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  • 1
    Publication Date: 2016-06-22
    Description: Reproductive traits in plants tend to evolve rapidly due to various causes that include plant-pollinator coevolution and pollen competition, but the genomic basis of reproductive trait evolution is still largely unknown. To characterize evolutionary patterns of genome wide gene expression in reproductive tissues in the gametophyte and to compare them to developmental stages of the sporophyte, we analyzed evolutionary conservation and genetic diversity of protein-coding genes using microarray-based transcriptome data from three plant species, Arabidopsis thaliana , rice ( Oryza sativa ), and soybean ( Glycine max ). In all three species a significant shift in gene expression occurs during gametogenesis in which genes of younger evolutionary age and higher genetic diversity contribute significantly more to the transcriptome than in other stages. We refer to this phenomenon as "evolutionary bulge" during plant reproductive development because it differentiates the gametophyte from the sporophyte. We show that multiple, not mutually exclusive, causes may explain the bulge pattern, most prominently reduced tissue complexity of the gametophyte, a varying extent of selection on reproductive traits during gametogenesis as well as differences between male and female tissues. This highlights the importance of plant reproduction for understanding evolutionary forces determining the relationship of genomic and phenotypic variation in plants.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 2
    Publication Date: 2018-09-18
    Description: Author(s): S. Augustin, M. Schulz, G. Schmid, K. Schnorr, E. V. Gryzlova, H. Lindenblatt, S. Meister, Y. F. Liu, F. Trost, L. Fechner, A. N. Grum-Grzhimailo, S. M. Burkov, M. Braune, R. Treusch, M. Gisselbrecht, C. D. Schröter, T. Pfeifer, and R. Moshammer A kinematically complete experiment on two-photon double ionization of Ar by free-electron laser radiation with a photon energy of 27.93 eV was performed. The electron energy spectra show that double ionization is dominated by the sequential process. Comparison of the electron angular distributions ... [Phys. Rev. A 98, 033408] Published Mon Sep 17, 2018
    Keywords: Atomic and molecular processes in external fields, including interactions with strong fields and short pulses
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
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  • 3
    Publication Date: 2018-02-09
    Description: Genetic resources are an important source of genetic variation for plant breeding. Genome-wide association studies (GWAS) and genomic prediction greatly facilitate the analysis and utilization of useful genetic diversity for improving complex phenotypic traits in crop plants. We explored the potential of GWAS and genomic prediction for improving curd-related traits in cauliflower ( Brassica oleracea var. botrytis ) by combining 174 randomly selected cauliflower gene bank accessions from two different gene banks. The collection was genotyped with genotyping-by-sequencing (GBS) and phenotyped for six curd-related traits at two locations and three growing seasons. A GWAS analysis based on 120,693 single-nucleotide polymorphisms identified a total of 24 significant associations for curd-related traits. The potential for genomic prediction was assessed with a genomic best linear unbiased prediction model and BayesB. Prediction abilities ranged from 0.10 to 0.66 for different traits and did not differ between prediction methods. Imputation of missing genotypes only slightly improved prediction ability. Our results demonstrate that GWAS and genomic prediction in combination with GBS and phenotyping of highly heritable traits can be used to identify useful quantitative trait loci and genotypes among genetically diverse gene bank material for subsequent utilization as genetic resources in cauliflower breeding.
    Electronic ISSN: 2160-1836
    Topics: Biology
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  • 4
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    American Association of Petroleum Geologists (AAPG)
    Publication Date: 2015-12-15
    Description: Thousands of shale gas wells have been drilled and hydraulically fractured across the state of Pennsylvania over the past decade, and more wells are being drilled each year. The drilled lengths of these wells and the amount of water being used to hydraulically fracture (frac) them continue to increase. These increases have led to an increase in the volume of wastewater being produced each year. However, the ratio of energy produced per barrel of wastewater has increased significantly over the past six years. Recent data show the volume of wastewater produced in one year is approximately 20% of the volume of frac water used in that same year. With changes in state policies, drilling companies in Pennsylvania have been recycling most of their wastewaters over the past few years. The development of various treatment technologies and brine-resistant frac mixtures has allowed companies to recycle this wastewater for use in future frac jobs. Use of this recycled water does not appear to be having a significant effect on production of oil or gas from wells. Recycling wastewater can be very cost-competitive when compared to options such as disposal via waste-treatment plants or injection wells.
    Print ISSN: 1075-9565
    Electronic ISSN: 1526-0984
    Topics: Geography , Geosciences
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  • 5
    Publication Date: 2015-11-17
    Description: The combination of Reverse Transcription (RT) and high-throughput sequencing has emerged as a powerful combination to detect modified nucleotides in RNA via analysis of either abortive RT-products or of the incorporation of mismatched dNTPs into cDNA. Here we simultaneously analyze both parameters in detail with respect to the occurrence of N -1-methyladenosine (m 1 A) in the template RNA. This naturally occurring modification is associated with structural effects, but it is also known as a mediator of antibiotic resistance in ribosomal RNA. In structural probing experiments with dimethylsulfate, m 1 A is routinely detected by RT-arrest. A specifically developed RNA-Seq protocol was tailored to the simultaneous analysis of RT-arrest and misincorporation patterns. By application to a variety of native and synthetic RNA preparations, we found a characteristic signature of m 1 A, which, in addition to an arrest rate, features misincorporation as a significant component. Detailed analysis suggests that the signature depends on RNA structure and on the nature of the nucleotide 3' of m 1 A in the template RNA, meaning it is sequence dependent. The RT-signature of m 1 A was used for inspection and confirmation of suspected modification sites and resulted in the identification of hitherto unknown m 1 A residues in trypanosomal tRNA.
    Keywords: Nucleic acid modification
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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