42 research outputs found
Nodeomics: Pathogen Detection in Vertebrate Lymph Nodes Using Meta-Transcriptomics
The ongoing emergence of human infections originating from wildlife highlights the need for better knowledge of the microbial community in wildlife species where traditional diagnostic approaches are limited. Here we evaluate the microbial biota in healthy mule deer (Odocoileus hemionus) by analyses of lymph node meta-transcriptomes. cDNA libraries from five individuals and two pools of samples were prepared from retropharyngeal lymph node RNA enriched for polyadenylated RNA and sequenced using Roche-454 Life Sciences technology. Protein-coding and 16S ribosomal RNA (rRNA) sequences were taxonomically profiled using protein and rRNA specific databases. Representatives of all bacterial phyla were detected in the seven libraries based on protein-coding transcripts indicating that viable microbiota were present in lymph nodes. Residents of skin and rumen, and those ubiquitous in mule deer habitat dominated classifiable bacterial species. Based on detection of both rRNA and protein-coding transcripts, we identified two new proteobacterial species; a Helicobacter closely related to Helicobacter cetorum in the Helicobacter pylori/Helicobacter acinonychis complex and an Acinetobacter related to Acinetobacter schindleri. Among viruses, a novel gamma retrovirus and other members of the Poxviridae and Retroviridae were identified. We additionally evaluated bacterial diversity by amplicon sequencing the hypervariable V6 region of 16S rRNA and demonstrate that overall taxonomic diversity is higher with the meta-transcriptomic approach. These data provide the most complete picture to date of the microbial diversity within a wildlife host. Our research advances the use of meta-transcriptomics to study microbiota in wildlife tissues, which will facilitate detection of novel organisms with pathogenic potential to human and animals
Examination of the Reactivity of Benzoxaboroles and Related Compounds with a <i>cis</i>-Diol
Benzoxaboroles have been emerging as an interesting and
useful
scaffold in drug discovery due to their apparently unique reactivity
toward diols under physiological conditions. In this work, the reaction
of benzoxaborole with the diol-containing, fluorescent dye Alizarin
Red S is probed. Steady-state and presteady-state experiments have
been conducted for the characterization of the reactions over a wide
range of pH. Results indicate that Alizarin Red S reacts with both
the boronic (neutral, trigonal) form as well as the boronate (anionic,
tetrahedral) form of benzoxaborole in a reaction largely analogous
to that previously determined for the simple phenylboronic acid. However,
in certain key aspects, the reactivity of the benzoxaborole was found
to differ from that of simple phenylboronic acid. The structural origin
of these differences has been explored by examination of compounds
related to both benzoxaborole and phenylboronic acid. These results
may be applied to rational drug discovery efforts aimed at expanding
the use of benzoxaboroles in medicine
Elucidation of the Mechanism of the Reaction between Phenylboronic Acid and a Model Diol, Alizarin Red S
In this work, the reaction between phenylboronic acid
and the diol-containing,
fluorescent dye Alizarin Red S (<b>ARS</b>) was probed. Fluorescence
titrations, <sup>11</sup>B NMR measurements, and both pre- and steady-state
kinetic experiments were used for the characterization of this reaction
over a large pH range (4–10.5). It was shown that <b>ARS</b> preferentially reacted with the
boronic (neutral, trigonal) form of phenylboronic acid; however, the
boronate (anionic, tetrahedral) form was also reactive. All in all,
four reactant species were implicated in the formation of four different
adduct species. The rate of a given adduct formation depended on the
combination of the solution pH and the p<i>K</i><sub>a</sub>’s of both <b>ARS</b> and the
arylboronic acid. The reaction was found to proceed in two distinct
kinetic steps with the products and starting materials in facile exchange.
In addition, the elucidation of the mechanism indicated the presence
of two fluorescent products with the structure of the major contributor
differing from what had been cited in the literature
Corrigendum to “The unique chemistry of benzoxaboroles: Current and emerging applications in biotechnology and therapeutic treatments” [Bioorg. Med. Chem. 22 (2014) 4462–4473]
Ring Structure and Aromatic Substituent Effects on the p<i>K</i><sub>a</sub> of the Benzoxaborole Pharmacophore
In this work, we present an investigation into the physical
properties
of a unique class of aromatic boronic acids, the benzoxaboroles. Using
spectrophotometric methods, the ionization constants of a family of
substituted benzoxaboroles are determined. Heterocyclic ring modifications
are examined to determine their effects on the ionization of the boronic
acid moiety. It is also shown that the substituent effects about the
aromatic ring follow a Hammett relationship with the compounds' measured
p<i>K</i><sub>a</sub> values. Finally, these substituent
effects are also shown to extend to the sugar binding properties of
these compounds under physiologically relevant conditions. Combined,
these data will inform medicinal chemists wishing to tailor the ionization
and/or ability of this class of compound to bind diol-containing biomolecules
Microtubule-assisted mechanism for functional metabolic macromolecular complex formation
Evidence has been presented for a metabolic multienzyme complex, the purinosome, that participates in de novo purine biosynthesis to form clusters in the cytoplasm of living cells under purine-depleted conditions. Here we identified, using fluorescent live cell imaging, that a microtubule network appears to physically control the spatial distribution of purinosomes in the cytoplasm. Application of a cell-based assay measuring the rate of de novo purine biosynthesis confirmed that the metabolic activity of purinosomes was significantly suppressed in the absence of microtubules. Collectively, we propose a microtubule-assisted mechanism for functional purinosome formation in HeLa cells
Protection of the Benzoxaborole Moiety: Synthesis and Functionalization of Zwitterionic Benzoxaborole Complexes
The synthesis and utility of three
benzoxaborole protecting groups
are reported. These protecting groups improve organic solubility and
allow otherwise incompatible reactions (oxidations, substitutions,
and mild reductions) to be achieved in the presence of the benzoxaborole
moiety. 3-(<i>N</i>,<i>N</i>-Dimethylamino)-1-propanol
was determined to be useful in one-step sequences and is readily cleaved
upon workup. Two other groups, <i>N</i>-methylsalicylidenimine
and 2-[1-(methylimino)ethyl]phenol, are suitable for multistep syntheses.
Deprotection with mild aqueous acid allows for chromatography-free
isolation of the benzoxaborole in high yields
Data from: Ancestral polyploidy in seed plants and angiosperms
Analysis1 - alignments and trees of 9 sequenced genomesAnalysis1.zipAnalysis2 - alignments and trees when basal angiosperms are consideredAnalysis2.zipAnalysis3 - alignments and trees when gymnosperms are consideredAnalysis3.zipAnalysis4 - alignments and trees when basal angiosperms and gymnosperms are consideredAnalysis4.zip,Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms1, 2, 3, especially plants. The success of angiosperms has been attributed, in part, to innovations associated with gene or whole-genome duplications4, 5, 6, but evidence for proposed ancient genome duplications pre-dating the divergence of monocots and eudicots remains equivocal in analyses of conserved gene order. Here we use comprehensive phylogenomic analyses of sequenced plant genomes and more than 12.6 million new expressed-sequence-tag sequences from phylogenetically pivotal lineages to elucidate two groups of ancient gene duplications—one in the common ancestor of extant seed plants and the other in the common ancestor of extant angiosperms. Gene duplication events were intensely concentrated around 319 and 192 million years ago, implicating two WGDs in ancestral lineages shortly before the diversification of extant seed plants and extant angiosperms, respectively. Significantly, these ancestral WGDs resulted in the diversification of regulatory genes important to seed and flower development, suggesting that they were involved in major innovations that ultimately contributed to the rise and eventual dominance of seed plants and angiosperms