The bracteatus pineapple genome and domestication of clonally propagated crops

Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a 'one-step operation'. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars 'Smooth Cayenne' and 'Queen' exhibited ancient and recent admixture, while 'Singapore Spanish' supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops

Forearm Posture and Mobility in Quadrupedal Dinosaurs

Quadrupedality evolved four independent times in dinosaurs; however, the constraints associated with these transitions in limb anatomy and function remain poorly understood, in particular the evolution of forearm posture and rotational ability (i.e., active pronation and supination). Results of previous qualitative studies are inconsistent, likely due to an inability to quantitatively assess the likelihood of their conclusions. We attempt to quantify antebrachial posture and mobility using the radius bone because its morphology is distinct between extant sprawled taxa with a limited active pronation ability and parasagittal taxa that have an enhanced ability to actively pronate the manus. We used a sliding semi-landmark, outline-based geometric morphometric approach of the proximal radial head and a measurement of the angle of curvature of the radius in a sample of 189 mammals, 49 dinosaurs, 35 squamates, 16 birds, and 5 crocodilians. Our results of radial head morphology showed that quadrupedal ceratopsians, bipedal non-hadrosaurid ornithopods, and theropods had limited pronation/supination ability, and sauropodomorphs have unique radial head morphology that likely allowed limited rotational ability. However, the curvature of the radius showed that no dinosaurian clade had the ability to cross the radius about the ulna, suggesting parallel antebrachial elements for all quadrupedal dinosaurs. We conclude that the bipedal origins of all quadrupedal dinosaur clades could have allowed for greater disparity in forelimb posture than previously appreciated, and future studies on dinosaur posture should not limit their classifications to the overly simplistic extant dichotomy

Activation of the Calcium-Regulated Thin Filament by Myosin Strong Binding

The current study was undertaken to investigate the relative contribution of calcium and myosin binding to thin filament activation. Using the in vitro motility assay, myosin strong binding to the thin filament was controlled by three mechanisms: 1), varying the myosin concentration of the motility surface, and adding either 2), inorganic phosphate (Pi) or 3), adenosine diphosphate (ADP) to the motility solutions. At saturating myosin conditions, Pi had no effect on thin filament motility. However, at subsaturating myosin concentrations, velocity was reduced at maximal and submaximal calcium in the presence of Pi. Adding ADP to the motility buffers reduced thin filament sliding velocity but increased the pCa(50) of the thin filament. Thus by limiting or increasing myosin strong binding (with the addition of Pi and ADP, respectively), the calcium concentration at which half maximal activation of the thin filament is achieved can be modulated. In experiments without ADP or Pi, the myosin concentration on the motility surface required to reach maximal velocity inversely correlated with the level of calcium activation. Through this approach, we demonstrate that myosin strong binding is essential for thin filament activation at both maximal and submaximal calcium levels, with the relative contribution of myosin strong binding being greatest at submaximal calcium. Furthermore, under conditions in which myosin strong binding is not rate limiting (i.e., saturating myosin conditions), our data suggest that a modulation of myosin cross-bridge kinetics is likely responsible for the graded response to calcium observed in the in vitro motility assay

Blood gene expression signatures associate with heart failure outcomes

Gene expression signatures in blood correlate with specific diseases. Such signatures may serve as valuable diagnostic and prognostic tools in disease management. Blood gene expression signatures associated with heart failure may be applied to predict prognosis, monitor disease progression, and optimize treatment. Blood gene expression profiles were generated for 71 subjects with heart failure and 15 controls without heart failure, using the Affymetrix GeneChip U133Plus2.0. Survival analysis identified 197 “mortality genes” that were significantly associated with patient outcome. Functional categorization showed that genes associated with T cell receptor signaling were most significantly overpresented. Cluster analysis of these T cell receptor signaling genes significantly categorized heart failure patients into three risk groups (P = 0.031) that were distinct from the three risk groups categorized by New York Heart Association (NYHA) Classification (P = 0.0002). By combining the analysis of clinical assessment (NYHA class) with T cell receptor signaling gene expression, we proposed a model that demonstrated an even greater differentiation of patients at risk (P = 0.0001). In this discovery study, we identified blood expression signatures associated with heart failure patient outcomes. Characterization of these mortality genes helped identify a set of T cell receptor signaling genes that may be of utility in predicting survival of heart failure patients. These data raise the possibility of prospectively risk stratifying patients with heart failure by integrating blood gene expression signatures with current clinical assessment

Linear Thermal Expansion Measurements of Lead Magnesium Niobate (PMN) Electroceramic Material for the Terrestrial Planet Finder Coronagraph

Linear thermal expansion measurements of nine samples of Lead Magnesium Niobate (PMN) electroceramic material were recently performed in support of NASA's Terrestrial Planet Finder Coronagraph (TPF-C) mission. The TPF-C mission is a visible light coronagraph designed to look at roughly 50 stars pre- selected as good candidates for possessing earth-like planets. Upon detection of an earth-like planet, TPF-C will analyze the visible-light signature of the planet's atmosphere for specific spectroscopic indicators that life may exist there. With this focus, the project's primary interest in PMN material is for use as a solid-state actuator for deformable mirrors or compensating optics. The nine test samples were machined from three distinct boules of PMN ceramic manufactured by Xinetics Inc. Thermal expansion measurements were performed in 2005 at NASA Jet Propulsion Laboratory (JPL) in their Cryogenic Dilatometer Facility. All measurements were performed in vacuum with sample temperature actively controlled over the range of 270K to 3 10K. Expansion and contraction of the test samples with temperature was measured using a JPL developed interferometric system capable of sub-nanometer accuracy. Presented in this paper is a discussion of the sample configuration, test facilities, test method, data analysis, test results, and future plans