Determination of ferroelectric compositional phase transition using novel virtual crystal approach

We employ a new method for studying compositionally disordered ferroelectric oxides. This method is based on the virtual crystal approximation (VCA), in which two or more component potentials are averaged into a composite atomic potential. In our method, we construct a virtual atom with the correctly averaged atomic size and atomic eigenvalues. We have used our new method to study the composition dependent phase transition in Pb(Zr_{1-x}Ti_x)O_3 lying between x=0.5 and x=0.4. We correctly predict the experimentally determined phase transition from the tetragonal phase to a low-temperature rhombohedral phase between these two compositions.Comment: 7 pages, 2 figures, Proceedings for Fundamental Physics of Ferroelectrics, Aspen, CO February 13-20, 200

Accurate construction of transition metal pseudopotentials

We generate a series of pseudopotentials to examine the relationship between pseudoatomic properties and solid-state results. We find that lattice constants and bulk moduli are quite sensitive to eigenvalue, total-energy difference and tail norm errors, and clear correlations emerge. These trends motivate our identification of two criteria for accurate transition metal pseudopotentials. We find that both the preservation of all-electron derivative of tail norm with respect to occupation and the preservation of all-electron derivative of eigenvalue with respect to occupation {[Phys. Rev. B {\bf 48}, 5031 (1993)]} are necessary to give accurate bulk metal lattice constants and bulk moduli. We also show how the fairly wide range of lattice constant and bulk modulus results found in the literature can be easily explained by pseudopotential effects.Comment: submitted to Phys. Rev

Wallerian degeneration: gaining perspective on inflammatory events after peripheral nerve injury

In this review, we first provide a brief historical perspective, discussing how peripheral nerve injury (PNI) may have caused World War I. We then consider the initiation, progression, and resolution of the cellular inflammatory response after PNI, before comparing the PNI inflammatory response with that induced by spinal cord injury (SCI)

Virtual-crystal approximation that works: Locating a composition phase boundary in Pb(Zr_{1-x}Ti_3)O_3

We present a new method for modeling disordered solid solutions, based on the virtual crystal approximation (VCA). The VCA is a tractable way of studying configurationally disordered systems; traditionally, the potentials which represent atoms of two or more elements are averaged into a composite atomic potential. We have overcome significant shortcomings of the standard VCA by developing a potential which yields averaged atomic properties. We perform the VCA on a ferroelectric oxide, determining the energy differences between the high-temperature rhombohedral, low-temperature rhombohedral and tetragonal phases of Pb(Zr_{1-x}Ti_x)O_3 at x=0.5 and comparing these results to superlattice calculations and experiment. We then use our new method to determine the preferred structural phase at x=0.4. We find that the low-temperature rhombohedral phase becomes the ground state at x=0.4, in agreement with experimental findings.Comment: 5 pages, no figure

A real-time PCR assay for accurate quantification of the individual members of the Altered Schaedler Flora microbiota in gnotobiotic mice

Changes in the gastrointestinal microbial community are frequently associated with chronic diseases such as Inflammatory Bowel Diseases. However, understanding the relationship of any individual taxon within the community to host physiology is made complex due to the diversity and individuality of the gut microbiota. Defined microbial communities such as the Altered Schaedler Flora (ASF) help alleviate the challenges of a diverse microbiota by allowing one to interrogate the relationship between individual bacterial species and host responses. An important aspect of studying these relationships with defined microbial communities is the ability to measure the population abundance and dynamics of each member. Herein, we describe the development of an improved ASF species-specific and sensitive real-time quantitative polymerase chain reaction (qPCR) for use with SYBR Green chemistry to accurately assess individual ASF member abundance. This approach targets hypervariable regions V1 through V3 of the 16S rRNA gene of each ASF taxon to enhance assay specificity. We demonstrate the reproducibility, sensitivity and application of this new method by quantifying each ASF bacterium in two inbred mouse lines. We also used it to assess changes in ASF member abundance before and after acute antibiotic perturbation of the community as well as in mice fed two different diets. Additionally, we describe a nested PCR assay for the detection of lowly abundant ASF members. Altogether, this improved qPCR method will facilitate gnotobiotic research involving the ASF community by allowing for reproducible quantification of its members under various physiological conditions

Experimental Evidence for Adaptation to Species-Specific Gut Microbiota in House Mice

The gut microbial communities of mammals have codiversified with host species, and changes in the gut microbiota can have profound effects on host fitness. Therefore, the gut microbiota may drive adaptation in mammalian species, but this possibility is underexplored. Here, we show that the gut microbiota has codiversified with mice in the genus Mus over the past 6 million years, and we present experimental evidence that the gut microbiota has driven adaptive evolution of the house mouse, Mus musculus domesticus. Phylogenetic analyses of metagenomeassembled bacterial genomic sequences revealed that gut bacterial lineages have been retained within and diversified alongside Mus species over evolutionary time. Transplantation of gut microbiotas from various Mus species into germfree M. m. domesticus showed that foreign gut microbiotas slowed growth rate and upregulated macrophage inflammatory protein in hosts. These results suggest adaptation by M. m. domesticus to its gut microbiota since it diverged from other Mus species

Home-site advantage for host species–specific gut microbiota

Mammalian species harbor compositionally distinct gut microbial communities, but the mechanisms that maintain specificity of symbionts to host species remain unclear. Here, we show that natural selection within house mice (Mus musculus domesticus) drives deterministic assembly of the house-mouse gut microbiota from mixtures of native and non-native microbiotas. Competing microbiotas from wild-derived lines of house mice and other mouse species (Mus and Peromyscus spp.) within germ-free wild-type (WT) and Rag1-knockout (Rag1−/−) house mice revealed widespread fitness advantages for native gut bacteria. Native bacterial lineages significantly outcompeted non-native lineages in both WT and Rag1−/− mice, indicating home-site advantage for native microbiota independent of host adaptive immunity. However, a minority of native Bacteriodetes and Firmicutes favored by selection in WT hosts were not favored or disfavored in Rag1−/− hosts, indicating that Rag1 mediates fitness advantages of these strains. This study demonstrates home-site advantage for native gut bacteria, consistent with local adaptation of gut microbiota to their mammalian species

A gut pathobiont synergizes with the microbiota to instigate inflammatory disease marked by immunoreactivity against other symbionts but not itself

Inflammatory bowel diseases (IBD) are likely driven by aberrant immune responses directed against the resident microbiota. Although IBD is commonly associated with a dysbiotic microbiota enriched in putative pathobionts, the etiological agents of IBD remain unknown. Using a pathobiont-induced intestinal inflammation model and a defined bacterial community, we provide new insights into the immune-microbiota interactions during disease. In this model system, the pathobiont Helicobacter bilis instigates disease following sub-pathological dextran sulfate sodium treatment. We show that H. bilis causes mild inflammation in mono-associated mice, but severe disease in the presence of a microbiota, demonstrating synergy between the pathobiont and microbiota in exacerbating pathology. Remarkably, inflammation depends on the presence of H. bilis, but is marked by a predominant Th17 response against specific members of the microbiota and not the pathobiont, even upon the removal of the most immune-dominant taxa. Neither increases in pathobiont burden nor unique changes in immune-targeted microbiota member abundances are observed during disease. Collectively, our findings demonstrate that a pathobiont instigates inflammation without being the primary target of a Th17 response or by altering the microbiota community structure. Moreover, our findings point toward monitoring pathobiont-induced changes in microbiota immune targeting as a new concept in IBD diagnotics

The waxy mutation in sorghum and other cereal grains reshapes the gut microbiome by reducing levels of multiple beneficial species

Waxy starches from cereal grains contain \u3e90% amylopectin due to naturally occurring mutations that block amylose biosynthesis. Waxy starches have unique organoleptic characteristics (e.g. sticky rice) as well as desirable physicochemical properties for food processing. Using isogenic pairs of wild type sorghum lines and their waxy derivatives, we studied the effects of waxy starches in the whole grain context on the human gut microbiome. In vitro fermentations with human stool microbiomes show that beneficial taxonomic and metabolic signatures driven by grain from wild type parental lines are lost in fermentations of grain from the waxy derivatives and the beneficial signatures can be restored by addition of resistant starch. These undesirable effects are conserved in fermentations of waxy maize, wheat, rice and millet. We also demonstrate that humanized gnotobiotic mice fed low fiber diets supplemented with 20% grain from isogenic pairs of waxy vs. wild type parental sorghum have significant differences in microbiome composition and show increased weight gain. We conclude that the benefits of waxy starches on food functionality can have unintended tradeoff effects on the gut microbiome and host physiology that could be particularly relevant in human populations consuming large amounts of waxy grains