Cluster analysis of 36Globodera pallida field populations using two sets of molecular markers

Thirty-six populations of the potato cyst nematodeGlobodera pallida, all collected in the Netherlands, were analysed twice: by two-dimensional gel electrophoresis of proteins (2-DGE) and by random amplified polymorphic DNA fingerprinting (RAPD). Two-DGE revealed frequencies of 21 alleles at eight putative loci in each population. The same populations were subjected to RAPD analysis. This qualitative technique revealed 38 polymorphic DNA fragments. Both datasets were independently processed to determine the intraspecific variation. UPGMA analysis resulted in a 2-DGE- and a RAPD-based dendrogram with cophenetic correlation coefficients of 0.755 and 0.838 respectively. The correlation between the genetic similarity values for the populations was 0.572. Comparison between the 2-DGE- and the RAPD-based dendrogram revealed that only thirteen of the 36 populations analysed were clustered identically. It is concluded that the gene pool similarity concept is only in some instances applicable to Dutch populations ofG. pallida. For populations that could not be differentiated unequivocally on the basis of molecular markers, markers closely linked to avirulence genes should be identified. Approaches that will lead to the identification of such markers are discussed.     

Towards complete and accurate reporting of studies of diagnostic accuracy: the STARD initiative

Background:  To comprehend the results of diagnostic accuracy studies, readers must understand the design, conduct, analysis, and results of such studies. That goal can be achieved only through complete transparency from authors.  Objective:  To improve the accuracy and completeness of reporting of studies of diagnostic accuracy to allow readers to assess the potential for bias in the study and to evaluate its generalisability.  Methods:  The Standards for Reporting of Diagnostic Accuracy (STARD) steering committee searched the literature to identify publications on the appropriate conduct and reporting of diagnostic studies and extracted potential items into an extensive list. Researchers, editors, and members of professional organisations shortened this list during a 2-day consensus meeting with the goal of developing a checklist and a generic flow diagram for studies of diagnostic accuracy.  Results:  The search for published guidelines on diagnostic research yielded 33 previously published checklists, from which we extracted a list of 75 potential items. The consensus meeting shortened the list to 25 items, using evidence on bias whenever available. A prototypical flow diagram provides information about the method of patient recruitment, the order of test execution and the numbers of patients undergoing the test under evaluation, the reference standard or both.  Conclusions:  Evaluation of research depends on complete and accurate reporting. If medical journals adopt the checklist and the flow diagram, the quality of reporting of studies of diagnostic accuracy should improve to the advantage of clinicians, researchers, reviewers, journals, and the public.     

Quantification of the spread of Mycoplasma hyopneumoniae in nursery pigs using transmission experiments

Mycoplasma hyopneumoniae (M. hyopneumoniae) is present in almost all swine herds worldwide, but transmission of the pathogen through herds is not yet fully clarified. The aim of this study, performed in 2003, was to investigate and to quantify the transmission of M. hyopneumoniae under experimental conditions by means of an adjusted reproduction ratio (R_n). This R_n-value, calculated according to the final size method, expresses the mean number of secondary infections due to one typical infectious piglet during the nursery period. The period lasted from 4 to 10 weeks of age, corresponding with the nursery period used in most European production systems. Additionally, a comparison was made between transmissions of highly virulent and low virulent isolates.

Forty-eight weaned piglets, free of M. hyopneumoniae, were housed in six separate pens. During 6 weeks, two animals experimentally infected with M. hyopneumoniae were housed together with six susceptible piglets. At the end of the study, the number of contact-infected animals was determined by the use of nPCR on bronchoalveolar lavage fluid. The R_n-values of the highly virulent and the low virulent isolates were estimated to be 1.47 (0.68–5.38) and 0.85 (0.33–3.39), respectively. No significant difference between the groups was found (P = 0.53). The overall R_n was estimated to be 1.16 (0.94–4.08). Under the present experimental conditions, the transmission of M. hyopneumoniae, assessed for the first time by a reproduction ratio, shows that one piglet infected before weaning will infect on average one penmate during the nursery phase.     

Gene-expression profiling of calves 6 and 9?months after inoculation with Mycobacterium avium subspecies paratuberculosis

Early detection of Johne’s disease (JD) caused by Mycobacterium avium subspecies paratuberculosis (MAP) is essential to reduce transmission; consequently, new diagnostic techniques and approaches to detect MAP or markers of early MAP infection are being explored. The objective was to identify biomarkers associated with MAP infection at 6 and 9 months after oral inoculation. Therefore, gene expression analysis was done using whole blood cells obtained from MAP-infected calves. All MAP-inoculated calves had a cell-mediated immune response (IFN-γ) to Johnin PPD specific antigens, and 60% had an antibody response to MAP antigens. Gene expression analysis at 6 months after inoculation revealed downregulation of chemoattractants, namely neutrophil beta-defensin-9 like peptide (BNBD9-Like), S100 calcium binding protein A9 (s100A9) and G protein coupled receptor 77 (GPR77) or C5a anaphylatoxin chemotactic receptor (C5a2). Furthermore, BOLA/MHC-1 intracellular antigen presentation gene was downregulated 9 months after inoculation. In parallel, qPCR experiments to evaluate the robustness of some differentially expressed genes revealed consistent downregulation of BOLA/MHC-I, BNBD9-Like and upregulation of CD46 at 3, 6, 9, 12, and 15 months after inoculation. In conclusion, measuring the expression of these genes has potential for implementation in a diagnostic tool for the early detection of MAP infection.

Electronic supplementary material

The online version of this article (doi:10.1186/s13567-014-0096-5) contains supplementary material, which is available to authorized users.     

Ascorbic acid concentration in Cv. conference pears during fruit development and postharvest storage

L-ascorbic acid (L-AA) concentration changes during the development of cv. Conference pears and the influence of postharvest handlings (gas condition, cooling rate, cooling duration) on L-AA breakdown were studied. L-AA concentration fluctuates in young fruits, remains stable during fruit maturation, and starts to decline 1 week before commercial harvest. The most rapid decrease in L-AA concentration was found during immediate controlled atmosphere. During short-term storage, only the gas condition was found to influence L-AA breakdown; no significant difference between gradually or immediately cooled pears was determined. Under air conditions, both cooling strategies did not differ from the L-AA breakdown in pears allowed to ripen on the tree up until 3 weeks after the optimal harvest date. During long-term storage, the cooling duration (1-3 weeks) had no effect whereas both O2 and CO2 had a significant effect on L-AA retention. After 7 months of storage, no difference was found in dehydroascorbic acid concentration; the L-AA and total L-AA concentrations, in contrast, were significantly lower in the 5% CO2 conditions.     

Air-liquid partition coefficients of aroma volatiles in frozen sugar solutions

Static headspace gas chromatography was used to measure air-solution partition coefficients of homologous series of methyl ketones and ethyl esters in aqueous sugar solutions. The measurements were performed in a temperature range from 25 to -25 degrees C. A rather unexpected temperature dependence of the partition coefficients was observed at subzero temperatures; that is, partition coefficients were found to increase in the temperature interval from 0 to -10 degrees C. A simple model, based on the freeze concentration effect, is proposed to explain the observed temperature dependence.