Duplication and diversification of the LEAFY HULL STERILE1 and Oryza sativa MADS5 SEPALLATA lineages in graminoid Poales

<p>Abstract</p> <p>Background</p> <p>Gene duplication and the subsequent divergence in function of the resulting paralogs via subfunctionalization and/or neofunctionalization is hypothesized to have played a major role in the evolution of plant form. The <it>LEAFY HULL STERILE1 (LHS1) SEPALLATA </it>(<it>SEP</it>) genes have been linked with the origin and diversification of the grass spikelet, but it is uncertain 1) when the duplication event that produced the <it>LHS1 </it>clade and its paralogous lineage <it>Oryza sativa MADS5 (OSM5) </it>occurred, and 2) how changes in gene structure and/or expression might have contributed to subfunctionalization and/or neofunctionalization in the two lineages.</p> <p>Methods</p> <p>Phylogenetic relationships among 84 <it>SEP </it>genes were estimated using Bayesian methods. RNA expression patterns were inferred using <it>in situ </it>hybridization. The patterns of protein sequence and RNA expression evolution were reconstructed using maximum parsimony (MP) and maximum likelihood (ML) methods, respectively.</p> <p>Results</p> <p>Phylogenetic analyses mapped the <it>LHS1/OSM5 </it>duplication event to the base of the grass family. MP character reconstructions estimated a change from cytosine to thymine in the first codon position of the first amino acid after the <it>Zea mays MADS3 </it>(<it>ZMM3</it>) domain converted a glutamine to a stop codon in the <it>OSM5 </it>ancestor following the <it>LHS1/OSM5 </it>duplication event. RNA expression analyses of <it>OSM5 </it>co-orthologs in <it>Avena sativa, Chasmanthium latifolium, Hordeum vulgare, Pennisetum glaucum</it>, and <it>Sorghum bicolor </it>followed by ML reconstructions of these data and previously published analyses estimated a complex pattern of gain and loss of <it>LHS1 </it>and <it>OSM5 </it>expression in different floral organs and different flowers within the spikelet or inflorescence.</p> <p>Conclusions</p> <p>Previous authors have reported that rice OSM5 and LHS1 proteins have different interaction partners indicating that the truncation of OSM5 following the <it>LHS1/OSM5 </it>duplication event has resulted in both partitioned and potentially novel gene functions. The complex pattern of <it>OSM5 </it>and <it>LHS1 </it>expression evolution is not consistent with a simple subfunctionalization model following the gene duplication event, but there is evidence of recent partitioning of <it>OSM5 </it>and <it>LHS1 </it>expression within different floral organs of <it>A. sativa, C. latifolium, P. glaucum </it>and <it>S. bicolor</it>, and between the upper and lower florets of the two-flowered maize spikelet.</p

Invest to Save: Report and Recommendations of the NSF-DELOS Working Group on Digital Archiving and Preservation

Digital archiving and preservation are important areas for research and development, but there is no agreed upon set of priorities or coherent plan for research in this area. Research projects in this area tend to be small and driven by particular institutional problems or concerns. As a consequence, proposed solutions from experimental projects and prototypes tend not to scale to millions of digital objects, nor do the results from disparate projects readily build on each other. It is also unclear whether it is worthwhile to seek general solutions or whether different strategies are needed for different types of digital objects and collections. The lack of coordination in both research and development means that there are some areas where researchers are reinventing the wheel while other areas are neglected. Digital archiving and preservation is an area that will benefit from an exercise in analysis, priority setting, and planning for future research. The WG aims to survey current research activities, identify gaps, and develop a white paper proposing future research directions in the area of digital preservation. Some of the potential areas for research include repository architectures and inter-operability among digital archives; automated tools for capture, ingest, and normalization of digital objects; and harmonization of preservation formats and metadata. There can also be opportunities for development of commercial products in the areas of mass storage systems, repositories and repository management systems, and data management software and tools.

Evidence for mechanical and chemical alteration of iron‐nickel meteorites on Mars: Process insights for Meridiani Planum

The weathering of meteorites found on Mars involves chemical and physical processes that can provide clues to climate conditions at the location of their discovery. Beginning on sol 1961, the Opportunity rover encountered three large iron meteorites within a few hundred meters of each other. In order of discovery, these rocks have been assigned the unofficial names Block Island, Shelter Island, and Mackinac Island. Each rock presents a unique but complimentary set of features that increase our understanding of weathering processes at Meridiani Planum. Significant morphologic characteristics interpretable as weathering features include (1) a large pit in Block Island, lined with delicate iron protrusions suggestive of inclusion removal by corrosive interaction; (2) differentially eroded kamacite and taenite lamellae in Block Island and Shelter Island, providing relative timing through crosscutting relationships with deposition of (3) an iron oxide&ndash;rich dark coating; (4) regmaglypted surfaces testifying to regions of minimal surface modification, with other regions in the same meteorites exhibiting (5) large‐scale, cavernous weathering (in Shelter Island and Mackinac Island). We conclude that the current size of the rocks is approximate to their original postfall contours. Their morphology thus likely results from a combination of atmospheric interaction and postfall weathering effects. Among our specific findings is evidence supporting (1) at least one possible episode of aqueous acidic exposure for Block Island; (2) ripple migration over portions of the meteorites; (3) a minimum of two separate episodes of wind abrasion; alternating with (4) at least one episode of coating‐forming chemical alteration, most likely at subzero temperatures

Lab-on-a-chip workshop activities for secondary school students

The ability to engage and inspire younger generations in novel areas of science is important for bringing new researchers into a burgeoning field, such as lab-on-a-chip. We recently held a lab-on-a-chip workshop for secondary school students, for which we developed a number of hands-on activities that explained various aspects of microfluidic technology, including fabrication (milling and moulding of microfluidic devices, and wax printing of microfluidic paper-based analytical devices, so-called μPADs), flow regimes (gradient formation via diffusive mixing), and applications (tissue analysis and μPADs). Questionnaires completed by the students indicated that they found the workshop both interesting and informative, with all activities proving successful, while providing feedback that could be incorporated into later iterations of the event

Opportunity Mars Rover mission: Overview and selected results from Purgatory ripple to traverses to Endeavour crater

Opportunity has been traversing the Meridiani plains since 25 January 2004 (sol 1), acquiring numerous observations of the atmosphere, soils, and rocks. This paper provides an overview of key discoveries between sols 511 and 2300, complementing earlier papers covering results from the initial phases of the mission. Key new results include (1) atmospheric argon measurements that demonstrate the importance of atmospheric transport to and from the winter carbon dioxide polar ice caps; (2) observations showing that aeolian ripples covering the plains were generated by easterly winds during an epoch with enhanced Hadley cell circulation; (3) the discovery and characterization of cobbles and boulders that include iron and stony‐iron meteorites and Martian impact ejecta; (4) measurements of wall rock strata within Erebus and Victoria craters that provide compelling evidence of formation by aeolian sand deposition, with local reworking within ephemeral lakes; (5) determination that the stratigraphy exposed in the walls of Victoria and Endurance craters show an enrichment of chlorine and depletion of magnesium and sulfur with increasing depth. This result implies that regional‐scale aqueous alteration took place before formation of these craters. Most recently, Opportunity has been traversing toward the ancient Endeavour crater. Orbital data show that clay minerals are exposed on its rim. Hydrated sulfate minerals are exposed in plains rocks adjacent to the rim, unlike the surfaces of plains outcrops observed thus far by Opportunity. With continued mechanical health, Opportunity will reach terrains on and around Endeavour&rsquo;s rim that will be markedly different from anything examined to date.Additional co-authors: RM Haberle, KE Herkenhoff, JA Herman, KD Iagnemma, BL Jolliff, JR Johnson, G Klingelhöfer, AH Knoll, AT Knudson, R Li, SM McLennan, DW Mittlefehldt, RV Morris, TJ Parker, MS Rice, LA Soderblom, SW Squyres, RJ Sullivan, MJ Wolf

Properties and distribution of paired candidate stony meteorites at Meridiani Planum, Mars

The Mars Exploration Rover Opportunity investigated four rocks, informally dubbed Barberton, Santa Catarina, Santorini, and Kasos, that are possible stony meteorites. Their chemical and mineralogical composition is similar to the howardite, eucrite, and diogenite group but with additional metal, similar to mesosiderite silicate clasts. Because of their virtually identical composition and because they appear to represent a relatively rare group of meteorites, they are probably paired. The four rocks were investigated serendipitously several kilometers apart, suggesting that Opportunity is driving across a larger population of similar rock fragments, maybe a meteorite strewn field. Small amounts of ferric Fe are a result of weathering. We did not observe evidence for fusion crusts. Four iron meteorites were found across the same area. Although mesosiderites are stony irons, a genetic link to these irons is unlikely. The stony meteorites probably fell later than the irons. The current atmosphere is sufficiently dense to land such meteorites at shallow entry angles, and it would disperse fragments over several kilometers upon atmospheric breakup. Alternatively, dispersion by spallation from an impacting meteoroid may have occurred. Santa Catarina and a large accumulation of similar rocks were found at the rim of Victoria crater. It is possible that they are associated with the impactor that created Victoria crater, but our limited knowledge about their distribution cannot exclude mere coincidence

Mineralogy and chemistry of cobbles at Meridiani Planum, Mars, investigated by the Mars Exploration Rover Opportunity

Numerous loose rocks with dimensions of a few centimeters to tens of centimeters and with no obvious physical relationship to outcrop rocks have been observed along the traverse of the Mars Exploration Rover Opportunity. To date, about a dozen of these rocks have been analyzed with Opportunity&rsquo;s contact instruments, providing information about elemental chemistry (Alpha Particle X‐ray Spectrometer), iron mineralogy and oxidation states (M&ouml;ssbauer Spectrometer) and texture (Microscopic Imager). These &ldquo;cobbles&rdquo; appear to be impact related, and three distinct groups can be identified on the basis of chemistry and mineralogy. The first group comprises bright fragments of the sulfate‐rich bedrock that are compositionally and texturally indistinguishable from outcrop rocks. All other cobbles are dark and are divided into two groups, referred to as the &ldquo;Barberton group&rdquo; and the &ldquo;Arkansas group,&rdquo; after the first specimen of each that was encountered by Opportunity. Barberton group cobbles are interpreted as meteorites with an overall chemistry and mineralogy consistent with a mesosiderite silicate clast composition. Arkansas group cobbles appear to be related to Meridiani outcrop and contain an additional basaltic component. They have brecciated textures, pointing to an impact‐related origin during which local bedrock and basaltic material were mixed

Searching for gravitational waves from known pulsars

We present upper limits on the amplitude of gravitational waves from 28 isolated pulsars using data from the second science run of LIGO. The results are also expressed as a constraint on the pulsars' equatorial ellipticities. We discuss a new way of presenting such ellipticity upper limits that takes account of the uncertainties of the pulsar moment of inertia. We also extend our previous method to search for known pulsars in binary systems, of which there are about 80 in the sensitive frequency range of LIGO and GEO 600.Comment: Accepted by CQG for the proceeding of GWDAW9, 7 pages, 2 figure

Science Programs for a 2 m-class Telescope at Dome C, Antarctica: PILOT, the Pathfinder for an International Large Optical Telescope

The cold, dry and stable air above the summits of the Antarctic plateau provides the best ground-based observing conditions from optical to sub-mm wavelengths to be found on the Earth. PILOT is a proposed 2 m telescope, to be built at Dome C in Antarctica, able to exploit these conditions for conducting astronomy at optical and infrared wavelengths. While PILOT is intended as a pathfinder towards the construction of future grand-design facilities, it will also be able to undertake a range of fundamental science investigations in its own right. This paper provides the performance specifications for PILOT, including its instrumentation. It then describes the kinds of science projects that it could best conduct. These range from planetary science to the search for other solar systems, from star formation within the Galaxy to the star formation history of the Universe, and from gravitational lensing caused by exo-planets to that produced by the cosmic web of dark matter. PILOT would be particularly powerful for wide-field imaging at infrared wavelengths, achieving near-diffraction limited performance with simple tip-tilt wavefront correction. PILOT would also be capable of near-diffraction limited performance in the optical wavebands, as well be able to open new wavebands for regular ground based observation; in the mid-IR from 17 to 40 microns and in the sub-mm at 200 microns.Comment: 74 pages, 14 figures, PASA, in pres

The Reflection Component from Cygnus X-1 in the Soft State Measured by NuSTAR and Suzaku

The black hole binary Cygnus X-1 was observed in late 2012 with the Nuclear Spectroscopic Telescope Array (NuSTAR) and Suzaku, providing spectral coverage over the ~1-300 keV range. The source was in the soft state with a multi-temperature blackbody, power law, and reflection components along with absorption from highly ionized material in the system. The high throughput of NuSTAR allows for a very high quality measurement of the complex iron line region as well as the rest of the reflection component. The iron line is clearly broadened and is well described by a relativistic blurring model, providing an opportunity to constrain the black hole spin. Although the spin constraint depends somewhat on which continuum model is used, we obtain ɑ_* > 0.83 for all models that provide a good description of the spectrum. However, none of our spectral fits give a disk inclination that is consistent with the most recently reported binary values for Cyg X-1. This may indicate that there is a >13° misalignment between the orbital plane and the inner accretion disk (i.e., a warped accretion disk) or that there is missing physics in the spectral models