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Sommer, D. D.

Publications and source records attributed to Sommer, D. D..

2 recordsLinked to original sources

BCR analysis of single-sorted, putative IgE+ memory B cells in food allergy: an ephemeral existence?

Immunoglobulin (Ig) E is the critical effector molecule in allergic reactions. Consequently, research efforts to understand the biology of IgE-expressing cells is of paramount importance. In particular, the role of IgE+ memory B cells (MBCs) in the perpetuation of allergic reactivity has been the subject of intense research. Studies in mice have convincingly established that IgE+ B cells are rare and transient and, therefore, an unlikely candidate to maintain allergic disease. In contrast, IgE+ MBCs have been detected by flow cytometry in the sputum and peripheral blood of humans and have been proposed as a clinical marker of allergic disease. We established a method to genetically validate, at the single-cell level, the putative IgE+ MBCs identified by flow cytometry from humans. We, then used this information to develop an enhanced flow cytometry protocol that more accurately identifies bona fide IgE+ MBCs. We found that IgE+ MBCs were detected in some patients with atopic dermatitis, but at a frequency that was ~100 times lower than previously reported. We also found that IgE+ MBCs were undetectable in PBMCs from peanut allergic patients. These findings provide tools to identify bona fide IgE+ MBCs, demonstrate their extreme rarity in circulation and are consistent with the lack of a central role for IgE+ MBCs in the maintenance of allergic sensitivity.\n\nOne Sentence SummaryThe frequency of IgE+ MBCs in the peripheral circulation of humans is orders of magnitude lower than previously reported and comparable between allergic and healthy donors, which cautions about the clinical utility of their assessment.

immunology↗

BLAST-based validation of metagenomic sequence assignments

When performing bioforensic casework, it is important to be able to reliably detect the presence of a particular organism in a metagenomic sample, even if the organism is only present in a trace amount. For this task, it is common to use a sequence classification program that determines the taxonomic affiliation of individual sequence reads by comparing them to reference database sequences. As metagenomic data sets often consist of millions or billions of reads that need to be compared to reference databases containing millions of sequences, such sequence classification programs typically use search heuristics and databases with reduced sequence diversity to speed up the analysis, which can lead to incorrect assignments. Thus, in a bioforensic setting where correct assignments are paramount, assignments of interest made by \"first-pass\" classifiers should be confirmed using the most precise methods and comprehensive databases available. In this study we present a O_SCPLOWBLASTC_SCPLOW-based method for validating the assignments made by less precise sequence classification programs, with optimal parameters for filtering of O_SCPLOWBLASTC_SCPLOW results determined via simulation of sequence reads from genomes of interest, and we apply the method to the detection of four pathogenic organisms. The software implementing the method is open source and freely available.

bioinformatics↗