Development of a method for Bayesian nonparametric ROC analysis with application to an ELISA for Johne's disease in dairy cattle

Six hundred and sixty-eight dairy cattle were tested for Johne's disease using a direct-fecal real-time polymerase chain reaction (rt-PCR), fecal culture, and serum enzyme-linked immunosorbent assay (ELISA). Likelihood ratios (LRs) were estimated for five categories of sample-to-positive (S/P) values for the ELISA: <0.1, 0.1-0.249, 0.25-0.399, 0.4-0.999, > or =1.0. The statistical method assumed a single multinomial model for cross-classified rt-PCR, fecal culture results, and ELISA category strata. Conditional dependence between tests was investigated by the inclusion of all possible pairwise dependence terms. Sensitivity covariance between ELISA and fecal culture was estimated as 0.017. Estimates for the accuracy of the ELISA at the usual cutoff of 0.25S/P was 67.2% and 95.2% for sensitivity and specificity, respectively for a model that adjusted for the dependence between ELISA and fecal culture. The area under the receiver-operating characteristic (ROC) curve (95% probability interval) for the ELISA was 0.867 (0.796, 0.928). Point estimates for likelihood ratios (95% probability intervals) were 0.24 (0.11, 0.38), 1.52 (0.48, 3.27), 2.49 (0.31, 13.4), 6.33 (2.54, 16.5), and 103 (25.0, 2412) for the categories <0.1, 0.1-0.249, 0.25-0.399, 0.4-0.999, >/=1.0, respectively. Assumptions concerning the underlying distribution of test results for infected and uninfected animals were not necessary and this model can be employed for the general estimation of LRs and ROC curves in absence of knowledge concerning true disease status.     

Involvement of mammalian Mus81 in genome integrity and tumor suppression

Mus81-Eme1 endonuclease has been implicated in the rescue of stalled replication forks and the resolution of meiotic recombination intermediates in yeast. We used gene targeting to study the physiological requirements of Mus81 in mammals. Mus81-/- mice are viable and fertile, which indicates that mammalian Mus81 is not essential for recombination processes associated with meiosis. Mus81-deficient mice and cells were hypersensitive to the DNA cross-linking agent mitomycin C but not to gamma-irradiation. Remarkably, both homozygous Mus81-/- and heterozygous Mus81+/- mice exhibited a similar susceptibility to spontaneous chromosomal damage and a profound and equivalent predisposition to lymphomas and other cancers. These studies demonstrate a critical role for the proper biallelic expression of the mammalian Mus81 in the maintenance of genomic integrity and tumor suppression.     

The ecoresponsive genome of Daphnia pulex

We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.     

Temperature variations during grain filling obtained in growth tunnel experiments and its influence on protein content,polymer build-up and gluten viscoelastic properties in wheat

The aim of this study was to investigate effects of temperature during grain filling on gluten quality characteristics at a lower to moderate temperature range. Experiments with two wheat varieties grown in field covered by polypropylene tunnels during grain filling were performed in two seasons. Mean day temperature differences achieved within the tunnel were approximately 2–2.5 °C from the open to the closed end. There were significant effects of temperature on grain maturity time, thousand grain weight and protein content. The resistance to stretching of the gluten doughs increased with the increasing day temperatures. This was reflected in the proportion of unextractable polymeric proteins (UPP). The results suggest that increases in temperature within this temperature range affect the polymerization of polymeric proteins, giving higher molecular weights, and hence increased Rmax and stronger gluten. The two varieties differed in their response to temperature. In addition, there were seasonal variations in gluten functionality that may be associated with fluctuations in day temperatures between the seasons.     

Nitrogen Availability from Compost in High Tunnel Tomato Production

High yield agricultural systems, such as high tunnel (HT) vegetable production, require a large supply of soil nutrients, especially nitrogen (N). Compost is a common amendment used by HT growers both to supply nutrients and to improve physical and biological soil properties. We examined commercially-available composts and their effects on soil N, plant N uptake, and tomato yield in HT cultivation. In addition, a laboratory study examined N and carbon (C) mineralization from the composts, and the usefulness of compost properties as predictors of compost N mineralization was assessed under field and laboratory conditions. The field study used a randomized complete block design with four replications to compare four compost treatments (all added at the rate of 300 kg total N ha^?1) with unamended soil and an inorganic N treatment (110 kg N ha^?1). Tomatoes were grown in Monmouth, Maine during the summers of 2013 and 2014. Compost NO₃^?-N and NH₄⁺-N application rates were significantly correlated with soil NO₃^?-N and NH₄⁺-N concentrations throughout the growing season. Marketable yield was positively correlated with compost total inorganic N and NO₃^?-N in both years, and with NH₄⁺-N in 2014. There were no significant differences among composts in percentage of organic N mineralized and no correlations were observed with any measured compost property. In the laboratory study, all compost-amended soils had relatively high rates of CO₂ release for the initial few days and then the rates declined. The compost-amended soils mineralized 4%–6% of the compost organic N. This study suggested compost inorganic N content controls N availability to plants in the first year after compost application.     

Identification of Arcanobacterium (Trueperella) abortisuis, a novel species of veterinary importance, by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)

In the present study A. (T.) abortisuis isolated from pigs and bovines could be reliably identified by determination of phenotypic properties, genotypically by polymerase chain reaction with the help of A. (T.) abortisuis 16s-23S rDNA intergenic spacer region specific oligonucleotide primer and by Matrix-Assisted Laser Desorption Ionization-Time Of Flight mass spectrometry (MALDI-TOF MS). The latter appeared to be a promising tool for fast and cost effective identification of this species and might help to elucidate the role A. (T.) abortisuis plays in infections of pigs, bovines, possibly other animals or humans.     

A preliminary investigation of Ehrlichia species in ticks, humans, dogs, and capybaras from Brazil

A molecular epidemiologic investigation in two Brazilian states (Rondônia and São Paulo) was undertaken to determine if Ehrlichia species responsible for human and animal ehrlichioses in North America could be found in Brazilian vectors, potential natural mammalian reservoirs and febrile human patients with a tick bite history. Samples, including 376 ticks comprising 9 Amblyomma species, 29 capybara (Hydrochaeris hydrochaeris) spleens, 5 canine blood, and 75 human blood samples from febrile patients with history of tick bites were tested by a real-time PCR assay targeting a fragment of the Ehrlichia dsb gene. Ehrlichia DNA was not detected in any tick, capybara or human samples. In contrast, 4 out of 5 dogs contained Ehrlichia canis DNA in their blood, which were sequenced, representing the first report of E. canis infecting dogs in the Amazon region of Brazil. Further studies are needed to evaluate the presence of other agents of human and animal ehrlichioses in Brazil.     

Measurement of serum IgG in foals by radial immunodiffusion and automated turbidimetric immunoassay

Hypogammaglobulinemia as a result of failure of transfer of passive immunity (FTPI) is an important risk factor for infectious disease in neonatal foals. The current gold standard for determining serum immunoglobulin concentrations is radial immunodiffusion (RID). The purpose of this study was to compare immunoglobulin concentrations measured by RID with those determined by an automated turbidimetric immunoassay (TIA), which has a much shorter turnaround time. Immunoglobulin concentrations were measured by both RID and TIA in serum collected from 84 neonatal foals. Sixty-seven foals had results within the linear range for both assays. Sensitivity and specificity of TIA for diagnosis of FTPI with IgG < or = 800 mg/dL were 0.81 (95% CI 0.70-0.88) and 0.86 (95% CI 0.76-0.93) and with IgG < or = 400 mg/dL were 0.63 (95% CI 0.35-0.86) and 0.92 (95% CI 0.87-0.95), respectively. A significant linear relationship was found between IgG concentrations determined by TIA and RID (TIA = 0.9511RID + 8.4354; R2 = .59, P < .0001). The coefficients of variation for between-run and within-run precision for the TIA were 2.5 and 3%, respectively. Storage of samples from 10 foals at -20 degrees C for 10-12 months resulted in a reduction in TIA-measured serum IgG concentration of -17.6% (SD = 3.7%), indicating that long-term storage of samples at -20 degrees C should be avoided. The results of this study indicate that measurement of serum IgG by TIA can be used to evaluate foals for FTPI.     

Lipid-like material as the source of the uncharacterized organic carbon in the ocean?

The composition and formation mechanisms of the uncharacterized fraction of oceanic particulate organic carbon (POC) are not well understood. We isolated biologically important compound classes and the acid-insoluble fraction, a proxy of the uncharacterized fraction, from sinking POC in the deep Northeast Pacific and measured carbon isotope ratios to constrain the source(s) of the uncharacterized fraction. Stable carbon and radiocarbon isotope signatures of the acid-insoluble fraction were similar to those of the lipid fraction, implying that the acid-insoluble fraction might be composed of selectively accumulated lipid-like macromolecules.