Salmonella Screening Procedure with Tests for β-Galactosidase and Flagellar Antigens

Differentiation of Salmonella from other gram-negative bacilli requires several biochemical and serological tests. A simplified 24-hr screening procedure has been devised which allows discarding of large numbers of isolates (picked from selective plating media) before they are subjected to this extensive testing. Cultures of gram-negative organisms isolated to triple sugar-iron slants during routine examination of products for Salmonella were tested for the presence of beta-galactosidase and Salmonella flagellar antigens. beta-Galactosidase-positive cultures which did not agglutinate in polyvalent flagellar antiserum were considered to be nonsalmonellae. Of 1,103 Salmonella cultures tested, none of the 61 different serotypes was missed by this procedure, whereas 673 (82.3%) of 818 nonsalmonellae were excluded from further testing. This screening procedure eliminates most nonsalmonellae and augments the proportion of cultures undergoing further biochemical and serological testing which will be confirmed as Salmonella.     

Use of multivariate linkage analysis for dissection of a complex cognitive trait

Replication of linkage results for complex traits has been exceedingly difficult, owing in part to the inability to measure the precise underlying phenotype, small sample sizes, genetic heterogeneity, and statistical methods employed in analysis. Often, in any particular study, multiple correlated traits have been collected, yet these have been analyzed independently or, at most, in bivariate analyses. Theoretical arguments suggest that full multivariate analysis of all available traits should offer more power to detect linkage; however, this has not yet been evaluated on a genomewide scale. Here, we conduct multivariate genomewide analyses of quantitative-trait loci that influence reading- and language-related measures in families affected with developmental dyslexia. The results of these analyses are substantially clearer than those of previous univariate analyses of the same data set, helping to resolve a number of key issues. These outcomes highlight the relevance of multivariate analysis for complex disorders for dissection of linkage results in correlated traits. The approach employed here may aid positional cloning of susceptibility genes in a wide spectrum of complex traits.     

Functional annotation signatures of disease susceptibility loci improve SNP association analysis

Background

Genetic association studies are conducted to discover genetic loci that contribute to an inherited trait, identify the variants behind these associations and ascertain their functional role in determining the phenotype. To date, functional annotations of the genetic variants have rarely played more than an indirect role in assessing evidence for association. Here, we demonstrate how these data can be systematically integrated into an association study’s analysis plan.

Results

We developed a Bayesian statistical model for the prior probability of phenotype–genotype association that incorporates data from past association studies and publicly available functional annotation data regarding the susceptibility variants under study. The model takes the form of a binary regression of association status on a set of annotation variables whose coefficients were estimated through an analysis of associated SNPs in the GWAS Catalog (GC). The functional predictors examined included measures that have been demonstrated to correlate with the association status of SNPs in the GC and some whose utility in this regard is speculative: summaries of the UCSC Human Genome Browser ENCODE super–track data, dbSNP function class, sequence conservation summaries, proximity to genomic variants in the Database of Genomic Variants and known regulatory elements in the Open Regulatory Annotation database, PolyPhen–2 probabilities and RegulomeDB categories. Because we expected that only a fraction of the annotations would contribute to predicting association, we employed a penalized likelihood method to reduce the impact of non–informative predictors and evaluated the model’s ability to predict GC SNPs not used to construct the model. We show that the functional data alone are predictive of a SNP’s presence in the GC. Further, using data from a genome–wide study of ovarian cancer, we demonstrate that their use as prior data when testing for association is practical at the genome–wide scale and improves power to detect associations.

Conclusions

We show how diverse functional annotations can be efficiently combined to create ‘functional signatures’ that predict the a priori odds of a variant’s association to a trait and how these signatures can be integrated into a standard genome–wide–scale association analysis, resulting in improved power to detect truly associated variants.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-398) contains supplementary material, which is available to authorized users.     

Host range of the European,rhizome-stem feeding scale Rhizaspidiotus donacis (Hemiptera: Diaspididae), a candidate biological control agent for giant reed,Arundo donax (Poales: Poaceae) in North America

The armored scale Rhizaspidiotus donacis (Leornardi) was evaluated as a potential biological control agent of the invasive reed grass Arundo donax in North America. No-choice tests, native range field surveys and non-target host exposures were used to determine the fundamental host range of the scale collected from Caloma, Spain and Perpignan, France. Thirty-five species, including two genotypes of A. donax and seven ecotypes of Phragmites australis, along with closely related grasses, economic grasses and habitat associates were tested. In quarantine no-choice testing using releases of 200 crawlers per plant, normal development of R. donacis was observed on A. donax and A. formosana, with very limited survival to the adult stage on Spartina alterniflora and Leptochloa spp. In follow-up studies using 1000 crawlers per plant, 10 live adult females were found on Leptochloa virgata, and one adult female on Spartina alterniflora, but average adult female abundance per plant was (2580%) 26-times lower on L. virgata and over (39,090%) 100-times lower on S. alterniflora than on A. donax. Field surveys were conducted at five locations in Spain and France at which A. donax infested with R. donacis, co-occurred with two non-target species of concern and R. donacis was only found on A. donax. Six-month field host exposures in Spain using potted Leptochloa plants entwined with heavily infested A. donax confirmed that R. donacis is specific to Arundo under field conditions. Based on our results, the scale R. donacis appears to be specific to the genus Arundo and is unlikely to harm native or cultivated plants in the Americas.     

Enantioselective microbial reduction of 3,5-dioxo-6-(benzyloxy) hexanoic acid, ethyl ester

The key chiral intermediate 3,5-dihydroxy-6-(benzyloxy) hexanoic acid, ethyl ester 2a, was made by the stereoselective microbial reduction of 3,5-dioxo-6-(benzyloxy) hexanoic acid, ethyl ester 1. Among various microbial cultures evaluated, cell suspensions of Acinetobacter calcoaceticus SC 13876 reduced 1 to 2a. The reaction yield of 85% and optical purity of 97% was obtained using glycerol-grown cells. The substrate was used at 2 g l⁻¹ and cells were used at 20% (w/v, wet cells) concentrations. The optimum pH for the reduction of 1 to 2a was 5.5 and the optimum temperature was 32°C. Cell extracts of A. calcoaceticus SC 13876 in the presence of NAD⁺, glucose, and glucose dehydrogenase reduced 1 to the corresponding monohydroxy compounds 3 and 4 [3-hydroxy-5-oxo-6-(benzyloxy) hexanoic acid ethyl ester 3, and 5-hydroxy-3-oxo-6-(benzyloxy) hexanoic acid ethyl ester 4]. Both 3 and 4 were further reduced to 2a by cell extracts. Reaction yield of 92% and optical purity of 99% were obtained when the reaction was carried out in a 1-l batch using cell extracts. The substrate was used at 10 g l⁻¹. Product 2a was isolated from the reaction mixture in 72% overall yield. The GC and HPLC area % purity of the isolated product was 99% and the optical purity was 99.5%. The reductase which converted 1 to 2a was purified about 200-fold from cell extracts of A. calcoaceticus SC 13876. The purified enzyme gave a single protein band on SDS-PAGE corresponding to 35,000 daltons.