Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana).

Sugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensive survey of the P. lambertiana transcriptome through deep sequencing of a variety of tissue types to generate more than 2.5 billion short reads. Third generation, long reads generated through PacBio Iso-Seq have been included for the first time in conifers to combat the challenges associated with de novo transcriptome assembly. A technology comparison is provided here to contribute to the otherwise scarce comparisons of second and third generation transcriptome sequencing approaches in plant species. In addition, the transcriptome reference was essential for gene model identification and quality assessment in the parallel project responsible for sequencing and assembly of the entire genome. In this study, the transcriptomic data were also used to address questions surrounding lineage-specific Dicer-like proteins in conifers. These proteins play a role in the control of transposable element proliferation and the related genome expansion in conifers

A Study of the Diverse T Dwarf Population Revealed by WISE

We report the discovery of 87 new T dwarfs uncovered with the Wide-field Infrared Survey Explorer (WISE) and 3 brown dwarfs with extremely red near-infrared colors that exhibit characteristics of both L and T dwarfs. Two of the new T dwarfs are likely binaries with L7 ± 1 primaries and mid-type T secondaries. In addition, our follow-up program has confirmed 10 previously identified T dwarfs and 4 photometrically selected L and T dwarf candidates in the literature. This sample, along with the previous WISE discoveries, triples the number of known brown dwarfs with spectral types later than T5. Using the WISE All-Sky Source Catalog we present updated color-color and color-type diagrams for all the WISE-discovered T and Y dwarfs. Near-infrared spectra of the new discoveries are presented along with spectral classifications. To accommodate later T dwarfs we have modified the integrated flux method of determining spectral indices to instead use the median flux. Furthermore, a newly defined J-narrow index differentiates the early-type Y dwarfs from late-type T dwarfs based on the J-band continuum slope. The K/J indices for this expanded sample show that 32% of late-type T dwarfs have suppressed K-band flux and are blue relative to the spectral standards, while only 11% are redder than the standards. Comparison of the Y/J and K/J index to models suggests diverse atmospheric conditions and supports the possible re-emergence of clouds after the L/T transition. We also discuss peculiar brown dwarfs and candidates that were found not to be substellar, including two young stellar objects and two active galactic nuclei. The substantial increase in the number of known late-type T dwarfs provides a population that will be used to test models of cold atmospheres and star formation. The coolest WISE-discovered brown dwarfs are the closest of their type and will remain the only sample of their kind for many years to come

Evidence for Direct Roles of Two Additional Factors, SECp43 and Soluble Liver Antigen, in the Selenoprotein Synthesis Machinery

Selenocysteine (Sec) is inserted into selenoproteins co-translationally with the help of various cis- and trans-acting factors. The specific mechanisms of Sec biosynthesis and insertion into protein in eukaryotic cells, however, are not known. Two proteins, SECp43 and the soluble liver antigen (SLA), were previously reported to interact with tRNA [Ser]Sec, but their functions remained elusive. Herein, we report that knockdown of SECp43 in NIH3T3 or TCMK-1 cells using RNA interference technology resulted in a reduction in the level of methylation at the 2’-hydroxylribosyl moiety in the wobble position (Um34) of Sec tRNA [Ser]Sec, and consequently reduced glutathione peroxidase 1 expression. Double knockdown of SECp43 and SLA resulted in decreased selenoprotein expression. SECp43 formed a complex with Sec tRNA [Ser]Sec and SLA, and the targeted removal of one of these proteins affected the binding of the other to Sec tRNA [Ser]Sec. SECp43 was located primarily in the nucleus, whereas SLA was found in the cytoplasm. Co-transfection of both proteins resulted in the nuclear translocation of SLA suggesting that SECp43 may also promote shuttling of SLA and Sec tRNA [Ser]Sec between different cellular compartments. Taken together, these data establish the role of SECp43 and SLA in selenoprotein biosynthesis through interaction with tRNA [Ser]Sec in a multiprotein complex. The data also reveal a role of SECp43 in regulation of selenoprotein expression by affecting the synthesis of Um34 on tRNA[ [Ser]Sec and the intracellular location of SLA

The Cenozoic Climatic and Topographic Evolution of the Western North American Cordillera

Herein we present oxygen isotope records from Cretaceous to Recent terrestrial sediments in the western North American Cordillera. The purpose of this analysis is to use oxygen isotope records to understand the coupled surface elevation and climate histories of this region through the Cenozoic. To do this we constructed δ¹⁸(O) maps of surface waters for time intervals that trace the development of topography of western North America. These maps are based on 4861 oxygen isotope analyses from both published (4478) and new (383) data. We determined the δ¹⁸(O) values of surface waters using paleotemperatures derived previously from floral assemblages and the appropriate isotope fractionation factors. These data suggest that in the late Cretaceous to early Eocene the Sevier hinterland formed a plateau of unknown height. Around 50 Ma, a topographic wave developed in British Columbia and eastern Washington that swept southward reaching northeastern Nevada at ~40 to 38 Ma, and southern Nevada ~23 Ma. This southward encroachment of an Eocene Plateau (SWEEP) caused reorganization of drainage patterns such that the intraforeland basins of Wyoming and Utah drainages extended deep within the Sevier hinterland as the wave swept southward. The landscape within the Sevier hinterland developed into a rugged and high mountain range with the hypsometric mean elevation of ~4 km and relief of ~1.5 km. This Eocene highland was bordered on the west by a high Sierra Nevada ramp and on the east by the intraforeland basins that captured water draining these growing highlands. The spatial and temporal evolution of this highland correlates with the timing of volcanism and extension. These observations support tectonic models that call for north to south removal of the Farallon slab or piecemeal removal of mantle lithosphere. The isotopic data show that prior to growth of this highland the North American Monsoon (NAM) penetrated much farther north in the Paleocene/Eocene than today. The combined effects of global cooling, increasing latitudinal temperature gradients, and the generation of the orographic barrier created by the growing north to south highland produced a southward migration of the NAM front. By the Oligocene the hydrologic regime that we observe today was in place. It has been modified since then as a result of Basin and Range extension and collapse of the highlands in the mid-Miocene. This collapse allowed the NAM to penetrate farther north into the Great Basin of Nevada and Utah

A Study of the Diverse T Dwarf Population Revealed by WISE

We report the discovery of 87 new T dwarfs uncovered with the Wide-field Infrared Survey Explorer (WISE) and three brown dwarfs with extremely red near-infrared colors that exhibit characteristics of both L and T dwarfs. Two of the new T dwarfs are likely binaries with L7+/-1 primaries and mid-type T secondaries. In addition, our follow-up program has confirmed 10 previously identified T dwarfs and four photometrically-selected L and T dwarf candidates in the literature. This sample, along with the previous WISE discoveries, triples the number of known brown dwarfs with spectral types later than T5. Using the WISE All-Sky Source Catalog we present updated color-color and color-type diagrams for all the WISE-discovered T and Y dwarfs. Near-infrared spectra of the new discoveries are presented, along with spectral classifications. To accommodate later T dwarfs we have modified the integrated flux method of determining spectral indices to instead use the median flux. Furthermore, a newly defined J-narrow index differentiates the early-type Y dwarfs from late-type T dwarfs based on the J-band continuum slope. The K/J indices for this expanded sample show that 32% of late-type T dwarfs have suppressed K-band flux and are blue relative to the spectral standards, while only 11% are redder than the standards. Comparison of the Y/J and K/J index to models suggests diverse atmospheric conditions and supports the possible re-emergence of clouds after the L/T transition. We also discuss peculiar brown dwarfs and candidates that were found not to be substellar, including two Young Stellar Objects and two Active Galactic Nuclei. The coolest WISE-discovered brown dwarfs are the closest of their type and will remain the only sample of their kind for many years to come.Comment: Accepted to ApJS on 15 January 2013; 99 pages in preprint format, 30 figures, 12 table

Arctic ocean chronology confirmed by accelerator 14C dating

The role of the Arctic Ocean in Earth's climatic and oceanographic development is significant but has become controversial because of disagreements concerning a reliable Arctic chronology. The first Arctic Ocean chronology based on U-Th and 14C data was in agreement with magnetostratigraphy developed later but these data have been challenged by recent amino acid diagenesis dates. New accelerator 14C data support the earlier U-Th-magnetostratigraphic dates and confirm the reliability of the established Arctic Ocean chronology

Plasmas and Controlled Nuclear Fusion

Contains reports on five research projects.U. S. Atomic Energy Commission (Contract AT(30-1)-3980

Plasmas and Controlled Nuclear Fusion

Contains reports on eleven research projects split into three section.U. S. Atomic Energy Commission (Contract AT(30-1)-3980

Plasmas and Controlled Nuclear Fusion

Contains research objectives and reports on four research projects.U. S. Atomic Energy Commission (Contract AT(30-1)-3980)U. S. Atomic Energy Commission (GK-2581