Hydrodynamics of strongly coupled non-conformal fluids from gauge/gravity duality

The subject of relativistic hydrodynamics is explored using the tools of gauge/gravity duality. A brief literature review of AdS/CFT and gauge/gravity duality is presented first. This is followed by a pedagogical introduction to the use of these methods in determining hydrodynamic dispersion relations, $w(q)$, of perturbations in a strongly coupled fluid. Shear and sound mode perturbations are examined in a special class of gravity duals: those where the matter supporting the metric is scalar in nature. Analytical solutions (to order $q^4$ and $q^3$ respectively) for the shear and sound mode dispersion relations are presented for a subset of these backgrounds. The work presented here is based on previous publications by the same author, though some previously unpublished results are also included. In particular, the subleading term in the shear mode dispersion relation is analyzed using the AdS/CFT correspondence without any reference to the black hole membrane paradigm.Comment: PhD thesis, 116 pages, 4 figure

A shear spectral sum rule in a non-conformal gravity dual

A sum rule which relates a stress-energy tensor correlator to thermodynamic functions is examined within the context of a simple non-conformal gravity dual. Such a sum rule was previously derived using AdS/CFT for conformal $\mathcal{N} = 4$ Supersymmetric Yang-Mills theory, but we show that it does not generalize to the non-conformal theory under consideration. We provide a generalized sum rule and numerically verify its validity. A useful byproduct of the calculation is the computation of the spectral density in a strongly coupled non-conformal theory. Qualitative features of the spectral densities and implications for lattice measurements of transport coefficients are discussed.Comment: 13 pages, 3 figures. v5: Typos in Eq. (60) fixed. v4: References added, matches published version. v3: Minor typographical corrections. v2: References and some discussion in Appendix A have been added; conclusions unchange

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Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome

BACKGROUND There is growing evidence for the prevalence of copy number variation (CNV) and its role in phenotypic variation in many eukaryotic species. Here we use array comparative genomic hybridization to explore the extent of this type of structural variation in domesticated barley cultivars and wild barleys. RESULTS A collection of 14 barley genotypes including eight cultivars and six wild barleys were used for comparative genomic hybridization. CNV affects 14.9% of all the sequences that were assessed. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. CNVs are enriched near the ends of all chromosomes except 4H, which exhibits the lowest frequency of CNVs. CNV affects 9.5% of the coding sequences represented on the array and the genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases. Sequence-based comparisons of CNV between cultivars Barke and Morex provided evidence that DNA repair mechanisms of double-strand breaks via single-stranded annealing and synthesis-dependent strand annealing play an important role in the origin of CNV in barley. CONCLUSIONS We present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley, and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance. We also identify potential mechanisms that can generate variation in copy number in plant genomes.This work was financially supported by the following grants: project GABI-BARLEX, German Federal Ministry of Education and Research (BMBF), #0314000 to MP, US, KFXM and NS; Triticeae Coordinated Agricultural Project, USDA-NIFA #2011-68002-30029 to GJM; and Agriculture and Food Research Initiative Plant Genome, Genetics and Breeding Program of USDA’s Cooperative State Research and Extension Service, #2009-65300- 05645 to GJM

Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome

BACKGROUND: There is growing evidence for the prevalence of copy number variation (CNV) and its role in phenotypic variation in many eukaryotic species. Here we use array comparative genomic hybridization to explore the extent of this type of structural variation in domesticated barley cultivars and wild barleys. RESULTS: A collection of 14 barley genotypes including eight cultivars and six wild barleys were used for comparative genomic hybridization. CNV affects 14.9% of all the sequences that were assessed. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. CNVs are enriched near the ends of all chromosomes except 4H, which exhibits the lowest frequency of CNVs. CNV affects 9.5% of the coding sequences represented on the array and the genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases. Sequence-based comparisons of CNV between cultivars Barke and Morex provided evidence that DNA repair mechanisms of double-strand breaks via single-stranded annealing and synthesis-dependent strand annealing play an important role in the origin of CNV in barley. CONCLUSIONS: We present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley, and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance. We also identify potential mechanisms that can generate variation in copy number in plant genomes

High-Resolution Genotyping via Whole Genome Hybridizations to Microarrays Containing Long Oligonucleotide Probes

To date, microarray-based genotyping of large, complex plant genomes has been complicated by the need to perform genome complexity reduction to obtain sufficiently strong hybridization signals. Genome complexity reduction techniques are, however, tedious and can introduce unwanted variables into genotyping assays. Here, we report a microarray-based genotyping technology for complex genomes (such as the 2.3 GB maize genome) that does not require genome complexity reduction prior to hybridization. Approximately 200,000 long oligonucleotide probes were identified as being polymorphic between the inbred parents of a mapping population and used to genotype two recombinant inbred lines. While multiple hybridization replicates provided ∼97% accuracy, even a single replicate provided ∼95% accuracy. Genotyping accuracy was further increased to >99% by utilizing information from adjacent probes. This microarray-based method provides a simple, high-density genotyping approach for large, complex genomes