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Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism
Get PDFPandemic influenza viruses modulate proinflammatory responses that can lead to immunopathogenesis. We present an extensive and systematic profiling of lipids, metabolites, and proteins in respiratory compartments of ferrets infected with either 1918 or 2009 human pandemic H1N1 influenza viruses. Integrative analysis of high-throughput omics data with virologic and histopathologic data uncovered relationships between host responses and phenotypic outcomes of viral infection. Proinflammatory lipid precursors in the trachea following 1918 infection correlated with severe tracheal lesions. Using an algorithm to infer cell quantity changes from gene expression data, we found enrichment of distinct T cell subpopulations in the trachea. There was also a predicted increase in inflammatory monocytes in the lung of 1918 virus-infected animals that was sustained throughout infection. This study presents a unique resource to the influenza research community and demonstrates the utility of an integrative systems approach for characterization of lipid metabolism alterations underlying respiratory responses to viruses
WeilandPopulationStructurePythiumSupFigure2.pdf
No full textPythium species are important soilborne pathogens occurring in the forest nursery industry of the Pacific Northwest. However, little is known about their genetic diversity or population structure and it is suspected that isolates are moved among forest nurseries on seedling stock and shared field equipment. In order to address these concerns, a total of 115 isolates of three Pythium species (P. irregulare, P. sylvaticum, and P. ultimum) were examined at three forest nurseries using simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers. Analyses revealed distinct patterns of intraspecific variation for the three species. P. sylvaticum exhibited the most diversity, followed by P. irregulare, while substantial clonality was found in P. ultimum. For both P. irregulare and P. sylvaticum, but not P. ultimum, there was evidence for significant variation among nurseries. However, all three species also exhibited at least two distinct lineages not associated with the nursery of origin. Finally, evidence was found that certain lineages and clonal genotypes, including fungicide-resistant isolates, are shared among nurseries, indicating that pathogen movement has occurred
ChristieSingleGenerationDomesticationSupplementaryData1.pdf
No full textThe genetic underpinnings associated with the earliest stages of plant and animal domestication have remained elusive. Because a genome-wide response to selection can take many generations, the earliest detectable changes associated with domestication may first manifest as heritable changes to global patterns of gene expression. Here, to test this hypothesis, we measured differential gene expression in the offspring of wild and first-generation hatchery steelhead trout (Oncorhynchus mykiss) reared in a common environment. Remarkably, we find that there were 723 genes differentially expressed between the two groups of offspring. Reciprocal crosses reveal that the differentially expressed genes could not be explained by maternal effects or by chance differences in the background levels of gene expression among unrelated families. Gene-enrichment analyses reveal that adaptation to the novel hatchery environment involved responses in wound healing, immunity and metabolism. These findings suggest that the earliest stages of domestication may involve adaptation to highly crowded conditions
ChristieSingleGenerationDomesticationSupplementarySoftware1.pdf
No full textThe genetic underpinnings associated with the earliest stages of plant and animal domestication have remained elusive. Because a genome-wide response to selection can take many generations, the earliest detectable changes associated with domestication may first manifest as heritable changes to global patterns of gene expression. Here, to test this hypothesis, we measured differential gene expression in the offspring of wild and first-generation hatchery steelhead trout (Oncorhynchus mykiss) reared in a common environment. Remarkably, we find that there were 723 genes differentially expressed between the two groups of offspring. Reciprocal crosses reveal that the differentially expressed genes could not be explained by maternal effects or by chance differences in the background levels of gene expression among unrelated families. Gene-enrichment analyses reveal that adaptation to the novel hatchery environment involved responses in wound healing, immunity and metabolism. These findings suggest that the earliest stages of domestication may involve adaptation to highly crowded conditions
Coal-Bed Methane Water Effects on Dill and Its Essential Oils
Get PDFPumping water from coal seams decreases the pressure in the seam and in turn releases trapped methane; this is the most common and economic method of methane extraction. The water that is pumped out is known as "coal-bed methane water" (CBMW), which is high in sodium and other salts. In the past 25 yr, the United States has seen a 16-fold increase in the production of coal bed methane gas, and trillions of cubic meters are yet to be extracted. There is no sustainable disposal method for CBMW, and there are very few studies investigating the effects of this water on plants and their secondary metabolites and on soil properties. This study was conducted to determine the effects of CBMW on soil chemical properties and on the biomass and essential oil yield and composition of dill (Anethum graveolens L.). This crop was grown in a greenhouse and was subjected to different levels of CBMW treatment: tap water only; 25% CBMW, 75% tap water; 50% CBMW, 50% tap water; 75% CBMW, 25% tap water; and 100% CBMW. The major dill oil constituents, limonene and α-phellandrene, were not affected by the treatments; however, the concentration of dill ether increased with increasing CBMW levels, whereas the concentration of carvone decreased. In soil, sodium level significantly increased with increasing level of treatment, but pH and cation exchange capacity were not much affected. Coal bed methane water could be used for irrigation of dill for one growing season, but longer-term studies may be needed to clarify the long-term effects on soil and plant
Trichinella Surveillance in Black Bears (Ursus Americanus) from Oregon, USA
Get PDFWe used serology and muscle digestion to test black bears (Ursus americanus) from western Oregon, USA, for Trichinella. Results indicate black bears in Oregon are not part of a sylvatic cycle for Trichinella, and risk of human exposure to Trichinella larvae from eating black bear meat from Oregon appears low
Objective past of a quantum universe: Redundant records of consistent histories
Get PDFMotivated by the advances of quantum Darwinism and recognizing the role played by redundancy in identifying the small subset of quantum states with resilience characteristic of objective classical reality, we explore the implications of redundant records for consistent histories. The consistent histories formalism is a tool for describing sequences of events taking place in an evolving closed quantum system. A set of histories is consistent when one can reason about them using Boolean logic, i.e., when probabilities of sequences of events that define histories are additive. However, the vast majority of the sets of histories that are merely consistent are flagrantly nonclassical in other respects. This embarras de richesses (known as the set selection problem) suggests that one must go beyond consistency to identify how the classical past arises in our quantum universe. The key intuition we follow is that the records of events that define the familiar objective past are inscribed in many distinct systems, e.g., subsystems of the environment, and are accessible locally in space and time to observers. We identify histories that are not just consistent but redundantly consistent using the partial-trace condition introduced by Finkelstein as a bridge between histories and decoherence. The existence of redundant records is a sufficient condition for redundant consistency. It selects, from the multitude of the alternative sets of consistent histories, a small subset endowed with redundant records characteristic of the objective classical past. The information about an objective history of the past is then simultaneously within reach of many, who can independently reconstruct it and arrive at compatible conclusions in the present
Resonant behavior in heat transfer across weak molecular interfaces
Get PDFMolecular dynamics (MD) simulations are used to study, in detail, the transfer of thermal (vibrational) energy between objects with discrete vibrational spectra to those with a semi-continuum of spectra. The transfer of energy is stochastic and strongly dependent on the instantaneous separation between the bodies. The insight from the MD simulations can be captured with a simple classical model that agrees well with quantum models. This model can be used to optimize systems for efficient frequency selective energy transfer, which can be used in designing a chemical sensor through nanomechanical resonance spectroscopy.Article Copyright 2013 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. This is the publisher’s final pdf. The published article can be found at: http://scitation.aip.org/content/aip/journal/jap
Powder Injection Molding of Ceria-Stabilized, Zirconia-Toughened Mullite Parts for UAV Engine Components
Get PDFPowder injection molding (PIM) of ceria-stabilized, zirconia-toughened mullite composites were investigated in the present article with the goal of obtaining performance enhancement in complex geometries for energy and transportation applications. A powder-polymer mixture (feedstock) was developed and characterized to determine its suitability for fabricating complex components using the PIM process. Test specimens were injection molded and subsequently debound and sintered. The sintered properties indicated suitable properties for engine component applications used in unmanned aerial vehicles (UAVs). The measured feedstock properties were used in computer simulations to assess the mold-filling behavior for a miniature turbine stator. The results from the measurements of rheological and thermal properties of the feedstock combined with the sintered properties of the ceria-stabilized, zirconia-toughened mullite strongly indicate the potential for enhancing the performance of complex geometries used in demanding operating conditions in UAV engines
New rRNA Gene-Based Phylogenies of the Alphaproteobacteria Provide Perspective on Major Groups, Mitochondrial Ancestry and Phylogenetic Instability
Get PDFBacteria in the class Alphaproteobacteria have a wide variety of lifestyles and physiologies. They include pathogens
of humans and livestock, agriculturally valuable strains, and several highly abundant marine groups. The ancestor of
mitochondria also originated in this clade. Despite significant effort to investigate the phylogeny of the
Alphaproteobacteria with a variety of methods, there remains considerable disparity in the placement of several
groups. Recent emphasis on phylogenies derived from multiple protein-coding genes remains contentious due to
disagreement over appropriate gene selection and the potential influences of systematic error. We revisited previous
investigations in this area using concatenated alignments of the small and large subunit (SSU and LSU) rRNA genes,
as we show here that these loci have much lower GC bias than whole genomes. This approach has allowed us to
update the canonical 16S rRNA gene tree of the Alphaproteobacteria with additional important taxa that were not
previously included, and with added resolution provided by concatenating the SSU and LSU genes. We investigated
the topological stability of the Alphaproteobacteria by varying alignment methods, rate models, taxon selection and
RY-recoding to circumvent GC content bias. We also introduce RYMK-recoding and show that it avoids some of the
information loss in RY-recoding. We demonstrate that the topology of the Alphaproteobacteria is sensitive to
inclusion of several groups of taxa, but it is less affected by the choice of alignment and rate methods. The majority of
topologies and comparative results from Approximately Unbiased tests provide support for positioning the
Rickettsiales and the mitochondrial branch within a clade. This composite clade is a sister group to the abundant
marine SAR11 clade (Pelagibacterales). Furthermore, we add support for taxonomic assignment of several recently
sequenced taxa. Accordingly, we propose three subclasses within the Alphaproteobacteria: the Caulobacteridae, the
Rickettsidae, and the Magnetococcidae