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  1. Abstract The response by vaccine developers to the COVID-19 pandemic has been extraordinary with effective vaccines authorized for emergency use in the United States within 1 year of the appearance of the first COVID-19 cases. However, the emergence of SARS-CoV-2 variants and obstacles with the global rollout of new vaccines highlight the need for platforms that are amenable to rapid tuning and stable formulation to facilitate the logistics of vaccine delivery worldwide. We developed a “designer nanoparticle” platform using phage-like particles (PLPs) derived from bacteriophage lambda for a multivalent display of antigens in rigorously defined ratios. Here, we engineered PLPsmore »that display the receptor-binding domain (RBD) protein from SARS-CoV-2 and MERS-CoV, alone (RBD SARS -PLPs and RBD MERS -PLPs) and in combination (hCoV-RBD PLPs). Functionalized particles possess physiochemical properties compatible with pharmaceutical standards and retain antigenicity. Following primary immunization, BALB/c mice immunized with RBD SARS - or RBD MERS -PLPs display serum RBD-specific IgG endpoint and live virus neutralization titers that, in the case of SARS-CoV-2, were comparable to those detected in convalescent plasma from infected patients. Further, these antibody levels remain elevated up to 6 months post-prime. In dose-response studies, immunization with as little as one microgram of RBD SARS -PLPs elicited robust neutralizing antibody responses. Finally, animals immunized with RBD SARS -PLPs, RBD MERS -PLPs, and hCoV-RBD PLPs were protected against SARS-CoV-2 and/or MERS-CoV lung infection and disease. Collectively, these data suggest that the designer PLP system provides a platform for facile and rapid generation of single and multi-target vaccines.« less
    Free, publicly-accessible full text available December 1, 2023
  2. Birol, Inanc (Ed.)
    Abstract Motivation Linking microbial community members to their ecological functions is a central goal of environmental microbiology. When assigned taxonomy, amplicon sequences of metabolic marker genes can suggest such links, thereby offering an overview of the phylogenetic structure underpinning particular ecosystem functions. However, inferring microbial taxonomy from metabolic marker gene sequences remains a challenge, particularly for the frequently sequenced nitrogen fixation marker gene, nitrogenase reductase (nifH). Horizontal gene transfer in recent nifH evolutionary history can confound taxonomic inferences drawn from the pairwise identity methods used in existing software. Other methods for inferring taxonomy are not standardized and require manual inspectionmore »that is difficult to scale. Results We present Phylogenetic Placement for Inferring Taxonomy (PPIT), an R package that infers microbial taxonomy from nifH amplicons using both phylogenetic and sequence identity approaches. After users place query sequences on a reference nifH gene tree provided by PPIT (n = 6317 full-length nifH sequences), PPIT searches the phylogenetic neighborhood of each query sequence and attempts to infer microbial taxonomy. An inference is drawn only if references in the phylogenetic neighborhood are: (1) taxonomically consistent and (2) share sufficient pairwise identity with the query, thereby avoiding erroneous inferences due to known horizontal gene transfer events. We find that PPIT returns a higher proportion of correct taxonomic inferences than BLAST-based approaches at the cost of fewer total inferences. We demonstrate PPIT on deep-sea sediment and find that Deltaproteobacteria are the most abundant potential diazotrophs. Using this dataset we show that emending PPIT inferences based on visual inspection of query sequence placement can achieve taxonomic inferences for nearly all sequences in a query set. We additionally discuss how users can apply PPIT to the analysis of other marker genes. Availability PPIT is freely available to non-commercial users at https://github.com/bkapili/ppit. Installation includes a vignette that demonstrates package use and reproduces the nifH amplicon analysis discussed here. The raw nifH amplicon sequence data have been deposited in the GenBank, EMBL, and DDBJ databases under BioProject number PRJEB37167. Supplementary information Supplementary data are available at Bioinformatics online.« less
  3. Abstract

    Diazotrophic microorganisms regulate marine productivity by alleviating nitrogen limitation. However, we know little about the identity and activity of diazotrophs in deep-sea sediments, a habitat covering nearly two-thirds of the planet. Here, we identify candidate diazotrophs from Pacific Ocean sediments collected at 2893 m water depth using15N-DNA stable isotope probing and a novel pipeline fornifHsequence analysis. Together, these approaches detect an unexpectedly diverse assemblage of active diazotrophs, including members of theAcidobacteria,Firmicutes,Nitrospirae,Gammaproteobacteria, andDeltaproteobacteria. Deltaproteobacteria, predominately members of theDesulfobacteralesandDesulfuromonadales, are the most abundant diazotrophs detected, and display the most microdiversity of associatednifHsequences. Some of the detected lineages, including those within theAcidobacteria, havemore »not previously been shown to fix nitrogen. The diazotrophs appear catabolically diverse, with the potential for using oxygen, nitrogen, iron, sulfur, and carbon as terminal electron acceptors. Therefore, benthic diazotrophy may persist throughout a range of geochemical conditions and provide a stable source of fixed nitrogen over geologic timescales. Our results suggest that nitrogen-fixing communities in deep-sea sediments are phylogenetically and catabolically diverse, and open a new line of inquiry into the ecology and biogeochemical impacts of deep-sea microorganisms.

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  4. Free, publicly-accessible full text available May 1, 2023
  5. In this work, we introduce a novel approach for the selective assembly of heterometallic complexes by unprecedented coordination of coinage metal cations to strained single ruthenium–boron bonds on a surface of icosahedral boron clusters. M( i ) cations (M = Cu, Ag, and Au) insert into B–Ru bonds of the (BB)–carboryne complex of ruthenium with the formation of four-membered B–M–Ru–B metalacycles. Results of theoretical calculations suggest that bonding within these metalacycles can be best described as unusual three-center-two-electron B–M⋯Ru interactions that are isolobal to B–H⋯Ru borane coordination for M = Cu and Ag, or the pairs of two-center-two electron B–Aumore »and Au–Ru interactions for M = Au. These transformations comprise the first synthetic route to exohedral coinage metal boryl complexes of icosahedral closo -{C 2 B 10 } clusters, which feature short Cu–B (2.029(2) Å) and Ag–B (2.182(3) Å) bonds and the shortest Au–B bond (2.027(2) Å) reported to date. The reported heterometallic complexes contain Cu( i ) and Au( i ) centers in uncharacteristic square-planar coordination environments. These findings pave the way to rational construction of a broader class of multimetallic architectures featuring M–B bonds.« less