Molecular organization and comparative analysis of chromosome 5B of the wild wheat ancestor Triticum dicoccoides

Wild emmer wheat, Triticum turgidum ssp. dicoccoides is the wild relative of Triticum turgidum, the progenitor of durum and bread wheat, and maintains a rich allelic diversity among its wild populations. The lack of adequate genetic and genomic resources, however, restricts its exploitation in wheat improvement. Here, we report next-generation sequencing of the flow-sorted chromosome 5B of T. dicoccoides to shed light into its genome structure, function and organization by exploring the repetitive elements, protein-encoding genes and putative microRNA and tRNA coding sequences. Comparative analyses with its counterparts in modern and wild wheats suggest clues into the B-genome evolution. Syntenic relationships of chromosome 5B with the model grasses can facilitate further efforts for fine-mapping of traits of interest. Mapping of 5B sequences onto the root transcriptomes of two additional T. dicoccoides genotypes, with contrasting drought tolerances, revealed several thousands of single nucleotide polymorphisms, of which 584 shared polymorphisms on 228 transcripts were specific to the drought-tolerant genotype. To our knowledge, this study presents the largest genomics resource currently available for T. dicoccoides, which, we believe, will encourage the exploitation of its genetic and genomic potential for wheat improvement to meet the increasing demand to feed the world

S-Band Transponder Multi-Network Compatibility, Space Environment and Radiation Testing

This paper presents the development and testing of the Software Define Radio (SDR) transceiver to meet the emerging needs for SmallSat communication and navigation. Vulcan Wireless and NASA Goddard Space Flight Center (GSFC) collaborated in testing the Vulcan Wireless S-band SDR engineering model. Apart from testing, communication link analysis was performed for a Low Earth Orbit (LEO) 400 km scenario. The results of the compatibility, radiation, environmental testing, and link analysis are presented. Also, this paper reviews a set of SmallSat missions under development at NASA GSFC

Ocean nutrient pathways associated with passage of a storm

Storms that affect ocean surface layer dynamics and primary production are a frequent occurrence in the open North Atlantic Ocean. In this study we use an interdisciplinary dataset collected in the region to quantify nutrient supply by two pathways associated with a storm event: entrainment of nutrients during a period of high wind forcing and subsequent shear-spiking at the pycnocline due to interactions of storm generated inertial currents with wind. The post-storm increase in surface layer nitrate (by ~20 mmol m?2) was predominantly driven by the first pathway: nutrient intrusion during the storm. Alignment of post-storm inertial currents and surface wind stress caused shear instabilities at the ocean pycnocline, forming the second pathway for nutrient transport into the euphotic zone. During the alignment period, pulses of high turbulent nitrate flux through the pycnocline (up to 1 mmol m?2 day?1; approximately 25 times higher than the background flux) were detected. However, the impact of the post-storm supply was an order of magnitude lower than during the storm due to the short duration of the pulses. Cumulatively, the storm passage was equivalent to 2.5-5 % of the nitrate supplied by winter convection and had a significant effect compared to previously reported (sub)-mesoscale dynamics in the region. As storms occur frequently, they can form an important component in local nutrient budgets

Physical mapping integrated with syntenic analysis to characterize the gene space of the long arm of wheat chromosome 1A

Background: Bread wheat (Triticum aestivum L.) is one of the most important crops worldwide and its production faces pressing challenges, the solution of which demands genome information. However, the large, highly repetitive hexaploid wheat genome has been considered intractable to standard sequencing approaches. Therefore the International Wheat Genome Sequencing Consortium (IWGSC) proposes to map and sequence the genome on a chromosome-by-chromosome basis. Methodology/Principal Findings: We have constructed a physical map of the long arm of bread wheat chromosome 1A using chromosome-specific BAC libraries by High Information Content Fingerprinting (HICF). Two alternative methods (FPC and LTC) were used to assemble the fingerprints into a high-resolution physical map of the chromosome arm. A total of 365 molecular markers were added to the map, in addition to 1122 putative unique transcripts that were identified by microarray hybridization. The final map consists of 1180 FPC based or 583 LTC based contigs. Conclusions/Significance: The physical map presented here marks an important step forward in mapping of hexaploid bread wheat. The map is orders of magnitude more detailed than previously available maps of this chromosome, and the assignment of over a thousand putative expressed gene sequences to specific map locations will greatly assist future functional studies. This map will be an essential tool for future sequencing of and positional cloning within chromosome 1A

SUSY GUTs under Siege : Proton Decay

SO(10) supersymmetric grand unified theories [SUSY GUTs] provide a beautiful framework for physics beyond the standard model. Experimental measurements of the three gauge couplings are consistent with unification at a scale $M_G \sim 3 \times 10^{16}$ GeV. In addition predictive models for fermion masses and mixing angles have been found which fit the low energy data, including the recent data for neutrino oscillations. SO(10) boundary conditions can be tested via the spectrum of superparticles. The simplest models also predict neutron and proton decay rates. In this paper we discuss nucleon decay rates and obtain reasonable upper bounds. A clear picture of the allowed SUSY spectra as constrained by nucleon decay is presented.Comment: 13 page

Annual Cycle of Turbulent Dissipation Estimated from Seagliders

The rate of dissipation of turbulent kinetic energy is estimated using Seaglider observations of vertical water velocity in the midlatitude North Atlantic. This estimate is based on the large‐eddy method, allowing the use of measurements of turbulent energy at large scales O(1–10 m) to diagnose the rate of energy dissipated through viscous processes at scales O(1 mm). The Seaglider data considered here were obtained in a region of high stratification (1 × 10−4<N < 1×10−2s−1), where previous implementations of this method fail. The large‐eddy method is generalized to high‐stratification by high‐pass filtering vertical velocity with a cutoff dependent on the local buoyancy frequency, producing a year‐long time series of dissipation rate spanning the uppermost 1,000 m with subdaily resolution. This is compared to the dissipation rate estimated from a moored 600 kHz acoustic Doppler current profiler. The variability of the Seaglider‐based dissipation correlates with one‐dimensional scalings of wind‐ and buoyancy‐driven mixed‐layer turbulence. Plain Language Summary Measuring ocean turbulence is crucial for understanding how heat and carbon dioxide are transferred from the atmosphere to the deep ocean. However, measurements of ocean turbulence are sparse. Here autonomous Seagliders are used to estimate turbulence in the surface kilometer of the North Atlantic Ocean. Using an estimate of the vertical water velocity from the flight of the Seaglider through the water, we estimate turbulence by assuming the energy of the largest turbulent fluctuations is representative of the energy dissipated at molecular scales. This approach has been used previously in an ocean region where the vertical gradient of density is small. Our results show that this previous approach fails when the vertical density gradient increases, as it does not account for other processes that are unrelated to turbulence. We introduce a generalized method that isolates only the turbulent processes by accounting for the strength of the vertical density gradient. We show that this new estimate agrees with other turbulence measurements. Our estimate also agrees well with a simple estimates of turbulence from atmospheric processes. This study therefore presents method that can be applied to existing and new Seaglider data to greatly increase our measurements of ocean turbulence

Unified Theories with U(2) Flavor Symmetry

A general operator expansion is presented for quark and lepton mass matrices in unified theories based on a U(2) flavor symmetry, with breaking parameter of order $V_{cb} \approx m_s/m_b \approx \sqrt{m_c/m_t}$. While solving the supersymmetric flavor-changing problem, a general form for the Yukawa couplings follows, leading to 9 relations among the fermion masses and mixings, 5 of which are precise. The combination of grand unified and U(2) symmetries provides a symmetry understanding for the anomalously small values of $m_u/m_c$ and $m_c/m_t$. A fit to the fermion mass data leads to a prediction for the angles of the CKM unitarity triangle, which will allow a significant test of these unified U(2) theories. A particular SO(10) model provides a simple realization of the general operator expansion. The lighter generation masses and the non-trivial structure of the CKM matrix are generated from the exchange of a single U(2) doublet of heavy vector generations. This model suggests that CP is spontaneously broken at the unification scale --- in which case there is a further reduction in the number of free parameters.Comment: 31 pages, 3 .eps figures include

Unique and conserved MicroRNAs in wheat chromosome 5D revealed by next-generation sequencing

MicroRNAs are a class of short, non-coding, single-stranded RNAs that act as post-transcriptional regulators in gene expression. miRNA analysis of Triticum aestivum chromosome 5D was performed on 454 GS FLX Titanium sequences of flow sorted chromosome 5D with a total of 3,208,630 good quality reads representing 1.34x and 1.61x coverage of the short (5DS) and long (5DL) arms of the chromosome respectively. In silico and structural analyses revealed a total of 55 miRNAs; 48 and 42 miRNAs were found to be present on 5DL and 5DS respectively, of which 35 were common to both chromosome arms, while 13 miRNAs were specific to 5DL and 7 miRNAs were specific to 5DS. In total, 14 of the predicted miRNAs were identified in wheat for the first time. Representation (the copy number of each miRNA) was also found to be higher in 5DL (1,949) compared to 5DS (1,191). Targets were predicted for each miRNA, while expression analysis gave evidence of expression for 6 out of 55 miRNAs. Occurrences of the same miRNAs were also found in Brachypodium distachyon and Oryza sativa genome sequences to identify syntenic miRNA coding sequences. Based on this analysis, two other miRNAs: miR1133 and miR167 were detected in B. distachyon syntenic region of wheat 5DS. Five of the predicted miRNA coding regions (miR6220, miR5070, miR169, miR5085, miR2118) were experimentally verified to be located to the 5D chromosome and three of them : miR2118, miR169 and miR5085, were shown to be 5D specific. Furthermore miR2118 was shown to be expressed in Chinese Spring adult leaves. miRNA genes identified in this study will expand our understanding of gene regulation in bread wheat

First report of the recently introduced, destructive powdery mildew Erysiphe corylacearum on hazelnut in Turkey

Hazelnut (Corylus avellana) is Turkey’s most valuable agricultural export, and an essential source of income for many families in the Black Sea Region. In spring 2013, hazelnut leaves, fruit clusters and shoots showing powdery mildew infection symptoms different from those observed previously were discovered in Giresun, Ordu and Trabzon provinces of Turkey. The disease has become epidemic throughout all hazelnut production areas spreading from east to west of the Black Sea Region over the subsequent years. Erysiphe corylacearum was identified as the causal agent of this new and highly destructive powdery mildew based on its morphological characteristics and analyses of DNA sequences of the internal transcribed spacer (ITS) and 28S regions of the ribosomal DNA. Pathogenicity of this species was examined in an infection test and proven for the first time. To our knowledge, this is the first report of E. corylacearum on Corylus avellana worldwide