Physical Sciences and Mathematics Commons^™

New Strategies To Reveal Protein Candidates In Protein-Protein Interactome Study, Meng-Chieh Chen

Open Access Theses

Comprehensive protein-protein interaction network analysis can help reveal protein functions in a system-wide manner. A reliable knowledgebase of interaction networks is not only important for selecting the candidates for drug therapies, but also for evaluating the disease risk. In current interaction databases, 322579 interactions comprised of 56460 proteins have been reported (statistical analysis from APID: Agile Protein Interaction DataAnalyzer; http://bioinfow.dep.usal.es/apid/index.htm). The huge datasets are contributed mainly by yeast -two -hybrid (Y2H) screening and affinity-purification followed by mass spectrometry (AP-MS). High false positive rates and failing to cover certain interaction categories are the limitations of these two methods. Here, we developed …

Nitrate Removal From Subsurface Drainage By Denitrifying Bioreactor, Erin Chichlowski

Open Access Theses

Denitrifying bioreactors are an edge-of-field best management practice that reduce nitrate in runoff and subsurface drainage waters with minimum surface foot print and management requirements. The objectives of this study included evaluating a 173 m3 wood chip bioreactor for nitrate reduction and removal rates, the effects on phosphorus, and the impacts of the bioreactor's physical characteristics on effective nitrate reduction During periods of flow, weekly water samples were collected for lab analysis of nitrate+nitrite (nitrate-N), total nitrogen (TN), soluble reactive phosphorus (SRP), and total phosphorus (TP) and measurements were made of water temperature, dissolved oxygen, pH, oxidation reduction potential, temperature, …

Profit-Maximizing Responses To Climate Change In Commodity Agriculture: Does Adaptation Matter?, Sajeev Erangu Purath Mohankumar

Open Access Theses

Accumulation of greenhouse gases in the atmosphere has led to rising temperatures, and is expected to lead to a change in climate. Crop yields are vulnerable to these changes. Adaptation is expected to be key to combating climate change impacts, but the effectiveness of adaptation strategies is not well understood. Hence, there is a need to assess the impacts of climate change on agriculture and devise profitable adaptation strategies to combat its effects. This study uses historical and three projected climate data sets to simulate yields using the crop model Daycent, empirical relationships between weather and agronomic variables that influence …

Liquid Swine Manure Application Timing And Instincttm Impacts On Net Soil Nitrogen Mineralization And Corn Yield, Min Xu

Open Access Theses

Nitrogen (N) is one of the most expensive variable input costs for corn production. Optimized manure management is essential to ensure maximum crop N utilization and to reduce the risk of N loss. A field study was conducted in central Indiana from 2011-2013 to assess liquid swine ( Sus scrofa L.) manure N availability when applied at different times or co-applied with InstinctTM , a microencapsulated form of nitrapyrin. Soil inorganic N contents, soil N mineralization, corn yield, grain N content, whole plant N concentrations of corn at the V6 growth stage, and ear leaf N concentrations of corn at …

Assessing Positional Accuracy And Correcting Point Data For Digital Soil Mapping At Varying Scales, Minerva J. Dorantes

Open Access Theses

Accuracy, timeliness, and the effect of scale of soil maps are rarely assessed. The recent increase in the use of GIS technologies and modelling software in natural resources and land management, has increased the demand for soil information at a finer resolution worldwide. Most of the world's developing countries rely on soils information at a scale that is too coarse for practical planning, and have obstacles impeding collection of new data, such as civil war and a lack of collection resources. The United States has an exhaustive collection of soils data at a fine scale. However, its location information is …

Vegetation And Soil Characteristics Of Pine Plantations And Naturally Regenerated Hardwood Forests On The Hoosier National Forest, Patrick James Duffy

Open Access Theses

During the 1930s there was widespread erosion on farmland and subsequent land abandonment. As a result, Pinus strobus L. (white pine), P. resinosa Aiton (red pine), and P. echinata Mill. (shortleaf pine) were planted in the Midwest to prevent erosion and rehabilitate sites. These species were selected due to their wide availability at the time. Currently, it is the goal of the U.S. Forest Service to provide a more natural and sustainable landscape, in part by removing these non-native Pinus stands and by replacing them with native hardwood species. The ultimate success of hardwood restoration depends, in part, on the …

Uncertainty, Irreversibility, And Investment In Secondgeneration Biofuels, Tanner Joseph Mccarty

Open Access Theses

The present study formalizes and quantifies the importance of uncertainty for investment in a corn-stover based cellulosic biofuel plant. Using a real options model we recover prices of gasoline that would trigger entry into the market and calculate the portion of that entry trigger price required to cover cost and the portion that corresponds to risk premium. We then discuss the effect of managerial flexibility on the entry risk premium and the prices of gasoline that would trigger mothballing, reactivation, and exit. Results show that the risk premium required by plants to enter the second-generation biofuel market is likely to …

The Effects Of Radar On Avian Behavior: Implications For Wildlife Management At Airports, Eleanor R. Sheridan

Open Access Theses

Airports are areas with a high availability of resources for wildlife to forage, breed, and roost. Airports also have different types of radars to assist with air traffic control as well as tracking of wildlife that could become a risk for aircraft. The effect of radar electromagnetic radiation on wildlife behavior is not well understood. The goal of this study was to determine if bird behavior is affected by radar in two contexts: static radar (e.g., surveillance radar) and approaching radar (e.g., aircraft weather radar). We used brown-headed cowbirds as a model species. In the static radar context, we performed …

Abcb11 Functions With B1 And B19 To Regulate Rootward Auxin Transport, Jesica Elyse Reemmer

Open Access Theses

Auxin transport is essential for the architecture and development of erect plants. In a network of transporters directing auxin flows, ATP-Binding Cassette (ABC) transporters are a ubiquitous family of proteins that actively transport important substrates, including auxins, across the plasma membrane. ABCB1 and ABCB19 have been shown to account for the majority of rootward auxin transport, but residual fluxes to the root tip in Arabidopsis b1b19 double mutants implies the involvement of at least one additional auxin transporter in this process. Of specific interest, the severe dwarfism seen in abcb1abcb19 is strikingly reminiscent of that seen in mutants defective in …

Characterization Of Water-Solid Interactions In Crystalline Ingredients And Development Of Deliquescence Measurement Recommendations, Matthew C. Allan

Open Access Theses

There are five major mechanisms of water-solid interactions. The primary focus of this thesis was on two of these: deliquescence and hydrate formation. Many crystalline food ingredients are deliquescent compounds (e.g., NaCl, sucrose, and ascorbic acid) and some are both deliquescent and hydrate formers (e.g., glucose, thiamine HCl, citric acid). Deliquescence is the first order phase transformation of a crystalline solid to a solution above a critical relative humidity (RH) known as the deliquescence point (RH0). A crystalline hydrate is a pseudo-polymorph in which water is incorporated into the crystal structure, altering the molecular formula and the physical properties.^ To …

Using The Microsoft Kinect To Assess Human Bimanual Coordination, Joshua James Liddy

Open Access Theses

Optical marker-based systems are the gold-standard for capturing three-dimensional (3D) human kinematics. However, these systems have various drawbacks including time consuming marker placement, soft tissue movement artifact, and are prohibitively expensive and non-portable. The Microsoft Kinect is an inexpensive, portable, depth camera that can be used to capture 3D human movement kinematics. Numerous investigations have assessed the Kinect's ability to capture postural control and gait, but to date, no study has evaluated it's capabilities for measuring spatiotemporal coordination. In order to investigate human coordination and coordination stability with the Kinect, a well-studied bimanual coordination paradigm (Kelso, 1984, Kelso; Scholz, & …

Physical And Chemical Attributes Of A Genetically Modified Fruit Pectin, Carl Patrick Littrell

Open Access Theses

Pectin is an important polymer used in the food industry as a thickening and gelling agent. Though pectin is ubiquitous in plants, chemical and structural differences among pectin molecules prevent most from being viable for industrial use. Enzymes found naturally in fruit cell walls during the ripening process impair many desirable attributes of fruit pectins, rendering them unsuitable for industrial applications. Pectin methylesterase (PME) is one such enzyme whose expression can be altered during ripening through the use of recombinant genetic engineering. Reduction in levels of PME results in increased degree of methylation and molecular size of pectin, greatly increasing …

Investigation Into The Control Of Melittin Secondary Structure And Antimicrobial Activity, Zachary B. Molinets

Open Access Theses

Antimicrobial resistance has been an exponentially growing problem since the discovery of antibiotics. Antibiotics have been misused for many years and this misuse has grown into a real problem for the medical community. While there are countless safeguards to prevent infection by a resistant strain of bacteria, there are still many plagued by it and must be treated with sometimes dangerous antibiotics. Melittin, along with many other peptides, contain potent antimicrobial properties, but are also toxic toward enthrocytes. The control of the secondary structure of peptides provides the key to adjusting their activity.

Field To Flight: A Techno-Economic Analysis Of Stover To Aviation Biofuels Supply Chain, Amanda C. Bittner

Open Access Theses

Greenhouse gas emissions have been a growing concern. The transportation sector contributes to one-third of GHG emissions in the United States from fossil fuel burning. The Renewable Fuel Standard set a requirement for 16 billion gallons (ethanol equivalent) of cellulosic biofuels to be used in the market. Aviation biofuels can help to meet both of these problems as well as improve U.S. energy security.

Investment in the biofuel industry carries a lot of risk. The biofuel industry is run by the private sector, but can be incentivized by government. Cellulosic biofuels carry even more risk than first generation biofuels, because …

Changes In Tundra Plant And Soil Organic Geochemical Composition In Response To Long-Term Increased Winter Precipitation In N. Alaska, Olivia Miller

Open Access Theses

Tundra ecosystem soils store half of the global soil organic carbon (SOC) pool and have the potential to release large amounts of greenhouse gases, primarily CH₄ and CO₂. As climates warm and permafrost thaws, the emissions of these gases as organic matter decomposition rates increase may become increasingly important to the chemistry of the atmosphere. Increases in precipitation that accompany warming, may shift tundra vegetative composition from moss/graminoid- to shrub-dominated systems. These vegetation shifts may result in important feedback effects as altered plant and litter chemistry may affect SOC storage in soils. Questions investigated include: 1) How …

Deforestation Of Cloud Forest In The Central Highlands Of Guatemala: Soil Erosion And Sustainability Implications For Q'Eqchi' Maya Communities, Ian Christopher Pope

Open Access Theses

Understanding the nexus between deforestation, food production, land degradation, and culture contributes knowledge that is useful for development practitioners working to enhance conservation and food security. Documenting deforestation and soil erosion in the Sierra Yalijux and Sierra Sacranix in the Central Highlands of Guatemala adds new knowledge about the rates and dynamics of deforestation and land degradation in areas with unique and sensitive cloud forest ecosystems. It also suggests possible areas of emphasis for efforts targeted at combining cloud forest conservation with sustainability for indigenous Q'eqchi' communities. In addition, this work contributes to a small but growing body of literature …

Determinants Of Energy Efficiency Across Countries, Guolin Yao

Open Access Theses

With economic development, environmental concerns become more important. Economies cannot be developed without energy consumption, which is the major source of greenhouse gas emissions. Higher energy efficiency is one means of reducing emissions, but what determines energy efficiency?

In this research we attempt to find answers to this question by using cross-sectional country data; that is, we examine a wide range of possible determinants of energy efficiency at the country level in an attempt to find the most important causal factors. All countries are divided into three income groups: high-income countries, middle-income countries, and low-income countries. Energy intensity is used …

Study Of The Sustainbility Issues Of Food Production Using Vertical Farm Methods In An Urban Environment Within The State Of Indiana, Victor Mendez Perez

Open Access Theses

There are several problems around the globe related to water scarcity, energy shortages, deforestation and loss of fertile land, and food security. Climate change is making environmental and social issues arise. Issues such as, changes in the agricultural landscape, increasing population (9 billion is the expected population for 2040), rising food borne illnesses, scarcity of drinking water, and more crop failure due to plant pathogens and insect pests, among other factors make this study specially significant. Vertical farming could be a potencial solution to some of these problems.

Due to these problems the present thesis analyzed vertical farming as a …

Pharmaceuticals And Personal Care Products: Emerging Contaminants In Aquatic Ecosystems, Jenny E. Zenobio

Open Access Theses

In recent years, the presence of pharmaceuticals and personal care products (PPCPs) in aquatic systems has led to research on their fate and effects. PPCPs have been found in mixture in wastewater effluents, surface, ground, and drinking water at low concentrations from areas of intense urbanization. Although adverse effects to human health from the current environmental concentrations are unlikely, the impacts to ecological receptors are not clear. We performed field and laboratory studies to quantify and evaluate effects of PPCPs on fish. First, a field study was conducted at the Baca National Wildlife Refuge, Colorado (2010-2012) because a portion of …