ALBERT

Description: Many phylogenomic studies based on transcriptomes have been limited to "single-copy" genes due to methodological challenges in homology and orthology inferences. Only a relatively small number of studies have explored analyses beyond reconstructing species relationships. We sampled 69 transcriptomes in the hyperdiverse plant clade Caryophyllales and 27 outgroups from annotated genomes across eudicots. Using a combined similarity- and phylogenetic tree-based approach, we recovered 10,960 homolog groups, where each was represented by at least eight ingroup taxa. By decomposing these homolog trees, and taking gene duplications into account, we obtained 17,273 ortholog groups, where each was represented by at least ten ingroup taxa. We reconstructed the species phylogeny using a 1,122-gene data set with a gene occupancy of 92.1%. From the homolog trees, we found that both synonymous and nonsynonymous substitution rates in herbaceous lineages are up to three times as fast as in their woody relatives. This is the first time such a pattern has been shown across thousands of nuclear genes with dense taxon sampling. We also pinpointed regions of the Caryophyllales tree that were characterized by relatively high frequencies of gene duplication, including three previously unrecognized whole-genome duplications. By further combining information from homolog tree topology and synonymous distance between paralog pairs, phylogenetic locations for 13 putative genome duplication events were identified. Genes that experienced the greatest gene family expansion were concentrated among those involved in signal transduction and oxidoreduction, including a cytochrome P450 gene that encodes a key enzyme in the betalain synthesis pathway. Our approach demonstrates a new approach for functional phylogenomic analysis in nonmodel species that is based on homolog groups in addition to inferred ortholog groups.

Description: Author(s): Kim Molvig, Nelson M. Hoffman, B. J. Albright, Eric M. Nelson, and Robert B. Webster Knudsen layer losses of tail fuel ions can significantly reduce the fusion reactivity of multi-keV DT in capsules with small fuel ρ r ; sizable yield reduction can result for small inertial confinement fusion (ICF) capsules. This effect is most pronounced when the distance from a burning DT gas region... [Phys. Rev. Lett. 109, 095001] Published Thu Aug 30, 2012

Description: The rs1061170T/C variant encoding the Y402H change in complement factor H (CFH) has been identified by genome-wide association studies as being significantly associated with age-related macular degeneration (AMD). However, the precise mechanism by which this CFH variant impacts the risk of AMD remains largely unknown. Oxidative stress plays an important...

Description: In gravel-bed rivers, bed topography and the bed surface grain size distribution evolve simultaneously, but it is not clear how feedbacks between topography and grain sorting affect channel morphology. In this, the second of a pair of papers examining interactions between bed topography and bed surface sorting in gravel bed rivers, we use a two-dimensional morphodynamic model to perform numerical experiments designed to explore the coevolution of both free and forced bars and bed surface patches. Model runs were carried out on a computational grid simulating a 200 m long, 2.75 m wide, straight, rectangular channel, with an initially flat bed at a slope of 0.0137. Over five numerical experiments, we varied a) whether an obstruction was present, b) whether the sediment was a gravel mixture or a single size, and c) whether the bed surface grain size feeds back on the hydraulic roughness field. Experiments with channel obstructions developed a train of alternate bars that became stationary and were connected to the obstruction. Freely migrating alternate bars formed in the experiments without channel obstructions. Simulations incorporating roughness feedbacks between the bed surface and flow field produced flatter, broader, and longer bars than simulations using constant roughness or uniform sediment. Our findings suggest that patches are not simply a byproduct of bed topography, but they interact with the evolving bed and influence morphologic evolution.

Description: Riverbeds frequently display a spatial structure where the sediment mixture composing the channel bed has been sorted into discrete patches of similar grain size. Even though patches are a fundamental feature in gravel-bed rivers, we have little understanding of how patches form, evolve, and interact. Here, we present a two-dimensional morphodynamic model that is used to examine in greater detail the mechanisms responsible for the development of forced bed surface patches and the coevolution of bed morphology and bed surface patchiness. The model computes the depth-averaged channel hydrodynamics, mixed-grain-size sediment transport, and bed evolution by coupling the river morphodynamic model FaSTMECH with a transport relation for gravel mixtures and the mixed-grain-size Exner equation using the active layer assumption. To test the model, we use it to simulate a flume experiment in which the bed developed a sequence of alternate bars and temporally and spatially persistent forced patches with a general pattern of coarse bar tops and fine pools. Cross-stream sediment flux causes sediment to be exported off of bars and imported into pools at a rate that balances downstream gradients in the streamwise sediment transport rate, allowing quasi-steady bar-pool topography to persist. The relative importance of lateral gravitational forces on the cross-stream component of sediment transport is a primary control on the amplitude of the bars. Because boundary shear stress declines as flow shoals over the bars, the lateral sediment transport is increasingly size-selective and leads to the development of coarse bar tops and fine pools.

Description: Galaxy clusters contain a large population of low-mass dwarf elliptical galaxies whose exact origin is unclear: their colours, structural properties and kinematics differ substantially from those of dwarf irregulars in the field. We use the Illustris cosmological simulation to study differences in the assembly histories of dwarf galaxies (3 x 10 8 〈 M * /M 〈 10 10 ) according to their environment. We find that cluster dwarfs achieve their maximum total and stellar mass on average ~8 and ~4.5 Gyr ago (or redshifts z  = 1.0 and 0.4, respectively), around the time of infall into the clusters. In contrast, field dwarfs not subjected to environmental stripping reach their maximum mass at z  = 0. These different assembly trajectories naturally produce a colour bimodality, with blue isolated dwarfs and redder cluster dwarfs exhibiting negligible star formation today. The cessation of star formation happens over median times 3.5–5 Gyr depending on stellar mass, and shows a large scatter (~1–8 Gyr), with the lower values associated with starburst events that occur at infall through the virial radius or pericentric passages. We argue that such starbursts together with the early assembly of cluster dwarfs can provide a natural explanation for the higher specific frequency of globular clusters (GCs) in cluster dwarfs, as found observationally. We present a simple model for the formation and stripping of GCs that supports this interpretation. The origin of dwarf ellipticals in clusters is, therefore, consistent with an environmentally driven evolution of field dwarf irregulars. However, the z  = 0 field analogues of cluster dwarf progenitors have today stellar masses a factor of ~3 larger – a difference arising from the early truncation of star formation in cluster dwarfs.

Description: Innervation of skeletal muscle by motor neurons occurs through the neuromuscular junction, a cholinergic synapse essential for normal muscle growth and function. Defects in nerve–muscle signaling cause a variety of neuromuscular disorders with features of ataxia, paralysis, skeletal muscle wasting, and degeneration. Here we show that the nuclear zinc finger...

Description: We present two numerical schemes for passive tracer particles in the hydrodynamical moving-mesh code arepo , and compare their performance for various problems, from simple set-ups to cosmological simulations. The purpose of tracer particles is to allow the flow to be followed in a Lagrangian way, tracing the evolution of the fluid with time, and allowing the thermodynamical history of individual fluid parcels to be recorded. We find that the commonly used ‘velocity field tracers’, which are advected using the fluid velocity field, do not in general follow the mass flow correctly, and explain why this is the case. This method can result in order-of-magnitude biases in simulations of driven turbulence and in cosmological simulations, rendering the velocity field tracers inappropriate for following these flows. We then discuss a novel implementation of ‘Monte Carlo tracers’, which are moved along with fluid cells and are exchanged probabilistically between them following the mass flux. This method reproduces the mass distribution of the fluid correctly. The main limitation of this approach is that it is more diffusive than the fluid itself. Nonetheless, we show that this novel approach is more reliable than that has been employed previously and demonstrate that it is appropriate for following hydrodynamical flows in mesh-based codes. The Monte Carlo tracers can also naturally be transferred between fluid cells and other types of particles, such as stellar particles, so that the mass flow in cosmological simulations can be followed in its entirety.

Description: Dilated cardiomyopathy (DCM) is a leading cause of heart failure. In families with autosomal-dominant DCM, heterozygous missense mutations were identified in RNA-binding motif protein 20 ( RBM20 ), a spliceosome protein induced during early cardiogenesis. Dermal fibroblasts from two unrelated patients harboring an RBM20 R636S missense mutation were reprogrammed to human induced pluripotent stem cells (hiPSCs) and differentiated to beating cardiomyocytes (CMs). Stage-specific transcriptome profiling identified differentially expressed genes ranging from angiogenesis regulator to embryonic heart transcription factor as initial molecular aberrations. Furthermore, gene expression analysis for RBM20- dependent splice variants affected sarcomeric ( TTN and LDB3 ) and calcium (Ca 2+ ) handling ( CAMK2D and CACNA1C ) genes. Indeed, RBM20 hiPSC-CMs exhibited increased sarcomeric length ( RBM20 : 1.747 ± 0.238 µm versus control: 1.404 ± 0.194 µm; P 〈 0.0001) and decreased sarcomeric width ( RBM20 : 0.791 ± 0.609 µm versus control: 0.943 ± 0.166 µm; P 〈 0.0001). Additionally, CMs showed defective Ca 2+ handling machinery with prolonged Ca 2+ levels in the cytoplasm as measured by greater area under the curve ( RBM20 : 814.718 ± 94.343 AU versus control: 206.941 ± 22.417 AU; P 〈 0.05) and higher Ca 2+ spike amplitude ( RBM20 : 35.281 ± 4.060 AU versus control:18.484 ± 1.518 AU; P 〈 0.05). β-adrenergic stress induced with 10 µ m norepinephrine demonstrated increased susceptibility to sarcomeric disorganization ( RBM20 : 86 ± 10.5% versus control: 40 ± 7%; P 〈 0.001). This study features the first hiPSC model of RBM20 familial DCM. By monitoring human cardiac disease according to stage-specific cardiogenesis, this study demonstrates RBM20 familial DCM is a developmental disorder initiated by molecular defects that pattern maladaptive cellular mechanisms of pathological cardiac remodeling. Indeed, hiPSC-CMs recapitulate RBM20 familial DCM phenotype in a dish and establish a tool to dissect disease-relevant defects in RBM20 splicing as a global regulator of heart function.

Description: Single-phase monoclinic aluminum–gallium oxide powders, β−(Al x Ga 1− x ) 2 O 3 , have been produced by solution combustion synthesis for Al fraction 0 ≤  x  〈 0.8. α−(Al x Ga 1− x ) 2 O 3 is observed for x  = 1, with mixed α + β for x  = 0.8. The contraction in lattice parameters and increase in band gap with increasing Al concentration were characterized by X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS), respectively, and are compared with a first-principles density-functional theory calculation. A novel filtering procedure is described to reduce the uncertainty involved in measuring band gap using photoemission, and to remove asymmetry in XPS line shapes caused by differential charging of loose powder. The lattice parameters vary linearly with Al fraction, but exhibit a change in slope at x  = 0.5 that is attributed to the difference between aluminum occupying tetrahedral and octahedral sites in the monoclinic lattice. The band gap changes linearly with local stoichiometry, including increasing when aluminum content at the surface is enriched relative to the interior, with a range of over 1.8 eV.