Physical Sciences and Mathematics Commons^™

Bringing Biodiversity To Development: Perceptions Of Integrating Eucalyptus And Forest-Corridors Around The Serra Do Brigadeiro, Brazil, Maggie R Stevens

Masters Theses

The Atlantic Forest of south-eastern Brazil is a hot-spot for biodiversity and should be conserved. It is also at the center of the largest municipalities in Brazil and therefore has a severely fragmented landscape. Iracambi, a working farm near the Serra do Brigadeiro state park in Minas Gerais, is working for conservation in an area of intense agricultural production and expanding forestry industry. Most households in this rural area have some amount of eucalyptus on their property and consequently the director of Iracambi is developing the preliminary foundation for a forest corridor program comprised of primarily eucalyptus with the goal …

Adaptation And Stochasticity Of Natural Complex Systems, Roy David Dar

Doctoral Dissertations

The methods that fueled the microscale revolution (top-down design/fabrication, combined with application of forces large enough to overpower stochasticity) constitute an approach that will not scale down to nanoscale systems. In contrast, in nanotechnology, we strive to embrace nature’s quite different paradigms to create functional systems, such as self-assembly to create structures, exploiting stochasticity, rather than overwhelming it, in order to create deterministic, yet highly adaptable, behavior. Nature’s approach, through billions of years of evolutionary development, has achieved self-assembling, self-duplicating, self-healing, adaptive systems. Compared to microprocessors, nature’s approach has achieved eight orders of magnitude higher memory density and three orders …

The ‘Helper’ Phenotype: A Symbiotic Interaction Between Prochlorococcus And Hydrogen Peroxide Scavenging Microorganisms, James Jeffrey Morris

Doctoral Dissertations

The unicellular cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism throughout the temperate and tropical open oceans, but it is difficult to grow in pure cultures. We developed a system for rendering spontaneous streptomycin-resistant mutants of Prochlorococcus axenic by diluting them to extinction in the presence of “helper” heterotrophic bacteria, allowing them to grow to high cell concentrations, and then killing the helpers with streptomycin. Using axenic strains obtained in this fashion, we demonstrated that Prochlorococcus experiences a number of growth defects in dilute axenic culture, including reduced growth rate, inability to form colonies on solid media, and higher incidence …

An Investigation Of Stratigraphic Evidence For An Abrupt Climatic Event 8200 Yr Bp In Valle De Las Morrenas, Costa Rica, Brian Thomas Watson

Masters Theses

Lago de las Morrenas 4 (9.498056° [degrees] N, 83.486111° [degrees] W, 3466 m elev.) is the lowest lake in a chain of glacial lakes located in the Valle de las Morrenas, a valley facing almost due north from Cerro Chirripó, the highest peak in the Cordillera de Talamanca in Costa Rica. Coarse resolution analyses of pollen, microscopic charcoal, and loss-on-ignition of a ca. 10,000 year sediment record from Lago de las Morrenas 4 was carried out to complement and extend previous research on the environmental history of the Chirripó highlands and to provide context for high-resolution sampling and analysis of …

Niche Of Harmful Alga Aureococcus Anophagefferens Revealed Through Ecogenomics, Christopher Gobler, Dianna Berry, Sonya Dyhrman, Steven Wilhelm

Microbiology Publications and Other Works

Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking, because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements showed that the harmful alga Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the genome of A. anophagefferens and compared its gene complement with those of six competing phytoplankton species identified through metaproteomics. …

Human Decomposition Ecology At The University Of Tennessee Anthropology Research Facility, Franklin Edward Damann

Doctoral Dissertations

The University of Tennessee Anthropology Research Facility (ARF) is well known for its unique history as a site of human decomposition research in a natural environment. It has been integral to our understanding of the processes of human decomposition. Over the last 30 years 1,089 bodies have decomposed at this 1.28 acre facility, producing a density of 850 corpses per acre of land. This project evaluated the abiotic and biotic characteristics of the soil exposed to various levels of human decomposition in order to determine the effect on the physicochemical properties and the indigenous bacterial communities.

Specifically, 75 soil samples …

Applied Ecosystem Services In Working Forests: A Direct Market Valuation, Darin Stuart Hale

Masters Theses

Ecosystem services, or the benefits humans obtain from natural ecosystems, have long been recognized as critical to human health. Efforts have been taken by many to determine the non-market values of these services but few have offered a direct market valuation. Increasing awareness, scarcity, and regulation have fostered transactions, and markets are emerging that can allow for direct valuation and could provide landowners the opportunity to merchandise this natural capital. This paper provides a valuation and comparison, as a case study, of a traditional management scheme, including the marketing of fiber and recreational leases, and an ecosystem services management scheme, …

Steps Toward Butternut (Juglans Cinerea L.) Restoration, Sunshine L. Brosi

Doctoral Dissertations

Butternut (Juglans cinerea L.), a lesser-known relative of black walnut (Juglans nigra L.), is a native tree species beneficial for wildlife, valuable for timber, and part of the great diversity of species in the eastern forests of North America. Populations of butternut are being devastated by butternut canker disease, caused by the fungus Sirococcus clavigignenti-juglandacearum (V.M.G. Nair, Kostichka, & Kuntz), which is thought to be introduced to North America. The disease causes multiple branch and stem cankers that eventually girdle trees. Small population sizes, lack of sprouting, and shade intolerance exacerbates the disease and results in permanent losses of butternut …

Spatiotemporal Dynamics In A Lower Montane Tropical Rainforest, Robert Michael Lawton

Doctoral Dissertations

Disturbance in a forest’s canopy, whether caused by treefall, limbfall, landslide, or fire determines not only the distribution of well-lit patches at any given time, but also the ways in which the forest changes over time. In this dissertation, I use a 25 year record of treefall gap formation find a novel and highly patterned process of forest disturbance and regeneration, providing a local mechanism by examining the factors that influence the likelihood of treefall. I then develop a stochastic cellular automaton for disturbance and regeneration based on the analysis of this long term data set and illustrate the potential …

The Maximum Clique Problem: Algorithms, Applications, And Implementations, John David Eblen

Doctoral Dissertations

Computationally hard problems are routinely encountered during the course of solving practical problems. This is commonly dealt with by settling for less than optimal solutions, through the use of heuristics or approximation algorithms. This dissertation examines the alternate possibility of solving such problems exactly, through a detailed study of one particular problem, the maximum clique problem. It discusses algorithms, implementations, and the application of maximum clique results to real-world problems. First, the theoretical roots of the algorithmic method employed are discussed. Then a practical approach is described, which separates out important algorithmic decisions so that the algorithm can be easily …

Optimal Control Of Species Augmentation Conservation Strategies, Erin Nicole Bodine

Doctoral Dissertations

Species augmentation is a method of reducing species loss via augmenting declining or threatened populations with individuals from captive-bred or stable, wild populations. In this dissertation, species augmentation is analyzed in an optimal control setting to determine the optimal augmentation strategies given various constraints and settings. In each setting, we consider the effects on both the target/endangered population and a reserve population from which the individuals translocated in the augmentation are harvested. Four different optimal control formulations are explored. The first two optimal control formulations model the underlying population dynamics with a system of ordinary differential equations. Each of these …

A Vegetation History From Emerald Pond, Great Abaco Island, The Bahamas, Based On Pollen Analysis, Ian Arthur Slayton

Masters Theses

Emerald Pond (26° 32' 12" N, 77° 06' 32" W) is a vertical-walled solution hole in the pine rocklands of Great Abaco Island, The Bahamas. In 2006, Sally Horn, Ken Orvis, and students recovered an 8.7 m-long sediment core from the center of the pond using a Colinvaux-Vohnout locking piston corer. AMS radiocarbon dates on macrofossils are in stratigraphic order and indicate that the sequence extends to ca. 8400 cal yr BP. Basal deposits consist of aeolian sands topped by a soil and then pond sediment, suggesting that the site began as a sheltered, dry hole during a Late Pleistocene …

Comparative Ecophysiology Of American Chestnut Under Different Planting Treatments On Reclaimed Mine Sites, Christopher Ryan Miller

Masters Theses

American chestnut was once an abundant species that dominated the Eastern U.S. deciduous forests. Although this species is currently functionally extinct due to the chestnut blight, researchers are working on blight-resistant hybrids in hopes of restoring the species. As one potential vector for chestnut reintroduction and dispersal, the reclamation of mine sites are being considered. Recent research has found that reforestation efforts on these reclaimed mine sites provide productive tree growth while also complying with mine-reclamation laws. Understanding how American chestnut performs physiologically on mine sites will aid in the restoration of this species and reclamation of mine sites.

The …

Classification And Fertility Of Soils In The Big South Fork National River And Recreation Area Based On Landscape Position And Geology, Ryan H. Blair

Masters Theses

The Big South Fork National River and Recreation Area encompasses more than 50,585 hectares (125,000 acres) of the Cumberland Plateau along the border of Tennessee and Kentucky. Highly dissected and steep terrain have made accessibility to much of the park limited, thus little work has been done to investigate the formation of these soils. Seven native soil profiles were selected for chemical and physical analysis representing Pennsylvanian-aged acidic sandstone and shale geology and landforms. The objectives of this study included the characterization of selected native profiles by physical and chemical analysis, as well as classification using US Soil Taxonomy, to …

The Construction And Analysis Of Marker Gene Libraries, S.M. Short, F. Chen, Steven Wilhelm

Microbiology Publications and Other Works

Marker genes for viruses are typically amplified from aquatic samples to determine whether specific viruses are present in the sample, or to examine the diversity of a group of related viruses. In this chapter, we will provide an overview of common methods used to amplify, clone, sequence, and analyze virus marker genes, and will focus our discussion on viruses infecting algae, bacteria, and heterotrophic flagellates. Within this chapter, we endeavor to highlight critical aspects and components of these methods. To this end, instead of providing a detailed experimental protocol for each of the steps involved in examining virus marker gene …

Determining Rates Of Virus Production In Aquatic Systems By The Virus Reduction Approach,, M.G. Weinbauer, J.M. Rowe, Steven Wilhelm

Microbiology Publications and Other Works

The reduction approach to assess virus production and the prokaryotic mortality by viral lysis stops new infection by reducing total virus abundance (and thus virus–host contacts). This allows for easy enumeration of viruses that originate from lysis of already infected cells due to the decreased abundance of free virus particles. This reoccurrence can be quantified and used to assess production and cell lysis rates. Several modifications of the method are presented and compared. The approaches have great potential for elucidating trends in virus production rates as well as for making generalized estimates of the quantitative effects of viruses on marine …

Biological Simulations And Biologically Inspired Adaptive Systems, Edgar Alfredo Duenez-Guzman

Doctoral Dissertations

Many of the most challenging problems in modern science lie at the interface of several fields. To study these problems, there is a pressing need for trans-disciplinary research incorporating computational and mathematical models. This dissertation presents a selection of new computational and mathematical techniques applied to biological simulations and problem solving: (i) The dynamics of alliance formation in primates are studied using a continuous time individual-based model. It is observed that increasing the cognitive abilities of individuals stabilizes alliances in a phase transition-like manner. Moreover, with strong cultural transmission an egalitarian regime is established in a few generations. (ii) A …

W229-Interpreting Mehlich 1 And 3 Soil Test Extractant Results For P And K In Tennessee, The University Of Tennessee Agricultural Extension Service

Field & Commercial Crops

The Mehlich 1 and 3 soil test extractants are the most widely used in laboratories of the southern United States today. Tennessee began using the Mehlich 1 extractant in December, 1981. Existing soil test calibration data in Tennessee are based on the Mehlich 1 soil test extractant,1,2 which became available in 1953.

Identifying The Source Of Unknown Microcystin Genes And Predicting Microcystin Variants By Comparing Genes Within Uncultured Cyanobacterial Cells, C.J. Allender, G.R. Lecleir, J.M. Rinta-Kanto, R.L. Small, M.F. Satchwell, G.L. Boyer, Steven Wilhelm

Microbiology Publications and Other Works

While multiple phylogenetic markers have been used in the culture independent study of microcystin producing cyanobacteria, in only a few instances have multiple markers been studied within individual cells, and in all cases these studies have been conducted with cultured isolates. Here, we isolate and evaluate large DNA fragments (> 6 kb) encompassing two genes involved in microcystin biosynthesis (mcyA2 and mcyB1) and use them to identify the source of gene fragments found in water samples. Further investigation of these gene loci from individual cyanobacterial cells allowed for improved analysis of the genetic diversity within microcystin producers as …

Actinorhodopsin Genes Discovered Diverse In Freshwater Habitats And Among Cultivated Actinobacteria, A.K. Sharma, K. Sommerfeld, G.S. Bullerjahn, A.R. Matteson, Steven Wilhelm, J. Jezbera, U. Brandt, W.F. Doolittle, M.W. Hahn

Microbiology Publications and Other Works

Microbial rhodopsins are membrane proteins that utilize a retinal chromophore to harvest sunlight for energetic and photosensory functions. Recently, a group of novel rhodopsin sequences named ‘actinorhodopsins’ (ActRs) was hypothesized to exist among uncultured planktonic Actinobacteria. ActRs were discovered by mining metagenomic data obtained during the Venter Institute’s Global Ocean Sampling expedition, from a hypersaline lagoon, two estuaries and a freshwater lake. On the basis of these findings, and many studies that show Actinobacteria are common inhabitants of lakes, we predicted that ActR genes would likely be present in other freshwater habitats and among the genomes of cultivated Actinobacteria …

The Effects Of Increased Pco2 And Temperature On The North Atlantic Spring Bloom: I. The Phytoplankton Community And Biogeochemical Response, Y. Feng, C.E. Hare, K. Leblanc, J.M. Rose, Y Zhang, G.R. Ditullio, P. Lee, Steven Wilhelm, J.M. Rowe, J. Sun, N. Nemcek, C. Gueguen, U. Passow, I. Benner, C. Brown, D.A. Hutchins

Microbiology Publications and Other Works

ABSTRACT: The North Atlantic spring bloom is one of the largest annual biological events in the ocean, and is characterized by dominance transitions from siliceous (diatoms) to calcareous (coccolithophores) algal groups. To study the effects of future global change on these phytoplankton and the biogeochemical cycles they mediate, a shipboard continuous culture experiment (Ecostat) was conducted in June 2005 during this transition period. Four treatments were examined: (1) 12°C and 390 ppm CO₂ (ambient control), (2) 12°C and 690 ppm CO₂ (high pCO₂), (3) 16°C and 390 ppm CO₂ (high temperature), and (4) 16°C and …

Effects Of Increased Pco2 And Temperature On The North Atlantic Spring Bloom: Iii. Dimethylsulfoniopropionate, P.A. Lee, J.R. Rudisill, A.R. Neeley, D.A. Hutchins, Y. Feng, C.E. Hare, K. Leblanc, J.M. Rose, Steven Wilhelm, J.M. Rowe, G.R. Ditullio

Microbiology Publications and Other Works

The CLAW hypothesis argues that a negative feedback mechanism involving phytoplankton-derived dimethylsulfoniopropionate (DMSP) could mitigate increasing sea surface temperatures that result from global warming. DMSP is converted to the climatically active dimethylsulfide (DMS), which is transferred to the atmosphere and photochemically oxidized to sulfate aerosols, leading to increases in planetary albedo and cooling of the Earth’s atmosphere. A shipboard incubation experiment was conducted to investigate the effects of increased temperature and pCO2 on the algal community structure of the North Atlantic spring bloom and their subsequent impact on particulate and dissolved DMSP concentrations (DMSP_p and DMSP_d). Under …

Distribution Of Calcifying And Silicifying Phytoplankton In Relation To Environmental And Biogeochemical Parameters During The Late Stages Of The 2005 North East Atlantic Spring Bloom, K. Leblanc, C.E. Hare, Y. Feng, G.M. Berg, G.R. Ditullio, A. Neeley, I. Benner, C. Sprengel, A. Beck, S.A. Sanudo-Wilhemy, U. Passow, K. Klinck, J.M. Rowe, Steven Wilhelm, C.W. Brown, D.A. Hutchins

Microbiology Publications and Other Works

The late stage of the North East Atlantic (NEA) spring bloom was investigated during June 2005 along a transect section from 45 to 66° N between 15 and 20° W in order to characterize the contribution of siliceous and calcareous phytoplankton groups and describe their distribution in relation to environmental factors. We measured several biogeochemical parameters such as nutrients, surface trace metals, algal pigments, biogenic silica (BSi), particulate inorganic carbon (PIC) or calcium carbonate, particulate organic carbon, nitrogen and phosphorus (POC, PON and POP, respectively), as well as transparent exopolymer particles (TEP). Results were compared with other studies undertaken in …

Past Fire Regimes Of Table Mountain Pine (Pinus Pungens L.) Stands In The Central Appalachian Mountains, Virginia, U.S.A., Georgina Deweese

Doctoral Dissertations

Table Mountain pine is an Appalachian endemic that occurs in a patchy distribution from Georgia to Pennsylvania and is prolific at sites with a history of fire disturbance. The purpose of this dissertation was to reconstruct the fire regimes of Table Mountain pine stands in the Jefferson National Forest, Virginia. Sections from firescarred Table Mountain pines were collected at four sites to analyze fire history, while increment cores and stand composition information were collected from macroplots within each fire history site to investigate the possible influence of fires that were more ecologically severe. Results show that fire was frequent before …

Beauveria Bassiana, A Cotton Endophyte With Biocontrol Activity Against Seedling Disease, Mary Ruth Griffin

Doctoral Dissertations

Beauveria bassiana isolate 11-98 is entomopathogenic, endophytic in tomato, and has biocontrol activity against Rhizoctonia solani on tomato. The objectives of this study were to determine 1) if B. bassiana is endophytic in cotton, following seed treatment; 2) if B. bassiana can protect cotton against seedling pathogens; 3) if different conidial rates, applied to seed, alter effectiveness of B. bassiana; and 4) mechanisms of biocontrol used by B. bassiana against plant pathogens. Cotton ‘Delta Pine 436’ seed was inoculated with isolate 11-98 conidia, sown in a gnotobiotic system, and then isolated from surfacesterilized seedlings on selective medium. Using scanning …

Seasonal Forage Availability And Diet Of Reintroduced Elk In The Cumberland Mountains, Tennessee, Jason Lee Lupardus

Masters Theses

The Tennessee Wildlife Resources Agency (TWRA) reintroduced elk (Cervus elaphus manitobensis) into the Cumberland Mountains, Tennessee over a 3-year period beginning in December 2000. We radio-collared 160 elk and monitored them by aerial telemetry from February 2001 to June 2003. Locations (n = 1450) were used in a geographic information system (GIS) to develop a core herd home range (789-ha sampling area) to assess elk seasonal forage use and availability. We monitored diet and resource availability from November 2003 to October 2004 by vegetation sampling and microhistological analysis of feces. Tall fescue (Festuca arundinacea; 35.1%) dominated …

Registros De Sedimentos Lacustres De La Vegetación Del Holoceno Y Historia Del Fuego En El Páramo De Costa Rica. (Lake-Sediment Records Of Holocene Vegetation And Fire History In The Costa Rican Páramos), Sally P Horn, Brandon L. League

Geography Publications and Other Works

We examined pollen, pteridophyte (ferns and fern-allies) spores, and charcoal in a 5.6 m long sediment core from Lago de las Morrenas 1, and charcoal in a 1.1 m long sediment core from Lago Chirripó, to reconstruct postglacial vegetation and fire history in the Chirripó páramo. Lago de las Morrenas 1, the largest lake in the Valle de las Morrenas of Chirripó National Park, is presently surrounded by treeless páramo vegetation and has apparently been so since deglaciation approximately 10,000 radiocarbon years ago. Pollen spectra suggest no pronounced changes in vegetation since ice retreat. Pollen percentages for Gramineae and other …

The Effect Of Carbon Dioxide Tension Upon The Ability Of Goldfish To Abosorb Oxygen At Low Tension, Thressa A. Hickman

Masters Theses

Within recent years much has been contributed to our knowledge of the physiology of respiration. Van Slyke (1921) in a study of the carbon dioxide carriers of the blood concluded that hemoglobin is almost as completely responsible for the transport of CO₂ in the blood as it is for the transport of oxygen. And that from 80% to 95%, sometimes possibly all, of the alkali furnished to neutralize the CO₂ that enters the venous blood comes from the hemoglobin.

Powers (1922) found that species of marine fishes have an optimum pH of more or less wide range for …