Showing papers by "Daniel McDonald published in 2014"
Broad Institute1, Emory University2, Cincinnati Children's Hospital Medical Center3, University of Colorado Boulder4, Harvard University5, University of Minnesota6, University of Toronto7, Women & Children's Hospital of Buffalo8, Boston Children's Hospital9, Mayo Clinic10, University of California, San Francisco11, Long Island Jewish Medical Center12, Children's Hospital of Philadelphia13, Children's Hospital of Eastern Ontario14, Nationwide Children's Hospital15, Howard Hughes Medical Institute16
TL;DR: Comparing the microbial signatures between the ileum, the rectum, and fecal samples indicates that at this early stage of disease, assessing the rectal mucosal-associated microbiome offers unique potential for convenient and early diagnosis of CD.
2,410 citations
TL;DR: A performance-optimized algorithm for assigning marker gene sequences generated on next-generation sequencing platforms to operational taxonomic units (OTUs) for microbial community analysis is presented and it is shown that subsampled open-reference OTU picking yields results that are highly correlated with those generated by “classic” open- reference OTUpicking through comparisons on three well-studied datasets.
Abstract: We present a performance-optimized algorithm, subsampled open-reference OTU picking, for assigning marker gene (e.g., 16S rRNA) sequences generated on next-generation sequencing platforms to operational taxonomic units (OTUs) for microbial community analysis. This algorithm provides benefits over de novo OTU picking (clustering can be performed largely in parallel, reducing runtime) and closed-reference OTU picking (all reads are clustered, not only those that match a reference database sequence with high similarity). Because more of our algorithm can be run in parallel relative to "classic" open-reference OTU picking, it makes open-reference OTU picking tractable on massive amplicon sequence data sets (though on smaller data sets, "classic" open-reference OTU clustering is often faster). We illustrate that here by applying it to the first 15,000 samples sequenced for the Earth Microbiome Project (1.3 billion V4 16S rRNA amplicons). To the best of our knowledge, this is the largest OTU picking run ever performed, and we estimate that our new algorithm runs in less than 1/5 the time than would be required of "classic" open reference OTU picking. We show that subsampled open-reference OTU picking yields results that are highly correlated with those generated by "classic" open-reference OTU picking through comparisons on three well-studied datasets. An implementation of this algorithm is provided in the popular QIIME software package, which uses uclust for read clustering. All analyses were performed using QIIME's uclust wrappers, though we provide details (aided by the open-source code in our GitHub repository) that will allow implementation of subsampled open-reference OTU picking independently of QIIME (e.g., in a compiled programming language, where runtimes should be further reduced). Our analyses should generalize to other implementations of these OTU picking algorithms. Finally, we present a comparison of parameter settings in QIIME's OTU picking workflows and make recommendations on settings for these free parameters to optimize runtime without reducing the quality of the results. These optimized parameters can vastly decrease the runtime of uclust-based OTU picking in QIIME.
491 citations
TL;DR: In this paper, the effects of intravaginal rings (IVRs) on the vaginal microbial communities were investigated in 6 women with recurrent genital HSV who used acyclovir IVR and compared to the communities developing in biofilms on the IVR surface.
21 citations
24 Jul 2014
4 citations
TL;DR: Evidence is provided that the GPCR microarray can identify GPCRs that contribute to the physiology of PASMC and can uncover new drug targets, such as GPR75 for PAH--a disease that requires therapies beyond those currently in use.
Abstract: Author(s): McDonald, Daniel Scott | Abstract: Pulmonary arterial hypertension (PAH) is characterized by increased pulmonary vascular resistance, in part due to increased proliferation of pulmonary artery smooth muscle cells (PASMC). Since the second messenger 3'5'-cyclic adenosine monophosphate (cAMP) decreases proliferation of PASMC, G protein-coupled receptors (GPCRs) that couple to G[alpha]s are attractive targets for PAH. We used a TaqMan ® GPCR array to identify the GPCRs expressed by PASMC isolated from normal subjects and from patients with PAH. The data revealed that human PASMC express g135 GPCRs, at least 50 of which regulate cAMP formation. We found that GPCR expression correlates with function e.g., of G[alpha]s-coupled GPCRs with formation of cAMP and inhibition of cell proliferation (a functional response to receptor activation), thus documenting that we had identified physiologically relevant GPCRs. Our studies of PAH-PASMC with GPCR arrays revealed that PAH is associated with an increase (g2-fold) in the expression of 41 GPCRs. The greatest increase in GPCR expression was of two orphan receptors, namely GPR113 and GPR75, whose expression was absent in normal PASMC. We also found the mRNA and protein expression of GPR113 and GPR75 were increased in animal models of PAH. Importantly, treatment of PAH-PASMC with a GPR75 antibody blunted the increased proliferation of PASMC and increased cellular cAMP levels. Taken together, the data in this thesis provide evidence that the GPCR microarray can identify GPCRs that contribute to the physiology of PASMC and can uncover new drug targets, such as GPR75 for PAH--a disease that requires therapies beyond those currently in use
3 citations
2 citations