Population Genomics of Adaptive Radiation.

Adaptive radiations are rich laboratories for exploring, testing, and understanding key theories in evolution and ecology because they offer spectacular displays of speciation and ecological adaptation. Particular challenges to the study of adaptive radiation include high levels of species richness, rapid speciation, and gene flow between species. Over the last decade, high-throughput sequencing technologies and access to population genomic data have lessened these challenges by enabling the analysis of samples from many individual organisms at whole-genome scales.

Comparison of source-location algorithms for atmospheric samplers.

Numerous algorithms have been developed to determine the source characteristics for an atmospheric radionuclide release, e.g., (Bieringer et al.

Nuclear explosion monitoring network design considerations.

Design of an efficient monitoring network requires information on the type and size of releases to be detected, the accuracy and reliability of the measuring equipment, and the desired network performance. This work provides a scientific basis for optimizing or minimizing networks of Xe samplers to achieve a desired performance level for different levels of release. The approach of this work varies the density of sampling locations to find optimal location subsets, and to explore the properties of variations of those subsets - how crucial is a specific subset; are substitutions problematic? The choice of possible station locations is arbitrary but constrained to some extent by the location of islands, land masses, difficult topography (mountains, etc.

An open database of computed bulk ternary transition metal dichalcogenides.

We present a dataset of structural relaxations of bulk ternary transition metal dichalcogenides (TMDs) computed via plane-wave density functional theory (DFT). We examined combinations of up to two chalcogenides with seven transition metals from groups 4-6 in octahedral (1T) or trigonal prismatic (2H) coordination. The full dataset consists of 672 unique stoichiometries, with a total of 50,337 individual configurations generated during structural relaxation.

Parallel shifts in trout feeding morphology suggest rapid adaptation to alpine lake environments.

Eco-evolutionary interactions following ecosystem change provide critical insight into the ability of organisms to adapt to shifting resource landscapes. Here we explore evidence for the rapid parallel evolution of trout feeding morphology following eco-evolutionary interactions with zooplankton in alpine lakes stocked at different points in time in the Wind River Range (Wyoming, USA). In this system, trout predation has altered the zooplankton species community and driven a decrease in average zooplankton size.

An experimental, computational, and uncertainty analysis study of the rates of iodoalkane trapping by DABCO in solution phase organic media.

NMR spectroscopy was used to measure the rates of the first and second substitution reactions between iodoalkane (R = Me, 1-butyl) and DABCO in methanol, acetonitrile and DMSO. Most of the reactions were recorded at three different temperatures, which permitted calculation of the activation parameters from Eyring and Arrhenius plots. Additionally, the reaction rate and heat of reaction for 1-iodobutane + DABCO in acetonitrile and DMSO were also measured using calorimetry.

Optimization of Thermal Conductance at Interfaces Using Machine Learning Algorithms.

Optimization of thermal transport across the interface of two different materials is critical to micro-/nanoscale electronic, photonic, and phononic devices. Although several examples of compositional intermixing at the interfaces having a positive effect on interfacial thermal conductance (ITC) have been reported, an optimum arrangement has not yet been determined because of the large number of potential atomic configurations and the significant computational cost of evaluation. On the other hand, computation-driven materials design efforts are rising in popularity and importance.

Hybridization decreases native cutthroat trout reproductive fitness.

Examining natural selection in wild populations is challenging, but crucial to understanding many ecological and evolutionary processes. Additionally, in hybridizing populations, natural selection may be an important determinant of the eventual outcome of hybridization. We characterized several components of relative fitness in hybridizing populations of Yellowstone cutthroat trout and rainbow trout in an effort to better understand the prolonged persistence of both parental species despite predictions of extirpation.

Enabling probabilistic retrospective transport modeling for accurate source detection.

Predicting source or background radionuclide emissions is limited by the effort needed to run gas/aerosol atmospheric transport models (ATMs). A high-performance surrogate model is developed for the HYSPLIT4 (NOAA) ATM to accelerate transport simulation through model reduction, code optimization, and improved scaling on high performance computing systems. The surrogate model parameters are a grid of short-duration transport simulations stored offline.

Invasion and rapid adaptation of guppies () across the Hawaiian Archipelago.

How much does natural selection, as opposed to genetic drift, admixture, and gene flow, contribute to the evolution of invasive species following introduction to a new environment? Here we assess how evolution can shape biological invasions by examining population genomic variation in non-native guppies () introduced to the Hawaiian Islands approximately a century ago. By examining 18 invasive populations from four Hawaiian islands and four populations from the native range in northern South America, we reconstructed the history of introductions and evaluated population structure as well as the extent of ongoing gene flow across watersheds and among islands. Patterns of differentiation indicate that guppies have developed significant population structure, with little natural or human-mediated gene flow having occurred among populations following introduction.

Source type estimation using noble gas samples.

A Bayesian source-term algorithm recently published by Eslinger et al. (2019) extended previous models by including the ability to discriminate between classes of releases such as nuclear explosions, nuclear power plants, or medical isotope production facilities when multiple isotopes are measured. Using 20 release cases from a synthetic data set previously published by Haas et al.

Source term estimation using multiple xenon isotopes in atmospheric samples.

Algorithms that estimate the location and magnitude of an atmospheric release using remotely sampled air concentrations typically involve a single chemical or radioactive isotope. A new Bayesian algorithm is presented that makes discrimination between possible types of releases (e.g.

A Mutation in the Transcription Factor Foxp3 Drives T Helper 2 Effector Function in Regulatory T Cells.

Regulatory T (Treg) cells maintain immune tolerance through the master transcription factor forkhead box P3 (FOXP3), which is crucial for Treg cell function and homeostasis. We identified an IPEX (immune dysregulation polyendocrinopathy enteropathy X-linked) syndrome patient with a FOXP3 mutation in the domain swap interface of the protein. Recapitulation of this Foxp3 variant in mice led to the development of an autoimmune syndrome consistent with an unrestrained T helper type 2 (Th2) immune response.

The chromatin-modifying enzyme Ezh2 is critical for the maintenance of regulatory T cell identity after activation.

Regulatory T cells (Treg cells) are required for immune homeostasis. Chromatin remodeling is essential for establishing diverse cellular identities, but how the epigenetic program in Treg cells is maintained throughout the dynamic activation process remains unclear. Here we have shown that CD28 co-stimulation, an extracellular cue intrinsically required for Treg cell maintenance, induced the chromatin-modifying enzyme, Ezh2.

Regulatory T cells suppress muscle inflammation and injury in muscular dystrophy.

We examined the hypothesis that regulatory T cells (Tregs) modulate muscle injury and inflammation in the mdx mouse model of Duchenne muscular dystrophy (DMD). Although Tregs were largely absent in the muscle of wild-type mice and normal human muscle, they were present in necrotic lesions, displayed an activated phenotype, and showed increased expression of interleukin-10 (IL-10) in dystrophic muscle from mdx mice. Depletion of Tregs exacerbated muscle injury and the severity of muscle inflammation, which was characterized by an enhanced interferon-γ (IFN-γ) response and activation of M1 macrophages.

Self-antigen-driven activation induces instability of regulatory T cells during an inflammatory autoimmune response.

Stable Foxp3 expression is crucial for regulatory T (Treg) cell function. We observed that antigen-driven activation and inflammation in the CNS promoted Foxp3 instability selectively in the autoreactive Treg cells that expressed high amounts of Foxp3 before experimental autoimmune encephalitis induction. Treg cells with a demethylated Treg-cell-specific demethylated region in the Foxp3 locus downregulated Foxp3 transcription in the inflamed CNS during the induction phase of the response.

microRNA-17-92 regulates IL-10 production by regulatory T cells and control of experimental autoimmune encephalomyelitis.

microRNAs (miRNA) are essential for regulatory T cell (Treg) function but little is known about the functional relevance of individual miRNA loci. We identified the miR-17-92 cluster as CD28 costimulation dependent, suggesting that it may be key for Treg development and function. Although overall immune homeostasis was maintained in mice with miR-17-92-deficient Tregs, expression of the miR-17-92 miRNA cluster was critical for Treg accumulation and function during an acute organ-specific autoimmune disease in vivo.

Culturing primary rat inner medullary collecting duct cells.

Arginine-vasopressin (AVP) facilitates water reabsorption by renal collecting duct principal cells and thereby fine-tunes body water homeostasis. AVP binds to vasopressin V2 receptors (V2R) on the surface of the cells and thereby induces synthesis of cAMP. This stimulates cellular signaling processes leading to changes in the phosphorylation of the water channel aquaporin-2 (AQP2).

Distinct genetic control of autoimmune neuropathy and diabetes in the non-obese diabetic background.

The non-obese diabetic (NOD) mouse is susceptible to the development of autoimmune diabetes but also multiple other autoimmune diseases. Over twenty susceptibility loci linked to diabetes have been identified in NOD mice and progress has been made in the definition of candidate genes at many of these loci (termed Idd for insulin-dependent diabetes). The susceptibility to multiple autoimmune diseases in the NOD background is a unique opportunity to examine susceptibility genes that confer a general propensity for autoimmunity versus susceptibility genes that control individual autoimmune diseases.