Doctor of Philosophy

dissertationWith the rapid proliferation of high-throughput sequencing methods, both the number and variety of genome assemblies have increased and require rigorous and sophisticated methods for genome annotation. As more species’ genomes are sequenced, the targets of genome annotation projects will more commonly be species with few closely related species that have been analyzed previously. This can be a serious challenge for genome annotation, here defined as the identification and demarcation of gene models in a genome assembly. My PhD research has focused on the application and development of genome annotation methods for non-model organisms. In the first chapter of my thesis, I present a review of the field of genome annotation, which discusses current challenges and bestpractice approaches. In the second chapter of my thesis, I present analyses of the important agronomic pest, Cronartium quercuum sp. fusiforme (CQF), which causes fusiform rust disease in loblolly pine trees. I annotated the genome and used genome-resequencing data to confirm results from a previous linkage mapping study that identified the location of virulence factor 1 (Avr1) and to identify candidate Avr1 genes

Transposable element islands facilitate adaptation to novel environments in an invasive species

Peer reviewe

On the correspondence between the transcriptomic response of a compound and its effects on its targets

Abstract Better understanding the transcriptomic response produced by a compound perturbing its targets can shed light on the underlying biological processes regulated by the compound. However, establishing the relationship between the induced transcriptomic response and the target of a compound is non-trivial, partly because targets are rarely differentially expressed. Therefore, connecting both modalities requires orthogonal information (e.g., pathway or functional information). Here, we present a comprehensive study aimed at exploring this relationship by leveraging thousands of transcriptomic experiments and target data for over 2000 compounds. Firstly, we confirm that compound-target information does not correlate as expected with the transcriptomic signatures induced by a compound. However, we reveal how the concordance between both modalities increases by connecting pathway and target information. Additionally, we investigate whether compounds that target the same proteins induce a similar transcriptomic response and conversely, whether compounds with similar transcriptomic responses share the same target proteins. While our findings suggest that this is generally not the case, we did observe that compounds with similar transcriptomic profiles are more likely to share at least one protein target and common therapeutic applications. Finally, we demonstrate how to exploit the relationship between both modalities for mechanism of action deconvolution by presenting a case scenario involving a few compound pairs with high similarity

Bimetallic Cooperativity with a 2-Phosphinoimidazole-Derived Pd(II) Dimer Enables Naphthalene Synthesis via dimeric Pd(III) Catalysis

We report the synthesis of bimetallic Pd(I) and Pd(II) complexes scaffolded on bidentate 2-phosphinoimidazole ligands. These complexes display unique catalytic activity and enable the expeditious formation of 1,3-disubstituted naphthalenes via an unprecedented coupling of aryl iodides and methyl ketones in the presence of silver triflate. Excellent substrate scope for naphthalene formation is also demonstrated. Mechanistic studies suggest that the transformation proceeds via Pd-catalyzed arylation of a methyl ketone, followed by cyclization with a second equivalent of ketone. Importantly, this ketone arylation processes occurs under oxidizing conditions, suggesting involvement of higher oxidation state dimeric Pd catalysts. Based on experiments and DFT calculations, we propose a mechanism involving high oxidation state Pd(III) bimetallic catalysis. These new bimetallic complexes possess reactivity that is not seen with monometallic Pd catalysts and we confirm the importance of the palladium catalyst for both arylation and cyclization for naphthalene formation

The genomic basis of evolutionary differentiation among honey bees

In contrast to the western honey bee, Apis mellifera, other honey bee species have been largely neglected despite their importance and diversity. The genetic basis of the evolutionary diversification of honey bees remains largely unknown. Here, we provide a genome-wide comparison of three honey bee species, each representing one of the three subgenera of honey bees, namely the dwarf (Apis florea), giant (A. dorsata), and cavity-nesting (A. mellifera) honey bees with bumblebees as an outgroup. Our analyses resolve the phylogeny of honey bees with the dwarf honey bees diverging first. We find that evolution of increased eusocial complexity in Apis proceeds via increases in the complexity of gene regulation, which is in agreement with previous studies. However, this process seems to be related to pathways other than transcriptional control. Positive selection patterns across Apis reveal a trade-off between maintaining genome stability and generating genetic diversity, with a rapidly evolving piRNA pathway leading to genomes depleted of transposable elements, and a rapidly evolving DNA repair pathway associated with high recombination rates in all Apis species. Diversification within Apis is accompanied by positive selection in several genes whose putative functions present candidate mechanisms for lineage-specific adaptations, such as migration, immunity, and nesting behavior

Genomic signatures of evolutionary transitions from solitary to group living

The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of 10 bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks

Rhinosinusitis: Developing guidance for clinical trials

The Rhinosinusitis Initiative was developed by 5 national societies. The current guidance document is an expansion of the 2004 publication, "Rhinosinusitis: Establishing definitions for clinical research and patient care" and provides templates for clinical trials in antimicrobial, anti-inflammatory, and symptom-relieving therapies for the following: (1) acute presumed bacterial rhinosinusitis, (2) chronic rhinosinusitis (CRS) without nasal polyps, (3) CRS with nasal polyps, and (4) classic allergic fungal rhinosinusitis. In addition to the templates for clinical trials and proposed study designs, the Rhinosinusitis Initiative has developed 6 appendices, which address (1) health outcomes, (2) nasal endoscopy and staging of CRS, (3) rardiologic imaging, (4) microbiology, (5) laboratory measures, and (6) biostatistical methods. (C) 2006 American Academy of Otolaryngology-Head and Neck Surgery Foundation, Inc. All rights reserved