Metagenome-enabled models improve genomic predictive ability and identification of herbivory-limiting genes in sweetpotato.

Plant-insect interactions are often influenced by host- or insect-associated metagenomic community members. The relative abundance of insects and the microbes that modulate their interactions were obtained from sweetpotato (Ipomoea batatas) leaf-associated metagenomes using quantitative reduced representation sequencing and strain/species-level profiling with the Qmatey software. Positive correlations were found between whitefly (Bemisia tabaci) and its endosymbionts (Candidatus Hamiltonella defensa, Candidatus Portiera aleyrodidarum, and Rickettsia spp.) and negative correlations with nitrogen-fixing bacteria that implicate nitric oxide in sweetpotato-whitefly interaction. Genome-wide associations using 252 975 dosage-based markers, and metagenomes as a covariate to reduce false positive rates, implicated ethylene and cell wall modification in sweetpotato-whitefly interaction. The predictive abilities (PA) for whitefly and Ocypus olens abundance were high in both populations (68%-69% and 33.3%-35.8%, respectively) and 69.9% for Frankliniella occidentalis. The metagBLUP (gBLUP) prediction model, which fits the background metagenome-based Cao dissimilarity matrix instead of the marker-based relationship matrix (G-matrix), revealed moderate PA (35.3%-49.1%) except for O. olens (3%-10.1%). A significant gain in PA after modeling the metagenome as a covariate (gGBLUP, ≤11%) confirms quantification accuracy and that the metagenome modulates phenotypic expression and might account for the missing heritability problem. Significant gains in PA were also revealed after fitting allele dosage (≤17.4%) and dominance effects (≤4.6%). Pseudo-diploidized genotype data underperformed for dominance models. Including segregation-distorted loci (SDL) increased PA by 6%-17.1%, suggesting that traits associated with fitness cost might benefit from the inclusion of SDL. Our findings confirm the holobiont theory of host-metagenome co-evolution and underscore its potential for breeding within the context of G × G × E interactions.

Qmatey: an automated pipeline for fast exact matching-based alignment and strain-level taxonomic binning and profiling of metagenomes.

Metagenomics is a powerful tool for understanding organismal interactions; however, classification, profiling and detection of interactions at the strain level remain challenging. We present an automated pipeline, quantitative metagenomic alignment and taxonomic exact matching (Qmatey), that performs a fast exact matching-based alignment and integration of taxonomic binning and profiling. It interrogates large databases without using metagenome-assembled genomes, curated pan-genes or k-mer spectra that limit resolution. Qmatey minimizes misclassification and maintains strain level resolution by using only diagnostic reads as shown in the analysis of amplicon, quantitative reduced representation and shotgun sequencing datasets. Using Qmatey to analyze shotgun data from a synthetic community with 35% of the 26 strains at low abundance (0.01-0.06%), we revealed a remarkable 85-96% strain recall and 92-100% species recall while maintaining 100% precision. Benchmarking revealed that the highly ranked Kraken2 and KrakenUniq tools identified 2-4 more taxa (92-100% recall) than Qmatey but produced 315-1752 false positive taxa and high penalty on precision (1-8%). The speed, accuracy and precision of the Qmatey pipeline positions it as a valuable tool for broad-spectrum profiling and for uncovering biologically relevant interactions.

Cholesterotic fibrous histiocytoma: Case report and literature review.

Cholesterotic fibrous histiocytoma is a particularly rare variant of dermatofibroma that is distinguished histopathologically by the presence of prominent cholesterol deposits within the lesion. We report the case of a 54-year-old male with poorly controlled hyperlipidemia who presented with a firm violaceous papule on the right shin, diagnosed as a cholesterotic fibrous histiocytoma. We also review and summarize the existing literature on this uncommon entity.

Allergic contact dermatitis from vitamin E: the experience at Mayo Clinic Arizona, 1987 to 2007.

BACKGROUND: Vitamin E, of which the most biologically active form is alpha-tocopherol, has become widely known for its antioxidant effects. It has been ingested or applied topically for purported anti-aging effects and for cosmetic enhancement. OBJECTIVE: To determine whether the incidence of allergic contact dermatitis from vitamin E has increased in recent years. METHODS: With the approval of the Mayo Clinic institutional review board, we retrospectively analyzed patch-test data from patients tested from June 1987 through December 2007. RESULTS: A total of 2,950 patients were patch-tested during this period, and 18 patients (0.61%) had positive reactions to alpha-tocopherol; 6 (0.53%) of 1,136 patients tested from June 1987 through December 1997 had positive results, and 12 (0.66%) of 1,814 patients tested from January 1998 through December 2007 had positive results (p = .69). CONCLUSION: Vitamin E appears to be a relatively rare contact allergen in our experience.

Allergic contact dermatitis from mercapto compounds.

Despite being well-known allergens, mercaptobenzothiazole and its derivatives continue to be widely used in natural and synthetic rubber, in the mining industry, and in a variety of nonrubber products. The purpose of this article is to review the epidemiology and the clinical characteristics of allergic contact dermatitis from mercapto compounds.