Phylogenetic analysis of within -host serially-sampled viral data

The primary goal of this dissertation is the study of patterns of viral evolution inferred from serially-sampled sequence data, i.e., sequence data obtained from strains isolated at consecutive time points from a single patient or host. RNA viral populations have an extremely high genetic variability, largely due to their astronomical population sizes within host systems, high replication rate, and short generation time. It is this aspect of their evolution that demands special attention and a different approach when studying the evolutionary relationships of serially-sampled sequence data. New methods that analyze serially-sampled data were developed shortly after a groundbreaking HIV-1 study of several patients from which viruses were isolated at recurring intervals over a period of 10 or more years. These methods assume a tree-like evolutionary model, while many RNA viruses have the capacity to exchange genetic material with one another using a process called recombination. ^ A genealogy involving recombination is best described by a network structure. A more general approach was implemented in a new computational tool, Sliding MinPD, one that is mindful of the sampling times of the input sequences and that reconstructs the viral evolutionary relationships in the form of a network structure with implicit representations of recombination events. The underlying network organization reveals unique patterns of viral evolution and could help explain the emergence of disease-associated mutants and drug-resistant strains, with implications for patient prognosis and treatment strategies. In order to comprehensively test the developed methods and to carry out comparison studies with other methods, synthetic data sets are critical. Therefore, appropriate sequence generators were also developed to simulate the evolution of serially-sampled recombinant viruses, new and more through evaluation criteria for recombination detection methods were established, and three major comparison studies were performed. The newly developed tools were also applied to "real" HIV-1 sequence data and it was shown that the results represented within an evolutionary network structure can be interpreted in biologically meaningful ways. ^

Tree Islands in Everglades Landscapes: Current Status, Historical Changes, and Hydrologic Impacts on Population Dynamics and Moisture Relations, First Annual Report

In 2005 we initiated a project designed to better understand tree island structure and function in the Everglades and the wetlands bordering it. Focus was on the raised portions at the upstream end of the islands, where tropical hardwood species adapted to well-drained conditions usually are the most prominent component of the vegetation. The study design is hierarchical, with four levels; in general, a large number of sites is to be surveyed once for a limited set of parameters, and increasingly small sets of islands are to be sampled more intensively, more frequently, and for more aspects of ecosystem function. During the first year of the 3-year study, we completed surveys of 41 Level 1 (i.e., the least intensive level) islands, and established permanent plots in two and three islands of Levels 2 and 4 intensity, respectively. Tree species richness and structural complexity was highest in Shark Slough “hammocks”, while islands in Northeast Shark Slough and Water Conservation Area 3B, which receive heavy human use, were simpler, more park-like communities. Initial monitoring of soil moisture in Level 4 hammocks indicated considerable local variation, presumably associated with antecedent rainfall and current water levels in the adjacent marsh. Tree islands throughout the study area were impacted significantly by Hurricanes Katrina and Wilma in 2005, but appear to be recovering rapidly. As the project continues to include more islands and repeated measurements, we expect to develop a better grasp of tree island dynamics across the Everglades ecosystem, especially with respect to moisture relations and water levels in the adjacent marsh. The detailed progress report which follows is also available online at http://www.fiu.edu/~serp1/projects/treeislands/tree_islands_2005_annual_report.pd

Soil Carbon Dioxide and Methane Efflux From an Everglades Tree Island and Ridge Landscape

The influence water levels have on CO2 and CH4 efflux were investigated at the Loxahatchee Impoundment Landscape Assessment (LILA) research facility, located in Boynton Beach, FL, USA. Measurements of CO2 efflux were taken for 24 h periods four times for one year from study plots. Laboratory incubations of intact soil cores were sampled for CO2, CH4, and redox potential. Additionally, soil cores from wet and dry condition were incubated for determination of enzyme activity and macronutrient limitation on decomposition of organic matter from study soils. Water levels had a significant negative influence on CO2 efflux and redox, but did not significantly influence CH4 efflux. Study plots were significantly different in CH4 efflux and redox potential. Labile carbon was more limiting to potential CO2 and CH4 production than phosphorus, with the effect significantly greater from dry conditions soils. Enzyme activity results were variable with greater macronutrient responses from dry condition soils.

Ghost Tree Social

GHOST TREE SOCIAL tells a coming out story of sorts. In terms of style, many of the poems are short, imagistic lyrics, though some are extended catalogues. Specific natural images—lakes, rivers, and snow—are often contrasted with cultural markers. The imagistic poems are thinking through the work of Sylvia Plath. The catalogue poems shift between diaristic, narrative, and critical modes, responding to the poetry of Elizabeth Bishop and the essays of Edouard Glissant. Voice-driven fragments disrupt the more traditional lyric poems. The fragments fall between formal lyrics like confetti from a gay club’s rafters; or the fragments hold the lyric poems in bondage. The lyric poem then re-signifies as form through resonances with the other discursive and poetic form of the fragment. Following critical writers such as Adrienne Rich and Audre Lorde, the re-signification of lyric form reflects the need for new signs for self and community organized queerly as opposed to more typical binary categories—man or woman, living or dead, rich or poor, white or black—where the first term is privileged and the second term often denigrated.