An Analytical Workflow for Metagenomic Data and its Application to the Study of Chronic Obstructive Pulmonary Disease (COPD)

Metagenomics is the culture-independent study of genetic material obtained directly from environmental samples. It has become a realistic approach to understanding microbial communities thanks to advances in high-throughput DNA sequencing technologies over the past decade. Current research has shown that different sites of the human body house varied bacterial communities. There is a strong correlation between an individual’s microbial community profile at a given site and disease. Metagenomics is being applied more often as a means of comparing microbial profiles in biomedical studies. The analysis of the data collected using metagenomics can be quite challenging and there exist a plethora of tools for interpreting the results. An automatic analytical workflow for metagenomic analyses has been implemented and tested using synthetic datasets of varying quality. It is able to accurately classify bacteria by taxa and correctly estimate the richness and diversity of each set. The workflow was then applied to the study of the airways microbiome in Chronic Obstructive Pulmonary Disease (COPD). COPD is a progressive lung disease resulting in narrowing of the airways and restricted airflow. Despite being the third leading cause of death in the United States, little is known about the differences in the lung microbial community profiles of healthy individuals and COPD patients. Bronchoalveolar lavage (BAL) samples were collected from COPD patients, active or ex-smokers, and never smokers and sequenced by 454 pyrosequencing. A total of 56 individuals were recruited for the study. Substantial colonization of the lungs was found in all subjects and differentially abundant genera in each group were identified. These discoveries are promising and may further our understanding of how the structure of the lung microbiome is modified as COPD progresses. It is also anticipated that the results will eventually lead to improved treatments for COPD.

"To Hold the World in Contempt": The British Empire, War, and the Irish and Indian Nationalist Press, 1899-1914

The era between the close of the nineteenth century and the onset of the First World War witnessed a marked increase in radical agitation among Indian and Irish nationalists. The most outspoken political leaders of the day founded a series of widely circulated newspapers in India and Ireland, placing these editors in the enviable position of both reporting and creating the news. Nationalist journalists were in the vanguard of those pressing vocally for an independent India and Ireland, and together constituted an increasingly problematic contingent for the British Empire. The advanced-nationalist press in Ireland and the nationalist press in India took the lead in facilitating the exchange of provocative ideas—raising awareness of perceived imperial injustices, offering strategic advice, and cementing international solidarity. Irish and Indian press coverage of Britain’s imperial wars constituted one of the premier weapons in the nationalists’ arsenal, permitting them to build support for their ideology and forward their agenda in a manner both rapid and definitive. Directing their readers’ attention to conflicts overseas proved instructive in how the Empire dealt with those who resisted its policies, and also showcased how it conducted its affairs with its allies. As such, critical press coverage of the Boxer Rebellion, Boer War, Russo-Japanese War, and World War I bred disaffection for the Empire, while attempts by the Empire to suppress the critiques further alienated the public. This dissertation offers the first comparative analysis of the major nationalist press organs in India and Ireland, using the prism of war to illustrate the increasingly persuasive role of the press in promoting resistance to the Empire. It focuses on how the leading Indian and Irish editors not only fostered a nationalist agenda within their own countries, but also worked in concert to construct a global anti-imperialist platform. By highlighting the anti-imperial rhetoric of the nationalist press in India and Ireland and illuminating their strategies for attaining self-government, this study deepens understanding of the seeds of nationalism, making a contribution to comparative imperial scholarship, and demonstrating the power of the media to alter imperial dynamics and effect political change.