body shape characters using principal component analysis and to morphologically classify the chicken genotypes using multivariate discriminant analysis. Data used were from 273 randomly selected 12-weeks-old indigenous chickens of normal-feathered (NF), frizzle-feathered (FF), naked-neck (NN) and Anak Titan (AT) genotypes. Phenotypic correlation among body weight and most biometric traits ranged from 0.227-0.876, -0.7-0.901, 0.034-0.968 and -0.207-0.849 for NF, NN and AT chickens, respectively. Factor analysis with varimax rotation of interrelated traits revealed three principal components which accounted for 83.1%, 74.4%, 78.8% and 76.5% of the total variance in NF, FF, NN and AT chickens in the order listed. Breast girth, keel length, thigh length, shank length and wing length were found to be the most discriminating variables to separate the chicken genotypes. The longest distance (72.54) occurred between AT and NF genotypes while the shortest distance (4.27) was recorded for FF and NN genotypes. Classification results showed that 85.2% of AT genotype was correctly classified into their source population. However, 22.7% of NF was misclassified as NN, while 33.3% of NN was misclassified as NF chickens. These results suggest that there is high rate of gene flow between these two indigenous chicken genotypes. Information obtained from this study may be considered useful in breed improvement programmes for selection, characterization, conservation and better management of Nigerian indigenous chickens.