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. ^

Serial evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains

Background The HIV virus is known for its ability to exploit numerous genetic and evolutionary mechanisms to ensure its proliferation, among them, high replication, mutation and recombination rates. Sliding MinPD, a recently introduced computational method [1], was used to investigate the patterns of evolution of serially-sampled HIV-1 sequence data from eight patients with a special focus on the emergence of X4 strains. Unlike other phylogenetic methods, Sliding MinPD combines distance-based inference with a nonparametric bootstrap procedure and automated recombination detection to reconstruct the evolutionary history of longitudinal sequence data. We present serial evolutionary networks as a longitudinal representation of the mutational pathways of a viral population in a within-host environment. The longitudinal representation of the evolutionary networks was complemented with charts of clinical markers to facilitate correlation analysis between pertinent clinical information and the evolutionary relationships. Results Analysis based on the predicted networks suggests the following:: significantly stronger recombination signals (p = 0.003) for the inferred ancestors of the X4 strains, recombination events between different lineages and recombination events between putative reservoir virus and those from a later population, an early star-like topology observed for four of the patients who died of AIDS. A significantly higher number of recombinants were predicted at sampling points that corresponded to peaks in the viral load levels (p = 0.0042). Conclusion Our results indicate that serial evolutionary networks of HIV sequences enable systematic statistical analysis of the implicit relations embedded in the topology of the structure and can greatly facilitate identification of patterns of evolution that can lead to specific hypotheses and new insights. The conclusions of applying our method to empirical HIV data support the conventional wisdom of the new generation HIV treatments, that in order to keep the virus in check, viral loads need to be suppressed to almost undetectable levels.

A study of leadership behaviors for Breaking Ranks leaders in public secondary schools

This research will investigate what it will take to develop principals who will embrace the recommendations of reform as proposed by National Association of Secondary School Principals (NASSP, 1996) in the Breaking Ranks document. Breaking Ranks is based on the belief that it is within the dynamics of the school culture that principals must gain insight into strategies for improving the schools for which they are held responsible. Given this context, it is important to examine perspectives that are held by principals who lead schools that embrace the concepts of reform as proposed by NASSP, thereby, could be deemed “Breaking Ranks” schools. It is within these schools that the new role of the principal develops. NASSP has identified seven key recommendations for leadership development; “attributes that need nourishing” (p. 12) for the success of school reform. The seven recommendations are included in Breaking Ranks. ^ The purpose of this study is to identify and describe how principals put the seven recommendations into practice as they function in their schools. In addition, this study will gather information on the characteristics, support, skills, and training these principals identify as critical aspects and components of their success. This is a study of principal leadership at four high school sites where “Breaking Ranks” principals have been identified. ^ This research plan will be designed to utilize an inquiry-based process with a panel of experts and four “Breaking Ranks” principals. This study will describe: (1) how a panel of experts identify what they believe needs to be done in order to put the recommendations of the Breaking Ranks document into practice and their identification of principals who are breaking ranks; (2) how identified principals say they have been able to put the recommendations of the Breaking Ranks document into practice; (3) How both groups identify and describe: (a) the characteristics and behaviors of a “Breaking Ranks” principal; (b) the new leadership skills as described by the seven recommendations identified in the Breaking Ranks document; (c) the support necessary in order to meet the recommendations in the Breaking Ranks document; and (d) The training needed in order to become “Breaking Ranks” principals; and (4) how the process of creating “Breaking Ranks” principals can be described by experts who have studied it theoretically and principals who have demonstrated it in their schools. ^

Canopy dynamics and light climates in a tropical moist deciduous forest in India

ABSTRACT. The canopy dynamics and light climates within a 20 by 60 m quadrat were studied in a disturbed moist deciduous forest near Bombay, India. A map was drawn of individual trees within the quadrat, the taxa were identified, and their phenology was followed from November 1984 to July 1985. The quadrat contained 14 species, the most common being Tectona grandis, Terminalia tomentosa, Butea monosperma, Mitragyne parviflora and Albizia procera. Some individuals were in leaf at all times, more so at the moister east end of the quadrat. In Novem- ber at the end of the rainy season, light measurements documented percentages of total daily photosynthetic photon fluence (PPF) at 10.0% of full sunlight; 44% of this flux was due to sun- flecks whose duration was approximately 17% of the daytime hours. Values for six sites were similar to mid-day measurements along a 40 m transect, and consistent with the 94% canopy cover of the sites, photographed with a fish-eye lens. The March dry season measurements re- vealed a more intense radiation environment (54% of solar PPF), and 59% of the photosyn- thetic photon flux density at mid-day along the transect. Canopy openings were increased to a mean of 59.4%. Light in the understorey in November was spectrally altered, with typical R:FR ratios of 0.30, compared to March values identical to those of sunlight, at 1.10.

Fluid dynamics and platelet deposition in a model arterial stenosis

The objective of this study was to gain further understanding and elucidation of the fluid dynamic factors and flow-induced mechanisms of the thrombogenic process of platelet deposition onto, and possible subsequent embolization from, the walls of an arterial stenosis. This has been accomplished by measurement of the axial dependence of platelet deposition within a modeled arterial stenosis for a transitional flow and a completely laminar flow field. The stenotic region of the model was collagen-coated to simulate a damaged endothelial lining of an artery. Fluid dynamics within a stenosis was studied using qualitative flow visualization, and was further compared to the in vitro platelet deposition studies. Normalized platelet density (NPD) measurements indicate decreased levels of NPD in the high shear throat region of the stenosis for a Reynolds number of 300 and a drastic increase in NPD at the throat for a Reynolds number of 175. This study provides further understanding of the flow dynamic effects on thrombus development within a stenosis. ^

Understanding anuran community dynamics in temporary wetlands: The interaction and importance of landscape and biotic processes

The major objective of this study was to determine the relative importance of landscape factors, local abiotic factors, and biotic interactions in influencing tadpole community structure in temporary wetlands. I also examined the influence of agricultural activities in South-central Florida by comparing tadpole communities in native prairie wetlands (a relatively unmodified habitat) at the Kissimmee Prairie Sanctuary (KPS) to tadpole communities in three agriculturally modified habitats found at MacArthur Agro-Ecology Research Center (MAERC). Environmental characteristics were measured in 24 isolated wetlands, and tadpoles were sampled using throw-traps and dipnets during the 1999 wet season (June–October). Landscape characteristics were expected to predominately influence all aspects of community structure because anurans associated with temporary wetland systems are likely to exist as metapopulations. Both landscape characteristics (wetland proximity to nearest woodland and the amount of woodland surrounding the wetland) and biotic interactions (fish predation) had the largest influence on tadpole community structure. Predatory fish influenced tadpole communities more than expected due to the ubiquity of wetlands, lack of topographic relief, and dispersal abilities of several fish species. Differences in tadpole community structure among habitat types were attributed to differences in woodland attributes and susceptibility to fish colonization. Furthermore, agricultural modification of prairie habitats in South-central Florida may benefit amphibian communities, particularly woodland-dwelling species that are unable to coexist with predatory fish. From a conservation standpoint, temporary wetlands proximal to woodland areas and isolated from permanent water sources appear to be most important to amphibians. In addition, the high tadpole densities attained in these wetlands suggest that these wetlands serve as biological hotspots within the landscape, and their benefits extend into the adjacent terrestrial matrix. Further research efforts are needed to quantify the biological productivity of these systems and determine spatial dynamics of anurans in surrounding terrestrial habitats. ^

Organic matter dynamics in the Florida coastal Everglades: A molecular marker and isotopic approach

Everglades National Park (ENP) is about to undergo the world's largest wetland restoration with the aim of improving the quality, timing and distribution of water flow. The changes in water flow are hypothesized to alter the nutrient fluxes and organic matter (OM) dynamics within ENP, especially in the estuarine areas. This study used a multi-proxy approach of molecular markers and stable δ 13C isotope measurements, to determine the present day OM dynamics in ENP. ^ OM dynamics in wetland soils/sediments have proved to be difficult to understand using traditional geochemical approaches. These are often inadequate to describe the multitude of OM sources (e.g. higher land plant, emergent vegetation, submerged vegetation) to the soils/sediments and the complex diagenetic processes that can alter the OM characteristics. A multi-proxy approach, however, that incorporates both molecular level and bulk parameter information is ideal to comprehend complex OM dynamics in aquatic environments. Therefore, biomass-specific molecular markers or proxies can be useful in tracing the sources and processing of OM. This approach was used to examine the OM dynamics in the two major drainage basins, Shark River Slough and Taylor River Slough, of ENP. Freshwater to marine transects were sampled in both systems for soils/sediments and suspended particulate organic matter (SPOM) to be characterized through bulk OM analyses, lipid biomarker determinations (e.g. sterols, fatty acids, hydrocarbons and triterpenoids) and compound-specific stable carbon isotope (δ 13C) determinations. ^ One key accomplishment of the research was the assessment of a molecular marker proxy (Paq) to distinguish between emergent/higher plant vegetation from submerged vegetation within ENP. This proxy proved to be quite useful at tracing OM inputs to the soils/sediments of ENP. A second key accomplishment was the development of a 3-way model using vegetation specific molecular markers. This novel, descriptive model was successfully applied to the estuarine areas of Taylor and Shark River sloughs, providing clear evidence of mixing of freshwater, estuarine and marine derived OM in these areas. In addition, diagenetic transformations of OM in these estuaries were found to be quite different between Taylor and Shark Rivers, and are likely a result of OM quality and hydrological differences. ^

The successional dynamics of lightning-initiated canopy gaps in the mangrove forests of Shark River, Everglades National Park, USA

Gap succession is a significant determinant of structure and development in most forest communities. Lightning strikes are an important source of canopy gaps in the mangrove forest of Everglades National Park. I investigated the successional dynamics of lightning-initiated canopy gaps to determine their influence on forest stand structure of the mixed mangrove forests ( Rhizophora mangle, Laguncularia racemosa, and Avicennia germinans ) of the Shark River. I measured gap size, gap shape, light environment, soil characteristics, woody debris, and fiddler crab abundance. I additionally measured the vegetative composition in a chronosequences of gap successional stages (new, recruiting, and growing gaps). I recorded survivorship, recruitment, growth and soil elevation dynamics within a subset of new and growing gaps. I determined the relationship between intact forest soil elevation and site hydrology in order to interpret the effects of lightning disturbance on soil elevation dynamics. ^ Gap size averaged 289 ± 20 m2 (± 1SE) and light transmittance decreased exponentially as gaps filled with saplings. Fine woody debris was highest in recruiting gaps. Soil strength was lower in the gaps than in the forest. The abundance of large and medium fiddler crab burrows increased linearly with total seedling abundance. Soil surface elevation declined in newly formed lightning gaps; this loss was due to a combination of superficial erosion (8.5 mm) and subsidence (60.9 mm). A distinct two-cohort recruitment pattern was evident in the seedling/sapling surveys, suggesting a partitioning of the succession between individuals present before and after lightning strike. In new gaps, the seedling recruitment rate was twice as high as in forest and the sapling population increased. At the growing gap stage, R. mangle seedling mortality was 10 times greater and sapling mortality was 13 times greater than recruitment. Growing gaps had reduced seedling stem elongation, sapling growth and adult growth. However, a few individuals (R. mangle saplings) were able to recruit into the adult life stage. In conclusion, the high density of R. mangle seedlings and saplings imply that lightning strike disturbances in these mangrove forests favor their recruitment over that of A. germinans and L. racemosa. ^

Coral disease dynamics and environmental drivers in the northern Florida Keys and Lee Stocking Island, Bahamas

Coral reefs are experiencing declines worldwide and recently coral diseases have been identified as significant contributors to coral mortality. However, little is known regarding the factors that drive coral disease distributions and dynamics. Current knowledge of the organisms that cause coral diseases is also limited, with pathogens having been identified for only 5 of the 21 described coral diseases. The study presented here describes coral disease dynamics in terms of occurrence, prevalence, spatial distribution, and host species susceptibility from 2002--2004 on reefs of the Northern Florida Keys (NFK) and Lee Stocking Island (LSI) in the Bahamas' Exuma chain. In addition, this research investigated the influence of temperature, sediment, and nutrient availability on coral disease prevalence and severity. Finally, microbial communities associated with a polymicrobial disease, black band, were examined to address spatial and temporal variability. ^ Four scleractinian diseases were observed in repeated surveys conducted during June-August of each year: black band disease (BBD), white plague type 2 (WP), dark spots syndrome (DSS), and yellow band disease-(YBD). Coral disease prevalence was generally low in both the NFK and LSI as compared to epizootic levels reported previously in the NFK and other regions of the Caribbean. Disease prevalence and species susceptibility varied spatially and temporally. Massive framework species, including Siderastrea siderea, Colpophyllia natans, and Montastraea annularis, along with relatively smaller colonies of Meandrina meandrites and Dichocoenia stokesi, were most susceptible to disease. Temperature, sedimentation, and dissolved inorganic nitrogen were positively correlated with BBD infections. Furthermore, experimental nutrient enrichment exacerbated coral tissue loss to BBD both in situ and in vivo. Profiling of BBD microbial communities using length heterogeneity PCR revealed variation over space and time, with significantly distinct bacterial assemblages in the NFK, LSI, and US Virgin Islands. ^ This study contributes to knowledge of the relationship between coral diseases and the environment, and facilitates predictions regarding potential changes in coral reef communities under differing environmental conditions. Additionally, this research provides further understanding of coral disease dynamics at both the host and microbial pathogen levels.^

A fresh look at decision making in international investment choices: Firm international coherence and home-host country relatedness

Understanding how decisions for international investments are made and how this affects the overall pattern of investments and firm’s performance is of particular importance both in strategy and international business research. This dissertation introduced first home-host country relatedness (HHCR) as the degree to which countries are efficiently combined within the investment portfolios of firms. It theorized and demonstrated that HHCR will vary with the motivation for investments along at least two key dimensions: the nature of foreign investments and the connectedness of potential host countries to the rest of the world. Drawing on cognitive psychology and decision-making research, it developed a theory of strategic decision making proposing that strategic solutions are chosen close to a convenient anchor. Building on research on memory imprinting, it also proposed that managers tend to rely on older knowledge representation. In the context of international investment decisions, managers use their home countries as an anchor and are more likely to choose as a site for foreign investments host countries that are ‘close’ to the home country. These decisions are also likely to rely more strongly on closeness to time invariant country factors of historic and geographic nature rather than time-variant institutions. Empirical tests using comprehensive investments data by all public multinational companies (MNC) worldwide, or over 15,000 MNCs with over half a million subsidiaries, support the claims. Finally, the dissertation introduced the concept of International Coherence (IC) defined as the degree to which an MNE’s network comprises countries that are related. It was hypothesized that maintaining a high level of coherence is important for firm performance and will enhance it. Also, the presence of international coherence mitigates some of the negative effects of unrelated product diversification. Empirical tests using data on foreign investments of over 20,000 public firms, while also developing a home-host country relatedness index for up to 24,300 home-host pairs, provided support for the theory advanced.

Sediment Dynamics of a Shallow Hypereutrophic lake: Lake Jesup, Florida, USA

Improved knowledge of sediment dynamics within a lake system is important for understanding lake water quality. This research was focused on an assessment of the vertical sediment flux in Lake Jesup, a shallow (1.3 m average depth) hypereutrophic lake of central Florida. Sediment dynamics were assessed at varying time scales (daily to weekly) to understand the transport of sediments from external forces; wind, waves, precipitation and/or runoff. Four stations were selected within the lake on the basis of water depth and the thicknesses of unconsolidated (floc) and consolidated sediments. At each of these stations, a 10:1 (length to diameter) high aspect ratio trap (STHA) was deployed to collect particulate matter for a one to two week period. The water and sediment samples were collected and analyzed for total carbon (TC), total phosphorus (TP) and total nitrogen (TN). Mass accumulation rates (MAR) collected by the traps varied from 77 to 418 g m-2 d-1 over seven deployments. TN, TP and TC sediment concentrations collected by the traps were consistently higher than the sediments collected by coring the lake bottom and is most likely associated with water column biomass. A yearly nutrient budget was determined from August 2009 to August 2010 with flux calculated as 2,033,882 mt yr-1.

The potential role of plant oxygen and sulphide dynamics in die-off events of the tropical seagrass, Thalassia testudinum

1 Oxygen and sulphide dynamics were examined, using microelectrode techniques, in meristems and rhizomes of the seagrass Thalassia testudinum at three different sites in Florida Bay, and in the laboratory, to evaluate the potential role of internal oxygen variability and sulphide invasion in episodes of sudden die-off. The sites differed with respect to shoot density and sediment composition, with an active die-off occurring at only one of the sites. 2 Meristematic oxygen content followed similar diel patterns at all sites with high oxygen content during the day and hyposaturation relative to the water column during the night. Minimum meristematic oxygen content was recorded around sunrise and varied among sites, with values close to zero at the die-off site. 3 Gaseous sulphide was detected within the sediment at all sites but at different concentrations among sites and within the die-off site. Spontaneous invasion of sulphide into Thalassia rhizomes was recorded at low internal oxygen partial pressure during darkness at the die-off site. 4 A laboratory experiment showed that the internal oxygen dynamics depended on light availability, and hence plant photosynthesis, and on the oxygen content of the water column controlling passive oxygen diffusion from water column to leaves and belowground tissues in the dark. 5 Sulphide invasion only occurred at low internal oxygen content, and the rate of invasion was highly dependent on the oxygen supply to roots and rhizomes. Sulphide was slowly depleted from the tissues when high oxygen partial pressures were re-established through leaf photosynthesis. Coexistence of sulphide and oxygen in the tissues and the slow rate of sulphide depletion suggest that sulphide reoxidation is not biologically mediated within the tissues of Thalassia. 6 Our results support the hypothesis that internal oxygen stress, caused by low water column oxygen content or poor plant performance governed by other environmental factors, allows invasion of sulphide and that the internal plant oxygen and sulphide dynamics potentially are key factors in the episodes of sudden die-off in beds of Thalassia testudinum . Root anoxia followed by sulphide invasion may be a more general mechanism determining the growth and survival of other rooted plants in sulphate-rich aquatic environments.

Multi-Scaled Grassland-Woody Plant Dynamics in the Heterogeneous Marl Prairies of the Southern Everglades

The Everglades freshwater marl prairie is a dynamic and spatially heterogeneous landscape, containing thousands of tree islands nested within a marsh matrix. Spatial processes underlie population and community dynamics across the mosaic, especially the balance between woody and graminoid components, and landscape patterns reflect interactions among multiple biotic and abiotic drivers. To better understand these complex, multi-scaled relationships we employed a three-tiered hierarchical design to investigate the effects of seed source, hydrology, and more indirectly fire on the establishment of new woody recruits in the marsh, and to assess current tree island patterning across the landscape. Our analyses were conducted at the ground level at two scales, which we term the micro- and meso-scapes, and results were related to remotely detected tree island distributions assessed in the broader landscape, that is, the macro-scape. Seed source and hydrologic effects on recruitment in the micro- and meso-scapes were analyzed via logistic regression, and spatial aggregation in the macro-scape was evaluated using a grid-based univariate O-ring function. Results varied among regions and scales but several general trends were observed. The patterning of adult populations was the strongest driver of recruitment in the micro- and meso-scape prairies, with recruits frequently aggregating around adults or tree islands. However in the macro-scape biologically associated (second order) aggregation was rare, suggesting that emergent woody patches are heavily controlled by underlying physical and environmental factors such as topography, hydrology, and fire.

Hydrologic Dynamics of the Ground-Water-Dependent Sian Ka’an Wetlands, Mexico, Derived from InSAR and SAR Data

The 5,280 km2 Sian Ka’an Biosphere Reserve includes pristine wetlands fed by ground water from the karst aquifer of the Yucatan Peninsula, Mexico. The inflow through underground karst structures is hard to observe making it difficult to understand, quantify, and predict the wetland dynamics. Remotely sensed Synthetic Aperture Radar (SAR) amplitude and phase observations offer new opportunities to obtain information on hydrologic dynamics useful for wetland management. Backscatter amplitude of SAR data can be used to map flooding extent. Interferometric processing of the backscattered SAR phase data (InSAR) produces temporal phase-changes that can be related to relative water level changes in vegetated wetlands. We used 56 RADARSAT-1 SAR acquisitions to calculate 38 interferograms and 13 flooding maps with 24 day and 48 day time intervals covering July 2006 to March 2008. Flooding extent varied between 1,067 km2 and 2,588 km2 during the study period, and main water input was seen to take place in sloughs during October–December. We propose that main water input areas are associated with water-filled faults that transport ground water from the catchment to the wetlands. InSAR and Landsat data revealed local-scale water divides and surface water flow directions within the wetlands.

Effects of hydrologic and water quality drivers on periphyton dynamics in the southern Everglades

Everglades periphyton mats are tightly-coupled autotrophic (algae and cyanobacteria) and heterotrophic (eubacteria, fungi and microinvertebrates) microbial assemblages. We investigated the effect of water column total phosphorus and nitrogen concentrations, water depth and hydroperiod on periphyton of net production, respiration, nutrient content, and biomass. Our study sites were located along four transects that extended southward with freshwater sheetflow through sawgrass-dominated marsh. The water source for two of the transects were canal-driven and anchored at canal inputs. The two other transects were rain-driven (ombrotrophic) and began in sawgrass-dominated marsh. Periphyton dynamics were examined for upstream and downstream effects within and across the four transects. Although all study sites were characterized as short hydroperiod and phosphorus-limited oligotrophic, they represent gradients of hydrologic regime, water source and water quality of the southern Everglades. Average periphyton net production of 1.08 mg C AFDW−1 h−1 and periphyton whole system respiration of 0.38 mg C AFDW−1 h−1 rates were net autotrophic. Biomass was generally highest at ombrotrophic sites and sites downstream of canal inputs. Mean biomass over all our study sites was high, 1517.30 g AFDW m−2. Periphyton was phosphorus-limited. Average periphyton total phosphorus content was 137.15 μg P g−1 and average periphyton total N:P ratio was 192:1. Periphyton N:P was a sensitive indicator of water source. Even at extremely low mean water total phosphorus concentrations ( ≤ 0.21 μmol l−1), we found canal source effects on periphyton dynamics at sites adjacent to canal inputs, but not downstream of inflows. These canal source effects were most pronounced at the onset of wet season with initial rewetting. Spatial and temporal variability in periphyton dynamics could not solely be ascribed to water quality, but was often associated with both hydrology and water source.