Phytochemical Composition and Biological Activity of the Essential Oil from Ericameria nauseosa Collected in Southwestern Montana, United States.

Ericameria nauseosa (Pall. ex Pursh) G.L. Nesom & G.I. Baird) is used in traditional medicine to treat various diseases; however, little is known about the immunomodulatory activity of essential oil from this plant. Thus, we isolated essential oil from the aerial parts of E. nauseosa and evaluated their chemical composition and biological activity. Compositional analysis of E. nauseosa essential oil revealed that the main (>2%) components were γ-decalactone (13.3%), cryptone (9.4%), terpinen-4-ol (9.3%), (E)-methyl cinnamate (6.0%), T-cadinol (4.7%), spathulenol (3.6%), 8Z-2,3-dihydromatricaria ester (3.1%), ß-phellandrene (3.0%), p-cymen-8-ol (2.2%), 3-ethoxy-2-cycloocten-1-one (2.2%), and trans-p-menth-2-en-1-ol (2.1%). Distinctive features were the lactones (up to 15%) and polyacetylenes (up to 3.1%), including (2Z,8Z)-matricaria ester and 8Z-2,3-dihydromatricaria ester. A comparison with other reported E. nauseosa essential oil samples showed that our samples were distinct from those collected in other areas of the country; however, they did have the most similarity to one sample collected in North Central Utah. Pharmacological studies showed that E. nauseosa essential oil activated human neutrophil Ca2+ influx, which desensitized these cells to subsequent agonist-induced functional responses. Based on our previously reported data that nerolidol, ß-pinene, spathulenol, sabinene, and γ-terpinene were active in human neutrophils, these compounds are the most likely constituents contributing to this immunomodulatory activity. However, the relatively high amount of polyacetylenes may also contribute, as these compounds have been characterized as potent immunomodulators.

Use of cellular CRISPR (clusters of regularly interspaced short palindromic repeats) spacer-based microarrays for detection of viruses in environmental samples.

It is currently difficult to detect unknown viruses in any given environment. The recent discovery of CRISPR (clusters of regularly interspaced short palindromic repeats) loci within bacterial and archaeal cellular genomes may provide an alternative approach to detect new viruses. It has been shown that the spacer sequences between the direct repeat units of the CRISPR loci are often derived from viruses and likely function as guide sequences to protect the cell from viral infection. The spacer sequences within the CRISPR loci may therefore serve as a record of the viruses that have replicated within the cell. We have cataloged the CRISPR spacer sequences from cellular metagenomic data from high-temperature (>80°C), acidic (pH < 4) hot spring environments located in Yellowstone National Park (YNP). We designed a microarray platform utilizing these CRISPR spacer sequences as potential probes to detect viruses present in YNP hot spring environments. We show that this microarray approach can detect viral sequences directly from virus-enriched environmental samples, detecting new viruses which have not been previously characterized. We further demonstrated that this microarray approach can be used to examine temporal changes in viral populations within the environment. Our results demonstrate that CRISPR spacer sequence-based microarrays will be useful tools for detecting and monitoring viruses from diverse environmental samples.

Virus movement maintains local virus population diversity.

Viruses are the largest reservoir of genetic material on the planet, yet little is known about the population dynamics of any virus within its natural environment. Over a 2-year period, we monitored the diversity of two archaeal viruses found in hot springs within Yellowstone National Park (YNP). Both temporal phylogeny and neutral biodiversity models reveal that virus diversity in these local environments is not being maintained by mutation but rather by high rates of immigration from a globally distributed metacommunity. These results indicate that geographically isolated hot springs are readily able to exchange viruses. The importance of virus movement is supported by the detection of virus particles in air samples collected over YNP hot springs and by their detection in metacommunity sequencing projects conducted in the Sargasso Sea. Rapid rates of virus movement are not expected to be unique to these archaeal viruses but rather a common feature among virus metacommunities. The finding that virus immigration rather than mutation can dominate community structure has significant implications for understanding virus circulation and the role that viruses play in ecology and evolution by providing a reservoir of mobile genetic material.

Fitting CRISPR-associated Cas3 into the helicase family tree.

Helicases utilize NTPs to modulate their binding to nucleic acids and many of these enzymes also unwind DNA or RNA duplexes in an NTP-dependent fashion. These proteins are phylogenetically related but functionally diverse, with essential roles in virtually all aspects of nucleic acid metabolism. A new class of helicases associated with RNA-guided adaptive immune systems in bacteria and archaea has recently been identified. Prokaryotes acquire resistance to invading genetic parasites by integrating short fragments of foreign nucleic acids into repetitive loci in the host chromosome known as CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats). CRISPR-associated gene 3 (cas3) encodes a conserved helicase protein that is essential for phage defense. Here we review recent advances in Cas3 biology, and provide a new phylogenetic framework that positions Cas3 in the helicase family tree. We anticipate that this Cas3 phylogeny will guide future biochemical and structural studies.

[FeFe]-hydrogenase in Yellowstone National Park: evidence for dispersal limitation and phylogenetic niche conservatism.

Hydrogen (H2) has an important role in the anaerobic degradation of organic carbon and is the basis for many syntrophic interactions that commonly occur in microbial communities. Little is known, however, with regard to the biotic and/or abiotic factors that control the distribution and phylogenetic diversity of organisms which produce H2 in microbial communities. In this study, we examined the [FeFe]-hydrogenase gene (hydA) as a proxy for fermentative bacterial H2 production along physical and chemical gradients in various geothermal springs in Yellowstone National Park (YNP), WY, USA. The distribution of hydA in YNP geothermal springs was constrained by pH to environments co-inhabited by oxygenic phototrophs and to environments predicted to have low inputs of abiotic H2. The individual HydA asssemblages from YNP springs were more closely related when compared with randomly assembled communities, which suggests ecological filtering. Model selection approaches revealed that geographic distance was the best explanatory variable to predict the phylogenetic relatedness of HydA communities. This evinces the dispersal limitation imposed by the geothermal spring environment on HydA phylogenetic diversity even at small spatial scales. pH differences between sites is the second highest ranked explanatory variable of HydA phylogenetic relatedness, which suggests that the ecology related to pH imposes strong phylogenetic niche conservatism. Collectively, these results indicate that pH has imposed strong niche conservatism on fermentative bacteria and that, within a narrow pH realm, YNP springs are dispersal limited with respect to fermentative bacterial communities.