ALBERT

Description: Genotyping microarrays are an important resource for genetic mapping, population genetics, and monitoring of the genetic integrity of laboratory stocks. We have developed the third generation of the Mouse Universal Genotyping Array (MUGA) series, GigaMUGA, a 143,259-probe Illumina Infinium II array for the house mouse ( Mus musculus ). The bulk of the content of GigaMUGA is optimized for genetic mapping in the Collaborative Cross and Diversity Outbred populations, and for substrain-level identification of laboratory mice. In addition to 141,090 single nucleotide polymorphism probes, GigaMUGA contains 2006 probes for copy number concentrated in structurally polymorphic regions of the mouse genome. The performance of the array is characterized in a set of 500 high-quality reference samples spanning laboratory inbred strains, recombinant inbred lines, outbred stocks, and wild-caught mice. GigaMUGA is highly informative across a wide range of genetically diverse samples, from laboratory substrains to other Mus species. In addition to describing the content and performance of the array, we provide detailed probe-level annotation and recommendations for quality control.

Description: Author(s): A. R. Konicek, D. S. Grierson, A. V. Sumant, T. A. Friedmann, J. P. Sullivan, P. U. P. A. Gilbert, W. G. Sawyer, and R. W. Carpick Highly s p 3 -bonded, nearly hydrogen-free carbon-based materials can exhibit extremely low friction and wear in the absence of any liquid lubricant, but this physical behavior is limited by the vapor environment. The effect of water vapor on friction and wear is examined as a function of applied norma... [Phys. Rev. B 85, 155448] Published Wed Apr 25, 2012

Description: Large eddy simulations of the Craik-Leibovich equations are used to assess the effect of misaligned Stokes drift and wind direction on Langmuir cells in the ocean mixed layer. Misalignments from 0° to 135° are examined and Langmuir turbulence structures are evident in all cases. The Stokes drift is modeled using a broadband empirical spectrum, and cases with and without the Coriolis effect, wind waves, and an initial mixed layer are examined. The expected scaling for the vertical velocity variance is recovered in the aligned simulations and is adapted here to the misaligned cases. The adjusted scaling projects the friction velocity (aligned with the wind stress) into the dominant axial direction of the Langmuir cells. The turbulent Langmuir number is generalized through a similar projection into the axial direction of the Langmuir cells, which reduces its value in realistic conditions. For known Langmuir cell orientations, the strength of Langmuir turbulence for misaligned cases can be estimated using the projected Langmuir number. A prediction for the angle between the wind stress and cell direction is obtained using the law of the wall; this prediction only requires the wind stress, Stokes drift, and boundary layer depth. Conditional analyses show that, with increasing misalignment, the typically antisymmetric Langmuir cell pairs become asymmetric. This asymmetry is due, in part, to the advection by cross cell flow of vorticity from one vortex tube onto the other, and in part due to an asymmetry induced by the stretching of vertical vorticity into cross cell vorticity.

Description: We present optical and near-infrared photometric and spectroscopic observations of SN 2013ej, in galaxy M74, from 1 to 450 d after the explosion. SN 2013ej is a hydrogen-rich supernova, classified as a Type IIL due to its relatively fast decline following the initial peak. It has a relatively high peak luminosity (absolute magnitude M V = –17.6) but a small 56 Ni production of ~0.023 M . Its photospheric evolution is similar to other Type II SNe, with shallow absorption in the H α profile typical for a Type IIL. During transition to the radioactive decay tail at ~100 d, we find the SN to grow bluer in B  –  V colour, in contrast to some other Type II supernovae. At late times, the bolometric light curve declined faster than expected from 56 Co decay and we observed unusually broad and asymmetric nebular emission lines. Based on comparison of nebular emission lines most sensitive to the progenitor core mass, we find our observations are best matched to synthesized spectral models with a M ZAMS  = 12–15 M progenitor. The derived mass range is similar to but not higher than the mass estimated for Type IIP progenitors. This is against the idea that Type IIL are from more massive stars. Observations are consistent with the SN having a progenitor with a relatively low-mass envelope.

Description: We present the analysis of 71 h of high-quality time series CCD photometry of the helium atmosphere pulsating white dwarf (DBV) EC 04207–4748 obtained using the facilities at Mt John University Observatory in New Zealand. The photometric data set consists of four week-long observing sessions covering the period 2011 March to November. A Fourier analysis of the light curves yielded clear evidence of four independent eigenmodes in the star with the dominant mode having a period of 447 s. The light-curve variations exhibit distinct non-sinusoidal shapes, which result in significant harmonics of the dominant frequency appearing in the Fourier transforms. These observed variations are interpreted in terms of non-linear contributions from the energy flux transmission through the sub-surface convection zone in the star. Our modelling of this mechanism, using the methods first introduced by Montgomery, yields a time-averaged convective response time of 0  ~ 150 s for the star, and this is shown to be broadly consistent with an MLT/α parameter value between 0.8 and 1.2. It is argued that for the DBV pulsators the measured value of 0 is a better estimate of the relative stellar surface temperatures than those obtained via spectroscopic techniques.

Description: Transcripts possessing a 5'-triphosphate are a hallmark of viral transcription and can trigger the host antiviral response. 5'-triphosphates are also found on common host transcripts transcribed by RNA polymerase III (RNAP III), yet how these transcripts remain non-immunostimulatory is incompletely understood. Most microRNAs (miRNAs) are 5'-monophosphorylated as a result of sequential endonucleolytic processing by Drosha and Dicer from longer RNA polymerase II (RNAP II)-transcribed primary transcripts. In contrast, bovine leukemia virus (BLV) expresses subgenomic RNAP III transcripts that give rise to miRNAs independent of Drosha processing. Here, we demonstrate that each BLV pre-miRNA is directly transcribed by RNAP III from individual, compact RNAP III type II genes. Thus, similar to manmade RNAP III-generated short hairpin RNAs (shRNAs), the BLV pre-miRNAs are initially 5'-triphosphorylated. Nonetheless, the derivative 5p miRNAs and shRNA-generated 5p small RNAs (sRNAs) possess a 5'-monophosphate. Our enzymatic characterization and small RNA sequencing data demonstrate that BLV 5p miRNAs are co-terminal with 5'-triphosphorylated miRNA precursors (pre-miRNAs). Thus, these results identify a 5'-tri-phosphatase activity that is involved in the biogenesis of BLV miRNAs and shRNA-generated sRNAs. This work advances our understanding of retroviral miRNA and shRNA biogenesis and may have implications regarding the immunostimulatory capacity of RNAP III transcripts.

Description: Rivers are increasingly recognized as providing nutritional subsidies (i.e., energy and nutrients) to adjacent terrestrial food webs via depredation of aquatic organisms (e.g., emergent aquatic insects, crayfish, fish) by terrestrial consumers. However, because these prey organisms assimilate energy from both aquatic (e.g., benthic algae, phytoplankton, aquatic macrophytes) and terrestrial (e.g., riparian leaf detritus) primary producers, river subsidies to terrestrial consumers represent a combination of aquatically and terrestrially derived energy. To date, the explicit contribution of energy derived from aquatic primary producers to terrestrial consumers has not been fully explored yet might be expected to be quantitatively important to terrestrial food webs. At 12 reaches along a 185-km segment of the sixth-order Scioto River system (Ohio, USA), we quantified the relative contribution of energy derived from aquatic primary producers to a suite of terrestrial riparian consumers that integrate the adjacent landscape across multiple spatial scales through their foraging activities (tetragnathid spiders, rove beetles, adult coenagrionid damselflies, riparian swallows, and raccoons). We used naturally abundant stable isotopes ( 13 C and 15 N) of periphyton, phytoplankton, macrophytes, and terrestrial vegetation to evaluate the energetic contribution of aquatic primary producers to terrestrial food webs. Shoreline tetragnathid spiders were most reliant on aquatic primary producers (50%), followed by wider-ranging raccoons (48%), damselflies (44%), and riparian swallows (41%). Of the primary producers, phytoplankton (19%) provisioned the greatest nutritional contribution to terrestrial consumers (considered collectively), followed by periphyton (14%) and macrophytes (11%). Our findings provide empirical evidence that aquatic primary producers of large streams and rivers can be a critical nutritional resource for terrestrial food webs. We also show that aquatically derived nutrition contributes to both shoreline and broader-ranging terrestrial consumers and thus may be an important landscape-scale energetic linkage between rivers and upland habitats.

Description: Journal of Physical Oceanography, Ahead of Print. 〈br/〉

Description: Abstract The addition of aluminum oxide (Al2O3) as a sintering aid to yttria‐stabilized zirconia (YSZ) reduces the required densification temperature. Sintering aids are incorporated using a number of processes which can lead to ambiguity when determining the effect of the sintering aid on the densification mechanism. In this study, a novel method for sintering aid addition, Particle Atomic Layer Deposition (ALD), was used to deposit an amorphous Al2O3 thin film on YSZ particles. Transmission electron microscopy confirmed the deposition of conformal Al2O3 thin films on the surface of the YSZ particles. The addition of Al2O3 to YSZ reduced the temperature at which densification began by ~75°C, and 2.2 wt% Al2O3 addition resulted in a minimum activation energy for the intermediate stage of densification. This concentration is well in excess of the solubility limit of Al2O3 in YSZ, showing that Al2O3 does not enhance the densification of YSZ solely by dissolving into the YSZ lattice and activating volume diffusion. The addition of 0.7 wt% Al2O3 with one Particle ALD cycle enhanced the ionic conductivity of YSZ by 23% after sintering at 1350°C for 2 hours, demonstrating that dense parts with high oxygen ion conductivities can be produced after sintering at reduced temperatures. One Particle ALD cycle is a fast, easily scaled‐up process that eliminates the use of solvents and has substantial cost/performance advantages over conventional processing.

Description: Abstract Artificial lighting at night (ALAN) is a global phenomenon that can be detrimental to organisms at individual and population levels, yet potential consequences for communities and ecosystem functions are less resolved. Riparian systems may be particularly vulnerable to ALAN. We investigated the impacts of ALAN on invertebrate community composition and food web characteristics for linked aquatic‐terrestrial ecosystems. We focused on food chain length (FCL), a central property of ecological communities that can influence their structure, function, and stability; and the contribution of aquatically derived energy (i.e., nutritional subsidies originating from stream periphyton). We collected terrestrial arthropods and emergent aquatic insects from a suite of stream and wetland sites in Columbus, Ohio, USA. Stable isotopes of carbon (13C) and nitrogen (15N) were used to infer FCL and contribution of aquatically derived energy. We found that moderate‐to‐high levels of ALAN altered invertebrate community composition, favoring primarily predators and detritivores. Impacts of ALAN, however, were very taxon specific as illustrated, for example, by the negative impact of ALAN on the abundance of orb‐web spiders belonging to the families Tetragnathidae and Araneidae: key invertebrate riparian predators. Most notably, we observed decreases in both invertebrate FCL and reliance on aquatically derived energy under ALAN (although aquatic energetic contributions appeared to increase again at higher levels of ALAN), in addition to shifts in the timing of reciprocal nutritional subsidies. Our study demonstrates that ALAN can alter the flows of energy between aquatic and terrestrial systems, thereby representing an environmental perturbation that can cross ecosystem boundaries. Given projections for global increases in ALAN, both in terms of coverage and intensity, these results have broad implications for stream ecosystem structure and function.