Identification and Characterization of MicroRNAs from Barley (Hordeum vulgare L.) by High-Throughput Sequencing

MicroRNAs (miRNAs) are a class of endogenous RNAs that regulates the gene expression involved in various biological and metabolic processes. Barley is one of the most important cereal crops worldwide and is a model organism for genetic and genomic studies in Triticeae species. However, the miRNA research in barley has lagged behind other model species in grass family. To obtain more information of miRNA genes in barley, we sequenced a small RNA library created from a pool of equal amounts of RNA from four different tissues using Solexa sequencing. In addition to 126 conserved miRNAs (58 families), 133 novel miRNAs belonging to 50 families were identified from this sequence data set. The miRNA* sequences of 15 novel miRNAs were also discovered, suggesting the additional evidence for existence of these miRNAs. qRT-PCR was used to examine the expression pattern of six randomly selected miRNAs. Some miRNAs involved in drought and salt stress response were also identified. Furthermore, the potential targets of these putative miRNAs were predicted using the psRNATarget tools. Our results significantly increased the number of novel miRNAs in barley, which should be useful for further investigation into the biological functions and evolution of miRNAs in barley and other species

Radiocarbon distributions in Southern Ocean dissolved and particulate organic matter

Dissolved organic carbon (DOC) is the largest actively exchanging pool of organic carbon in the ocean, yet its sources and sinks are not well constrained. The average C-14 ages of DOC in the deep N. Atlantic and N. Pacific Oceans are 4,000 [Bauer et al., 1992; Druffel et al., 1992] and 6,000 years [Williams and Druffel, 1987], respectively, and represent the beginning and end of the deep ocean conveyor [Broecker, 1991]. Here we report that the deep Southern Ocean DOC has a C-14 age (5,600 y) much closer to that of the deep N. Pacific, but its concentration in seawater (41 +/- 2 mu M) is nearly equal to that of the deep N. Atlantic. The radiocarbon and concentration data indicate that most, but not all, deep DOC is transported conservatively with the ocean\u27s conveyor. A younger (post-bomb) source of DOC to the N. Atlantic is the most likely explanation for the large age difference we observe between deep DOC in the Atlantic and Southern Oceans. Other possibilities are a source of older DOC or a smaller microbial sink in the S. Ocean, or perhaps a possible slowdown of S. Ocean deep water formation during the past century [Broecker et at, 1999]

BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L.)

Background: Although second generation sequencing (2GS) technologies allow re-sequencing of previously gold-standard-sequenced genomes, whole genome shotgun sequencing and de novo assembly of large and complex eukaryotic genomes is still difficult. Availability of a genome-wide physical map is therefore still a prerequisite for whole genome sequencing for genomes like barley. To start such an endeavor, large insert genomic libraries, i.e. Bacterial Artificial Chromosome (BAC) libraries, which are unbiased and representing deep haploid genome coverage, need to be ready in place. Result: Five new BAC libraries were constructed for barley (Hordeum vulgare L.) cultivar Morex. These libraries were constructed in different cloning sites (HindIII, EcoRI, MboI and BstXI) of the respective vectors. In order to enhance unbiased genome representation and to minimize the number of gaps between BAC contigs, which are often due to uneven distribution of restriction sites, a mechanically sheared library was also generated. The new BAC libraries were fully characterized in depth by scrutinizing the major quality parameters such as average insert size, degree of contamination (plate wide, neighboring, and chloroplast), empty wells and off-scale clones (clones with 250 fragments). Additionally a set of gene-based probes were hybridized to high density BAC filters and showed that genome coverage of each library is between 2.4 and 6.6 X. Conclusion: BAC libraries representing >20 haploid genomes are available as a new resource to the barley research community. Systematic utilization of these libraries in high-throughput BAC fingerprinting should allow developing a genome-wide physical map for the barley genome, which will be instrumental for map-based gene isolation and genome sequencing.Daniela Schulte, Ruvini Ariyadasa, Bujun Shi, Delphine Fleury, Chris Saski, Michael Atkins, Pieter deJong, Cheng-Cang Wu, Andreas Graner, Peter Langridge and Nils Stei

First narrow-band search for continuous gravitational waves from known pulsars in advanced detector data

Spinning neutron stars asymmetric with respect to their rotation axis are potential sources of continuous gravitational waves for ground-based interferometric detectors. In the case of known pulsars a fully coherent search, based on matched filtering, which uses the position and rotational parameters obtained from electromagnetic observations, can be carried out. Matched filtering maximizes the signalto- noise (SNR) ratio, but a large sensitivity loss is expected in case of even a very small mismatch between the assumed and the true signal parameters. For this reason, narrow-band analysis methods have been developed, allowing a fully coherent search for gravitational waves from known pulsars over a fraction of a hertz and several spin-down values. In this paper we describe a narrow-band search of 11 pulsars using data from Advanced LIGO’s first observing run. Although we have found several initial outliers, further studies show no significant evidence for the presence of a gravitational wave signal. Finally, we have placed upper limits on the signal strain amplitude lower than the spin-down limit for 5 of the 11 targets over the bands searched; in the case of J1813-1749 the spin-down limit has been beaten for the first time. For an additional 3 targets, the median upper limit across the search bands is below the spin-down limit. This is the most sensitive narrow-band search for continuous gravitational waves carried out so far

Sources and cycling of dissolved and particulate organic radiocarbon in the northwest Atlantic continental margin

Continental shelves and slopes are productive and dynamic ocean margin systems that also regulate the fluxes of terrestrial, riverine, and estuarine materials between the continents and oceans. In order to evaluate the ages, potential sources, and transformations of organic matter in an ocean margin system, we measured the radiocarbon (Delta (14)C and delta (13)C distributions of total dissolved organic carbon (DOC), suspended particulate organic carbon (POC), and dissolved inorganic carbon (DIC) in waters of the Middle Atlantic Bight (MAB) continental shelf and slope in April-May 1994. The Delta (14)C of DOC was greatest (as high as -39 parts per thousand) in surface waters of the shelf, decreasing rapidly offshore and with depth, even in relatively shallow (25-50 in depth) shelf waters. The lowest Delta (14)C-DOC values were observed in deep slope waters, where they were significantly lower than values measured previously for the deep Sargasso Sea. There was a strong inverse relationship between Delta (14)C-DOC and delta (-13)C-DOC in all shelf and surface slope waters of the MAB, which is likely attributable to varying contributions of young, (14)C-enriched organic matter of terrestrial and/or riverine origin. The more highly (14)C-depleted DOC in deep : slope waters (as low as -442 parts per thousand) generally had a correspondingly lower delta (13)C (as low as -22.3 parts per thousand) component. However, this must originate from relic terrestrial material either in the MAB itself or be discharged to the MAB from rivers and estuaries. The isotopic signatures of POC were clearly differentiable from DOC and indicate that this pool also contained a broad range of both old and young material of terrestrial (delta (13)C as low as -24.9 parts per thousand) and marine (delta (13)C as high as -19.9 parts per thousand) origin throughout the MAB shelf and slope. The highest Delta (14)C-POC values (up to 78 parts per thousand) were observed in shallow shelf waters of the southern MAR Conversely, the lowest Delta (14)C-POC values (as low as -394 parts per thousand) were found in MAB deep slope waters and were also significantly more depleted in (14)C than POC from the central north Atlantic (Sargasso Sea). A multiple-source isotopic mass balance model employing both (14)C and (13)C was used to evaluate the relative contributions of both young and old terrigenous versus marine organic matter to DOC and POC in the MAR The results indicate that shelf and slope DOC is comprised of an old marine fraction (represented by offshore Sargasso Sea material) and either a young terrestrial/riverine/estuarine (TRE) component (in shelf and shallow slope waters) or a relic TRE component (in deep and some shallow slope waters). In contrast, suspended POC from the MAB appears to originate predominantly from a mixture of recent MAB primary production and an old, TRE component, similar to that observed in one of the major subestuaries of the Chesapeake Bay. These results suggest that both young and old sources of terrestrial and riverine organic matter can comprise a significant fraction of the DOC and POC in ocean margins. Preliminary calculations indicate that the export of this compositionally unique DOC and suspended POC may be significant terms in the organic carbon budgets of the MAB and other margin systems

Evidence of causal effect of major depression on alcohol dependence: findings from the psychiatric genomics consortium

BACKGROUND Despite established clinical associations among major depression (MD), alcohol dependence (AD), and alcohol consumption (AC), the nature of the causal relationship between them is not completely understood. We leveraged genome-wide data from the Psychiatric Genomics Consortium (PGC) and UK Biobank to test for the presence of shared genetic mechanisms and causal relationships among MD, AD, and AC. METHODS Linkage disequilibrium score regression and Mendelian randomization (MR) were performed using genome-wide data from the PGC (MD: 135 458 cases and 344 901 controls; AD: 10 206 cases and 28 480 controls) and UK Biobank (AC-frequency: 438 308 individuals; AC-quantity: 307 098 individuals). RESULTS Positive genetic correlation was observed between MD and AD (rgMD−AD = + 0.47, P = 6.6 × 10−10). AC-quantity showed positive genetic correlation with both AD (rgAD−AC quantity = + 0.75, P = 1.8 × 10−14) and MD (rgMD−AC quantity = + 0.14, P = 2.9 × 10−7), while there was negative correlation of AC-frequency with MD (rgMD−AC frequency = −0.17, P = 1.5 × 10−10) and a non-significant result with AD. MR analyses confirmed the presence of pleiotropy among these four traits. However, the MD-AD results reflect a mediated-pleiotropy mechanism (i.e. causal relationship) with an effect of MD on AD (beta = 0.28, P = 1.29 × 10−6). There was no evidence for reverse causation. CONCLUSION This study supports a causal role for genetic liability of MD on AD based on genetic datasets including thousands of individuals. Understanding mechanisms underlying MD-AD comorbidity addresses important public health concerns and has the potential to facilitate prevention and intervention efforts