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.     

Amino acid digestibility of heat damaged distillers dried grains with solubles fed to pigs

The primary objective of this experiment was to determine the effects of heat treatment on the standardized ileal digestibility(SID) of amino acids(AA) in corn distillers dried grains with solubles(DDGS) fed to growing pigs. The second objective was to develop regression equations that may be used to predict the concentration of SID AA in corn DDGS. A source of corn DDGS was divided into 4 batches that were either not autoclaved or autoclaved at130°C for 10, 20, or 30 min. Four diets containing DDGS from each of the 4 batches were formulated with DDGS being the only source of AA and CP in the diets. A N-free diet also was formulated and used to determine the basal endogenous losses of CP and AA. Ten growing pigs(initial BW: 53.5 ± 3.9 kg) were surgically equipped with a T-cannula in the distal ileum and allotted to a replicated 5 × 4 Youden square design with 5 diets and 4 periods in each square. The SID of CP decreased linearly(P 0.05) from 77.9% in non-autoclaved DDGS to 72.1, 66.1, and 68.5% in the DDGS samples that were autoclaved for 10, 20, or 30 min, respectively. The SID of lysine was quadratically reduced(P 0.05) from 66.8% in the non-autoclaved DDGS to 54.9, 55.3, and 51.9% in the DDGS autoclaved for 10, 20, or30 min, respectively. The concentrations of SID Arginine, Histidine, Leucine, Lysine, Methionine, Phenylalanine, or Threonine may be best predicted by equations that include the concentration of acid detergent insoluble N in the model(r2= 0.76, 0.68, 0.67, 0.84, 0.76, 0.73, or 0.54, respectively). The concentrations of SID Isoleucine and Valine were predicted(r2= 0.58 and 0.54, respectively) by the Lysine:CP ratio, whereas the concentration of SID Tryptophan was predicted(r2= 0.70) by the analyzed concentration of Tryptophan in DDGS. In conclusion, the SID of AA is decreased as a result of heat damage and the concentration of SID AA in heat-damaged DDGS may be predicted by regression equations developed in this experiment.     

Global and Phylogenetic Distribution of Quorum Sensing Signals,Acyl Homoserine Lactones,in the Family of Vibrionaceae

Bacterial quorum sensing (QS) and the corresponding signals, acyl homoserine lactones (AHLs), were first described for a luminescent Vibrio species. Since then, detailed knowledge has been gained on the functional level of QS; however, the abundance of AHLs in the family of Vibrionaceae in the environment has remained unclear. Three hundred and one Vibrionaceae strains were collected on a global research cruise and the prevalence and profile of AHL signals in this global collection were determined. AHLs were detected in 32 of the 301 strains using Agrobacterium tumefaciens and Chromobacterium violaceum reporter strains. Ethyl acetate extracts of the cultures were analysed by ultra-high performance liquid chromatography-high resolution mass spectrometry (MS) with automated tandem MS confirmation for AHLs. N-(3-hydroxy-hexanoyl) (OH-C6) and N-(3-hydroxy-decanoyl) (OH-C10) homoserine lactones were the most common AHLs found in 17 and 12 strains, respectively. Several strains produced a diversity of different AHLs, including N-heptanoyl (C7) HL. AHL-producing Vibrionaceae were found in polar, temperate and tropical waters. The AHL profiles correlated with strain phylogeny based on gene sequence homology, however not with geographical location. In conclusion, a wide range of AHL signals are produced by a number of clades in the Vibrionaceae family and these results will allow future investigations of inter- and intra-species interactions within this cosmopolitan family of marine bacteria.     

Accurate Dereplication of Bioactive Secondary Metabolites from Marine-Derived Fungi by UHPLC-DAD-QTOFMS and a MS/HRMS Library

In drug discovery, reliable and fast dereplication of known compounds is essential for identification of novel bioactive compounds. Here, we show an integrated approach using ultra-high performance liquid chromatography-diode array detection-quadrupole time of flight mass spectrometry (UHPLC-DAD-QTOFMS) providing both accurate mass full-scan mass spectrometry (MS) and tandem high resolution MS (MS/HRMS) data. The methodology was demonstrated on compounds from bioactive marine-derived strains of Aspergillus, Penicillium, and Emericellopsis, including small polyketides, non-ribosomal peptides, terpenes, and meroterpenoids. The MS/HRMS data were then searched against an in-house MS/HRMS library of ~1300 compounds for unambiguous identification. The full scan MS data was used for dereplication of compounds not in the MS/HRMS library, combined with ultraviolet/visual (UV/Vis) and MS/HRMS data for faster exclusion of database search results. This led to the identification of four novel isomers of the known anticancer compound, asperphenamate. Except for very low intensity peaks, no false negatives were found using the MS/HRMS approach, which proved to be robust against poor data quality caused by system overload or loss of lock-mass. Only for small polyketides, like patulin, were both retention time and UV/Vis spectra necessary for unambiguous identification. For the ophiobolin family with many structurally similar analogues partly co-eluting, the peaks could be assigned correctly by combining MS/HRMS data and m/z of the [M + Na]⁺ ions.     

A model ensemble approach to determine the humus building efficiency of organic amendments in incubation experiments

Organic amendments are important to sustain soil organic matter (SOM) and soil functions in agricultural soils. Information about the contribution of organic amendments to SOM can be derived from incubation experiments. In this study, data from 72 incubated organic amendments including plant residues, digestates and manure were analysed. The incubation data was compiled from three experimental setups with varying incubation times, soils and incubation temperatures, in which CO₂ release was measured continuously. The analysis of the incubation data was performed with an approach relying on conceptual parts of C-TOOL, CCB, Century, ICBM, RothC and Yasso which are all well-approved first-order carbon models that differ in structure and abstraction level. All models are an approximation of reality, whereby each model differs in understanding of the processes involved in soil carbon dynamics. To accumulate the advantages from each model a model ensemble was performed for each substrate. With the ability of each carbon model to compute the distribution of carbon into specific SOM pools a new approach for evaluating organic amendments in terms of humus building efficiency is presented that, depends on the weighted model fit of each ensemble member. Depending on the organic substrate added to the soil, the time course of CO₂ release in the incubation studies was predicted with different accuracy by the individual model concepts. Averaging the output of the individual models leads to more robust prediction of SOM dynamics. The E_HUM value is easy to interpret and the results are in accordance with the literature.     

A quick microtechnique for inspection of potato periderm or wound periderm formation

Summary A method for a quick inspection of wound periderm formation is described. Sections are freehand cut into a stain solution, and microscopic examination is accomplished with an epiplanatic lens.     

The occurrence of summer mastitis in Jutland (Denmark) in relation to meteorological factors

Data for incidence of summer mastitis in 14 veterinary practices in Jutland (Denmark) were related to meteorological factors using statistical methods. A correlation and regression analysis showed that summer mastitis occurred earlier in years with high temperature and precipitation in early summer. The annual number of cases markedly increased over the years 1953 to 1980. This increase was described by applying a linear increase with with year to a logarithmic transformation of the annual incidence.Analysis of 10-day incidences from the veterinary practices and daily incidence from a test site at St. Vildmose (Jutland) showed that incidence of summer mastitis could be related to temperature and wind velocity within the previous 10 days. High temperature and low wind velocity in this period increase the incidence. This indicates that the incubation period of summer mastitis is at maximum about 10 days. The activity of the fly (Hydrotaea irritans Fall), which acts as mechanical vector for the bacteria is influenced by temperature and wind velocity. This may explain the variation in incidence of summer mastitis during the season and from year to year.     

Effects of breeding season length and calving season on range beef cow productivity

A 5-yr study was conducted beginning in 1983 with 460 cows to evaluate the effects of three breeding seasons (30, 45, and 70 d in length) and two times of spring calving, March (early) and April (late), on cattle production under Nebraska Sandhills range conditions. Criteria evaluated included pregnancy and weaning percentages, calving date and distribution, cow weights and body condition at four intervals, calf birth and weaning weights, and cow productivity. The 30-d breeding season included a 10-d estrus synchronization and AI period; in the other breeding seasons only natural breeding was used. The same sires were used over the entire study period. Percentage of cows pregnant and percentage of calves weaned were lower (P less than .01) for cows bred for 30 d than for cows bred for 45 or 70 d. Average calving dates were similar among the breeding groups within the early and late calving herds. Pregnancy rates from AI were higher (P less than .01) for the cows calving in April (64%) than for the cows calving in March (41%). Cows calving in April lost less weight between precalving and prebreeding and were heavier (P less than .05) at prebreeding time than the cows calving in March. Calf weaning weights were not different (P greater than .10) among any of the breeding season groups or between the two calving herds when calves were weaned at a similar age. Cow productivity (calf weaning weight per breeding female) was highest (P less than .05) for the cows bred for 70 d (186 kg), intermediate for the cows bred for 45 d (172 kg), and lowest for cows bred for 30 d (162 kg).(ABSTRACT TRUNCATED AT 250 WORDS)