Life Sciences Commons^™

Quantifying Terrestrial Ecosystem Carbon Dynamics With Mechanistically-Based Biogeochemistry Models And In Situ And Remotely Sensed Data, Shaoqing Liu

Open Access Dissertations

Terrestrial ecosystem plays a critical role in the global carbon cycle and climate system. Therefore, it is important to accurately quantify the carbon dynamics of terrestrial ecosystem under future climatic change condition. This dissertation evaluates the regional carbon dynamics by using upscaling approach, mechanistically-based biogeochemistry models and in situ and remotely sensed data.

The upscaling studies based on FLUXNET network has provided us the spatial and temporal pattern of the carbon fluxes but it fails to consider the atmospheric CO2 effect given its important physiological role in carbon assimilation. In the second chapter, we consider the effect of atmospheric CO2 …

Ros Regulation Of Axonal Mitochondrial Transport, Pin-Chao Liao

Open Access Dissertations

Mitochondria perform critical functions including aerobic ATP production and calcium (Ca2+) homeostasis, but are also a major source of reactive oxygen species (ROS) production. To maintain cellular function and survival in neurons, mitochondria are transported along axons, and accumulate in regions with high demand for their functions. Oxidative stress and abnormal mitochondrial axonal transport are associated with neurodegenerative disorders. However, we know little about the connection between these two. Using primaryDrosophila neuronal cell culture and the third instar larval nervous system as in vitro and in vivo models, respectively, we studied mitochondrial transport under oxidative stress conditions. In vitro …

Annual Forage Cropping-Systems For Midwestern Ruminant Livestock Production, John Ernest Mcmillan

Open Access Dissertations

Annual forage cropping systems are a vital aspect of livestock forage production. One area where this production system can be enhanced is the integration of novel annual forages into conventional cropping systems. Two separate projects were conducted to investigate alternative forage options in annual forage production. In the first discussed research trial, two sets of crops were sown following soft red winter wheat (Triticum aestivum L.) grain harvest, at two nitrogen application rates 56 and 112 kg ha-1 . The first set of crops were C4 summer annuals seeded within two weeks of wheat grain harvest and included, brown …

Managing Bacterial Wilt, Caused By Erwinia Tracheiphila, On Muskmelon With Early Control Of Striped Cucumber Beetle ( Acalymma Vittatum (F)), And Through Varietal Selection, Ahmad Shah Mohammadi

Open Access Dissertations

Muskmelon (Cucumis melo L), is an important vegetable crop in the United States. It is grown throughout the US, and Indiana ranked 4th in production after California, Arizona and Georgia with 12.4 thousand metric tons and market value of $7.6 million in 2015. Bacterial wilt of cucurbits, which is caused by Erwinia tracheiphila (E. F. Smith), and vectored by striped cucumber beetle (Acalymma vittatum (F)), is one of the most serious diseases of muskmelon that influences muskmelon quality and yield. Many cultivars of muskmelon are grown around the United States, especially in the Midwest. Muskmelon cultivars differ in …

Investigating The Effects Of Ph On Alphaviral E3-E2 Glycoprotein Association, Organization, And Cellular Tropism, Jason Michael Sequra

Open Access Dissertations

In alphaviruses the role of E3 is required in protecting the fusion peptide region of E1 during intracellular transport. Throughout viral processing, the association of E2 and E3 is required for the successful trafficking and incorporation of E1 into the mature virion. This E3-E2 association has been observed to extend to mature virions in the solved structure for the envelope of Semliki Forest virus (SFV) and supported by the solved structure for the entire Venezuelan equine encephalitis virion (VEEV) with exclusive contacts being made between E3-E2. Immunization with monoclonal antibodies against VEEV E3 provided protection for mice challenged by lethal …

Characterizing The Effects Of Repetitive Head Trauma In Female Soccer Athletes For Prevention Of Mild Traumatic Brain Injury, Diana Otero Svaldi

Open Access Dissertations

As participation in women’s soccer continues to grow and the longevity of female athletes’ careers continues to increase, prevention of mTBI in women’s soccer has become a major concern for female athletes as the long-term risks associated with a history of mTBI are well documented. Among women’s sports, soccer exhibits the highest concussion rates, on par with those of men’s football at the collegiate level. Head impact monitoring technology has revealed that “concussive hits” occurring directly before symptomatic injury are not predictive of mTBI, suggesting that the cumulative effect of repetitive head impacts experienced by collision sport athletes should be …

Improving And Elucidating Factors Regulating Black Walnut (Juglans Nigra L.) Clonal Propagation, Micah E. Stevens

Open Access Dissertations

Black walnut (Juglans nigra L.) is a fine hardwood tree species native to the central hardwood region of the United States. High-quality black walnut timber is highly desirable. Traded in both regional and global markets, it has been used for veneer, and the manufacture of high-end products such as cabinets, furniture, and gunstocks. As a result of its high economic value, black walnut has been commercially cultivated for many years, and breeding programs have generated superior timber genotypes with improved marketable traits. Once elite genotypes were developed, it was quickly recognized that black walnut was recalcitrant to clonal propagation …

The Role Of Seed Attributes In Eastern Gray Squirrel Foraging, Mekala Sundaram

Open Access Dissertations

Seed attributes are important predictors of rodent foraging behaviors. I examined the role of seed attributes in eastern gray squirrel (Sciurus carolinensis) foraging behavior from an evolutionary, economic, ecological and biochemical perspective. From an evolutionary perspective (chapter 2), I found that squirrel foraging behaviors are influenced by a combination of phylogenetically conserved and evolutionarily labile seed traits, which supports a diffuse coevolutionary relationship between hardwood trees and squirrels and provides indirect evidence supporting the Janzen-Connell and handling time hypotheses. From an economic perspective (chapter 3), I found that eastern gray squirrels are homogenous with respect to their preferences for seed …

The Relationship Between Protein And Phosphorus Digestion And Retention In Growing Pigs And Broiler Chickens, Pengcheng Xue

Open Access Dissertations

Xue, Pengcheng. Ph.D., Purdue University, December 2016. The Relationship between Protein and Phosphorus Digestion and Retention in Growing Pigs and Broiler Chickens. Major Professor: Dr. Layi Adeola. The objective of this study was to investigate the relationship between protein and P digestion and retention in growing pigs and broiler chickens. The methodology of determining the digestibility of AA and P and the effect of dietary N and P on the digestion and retention of these two nutrients were investigated.

An experiment was conducted in growing pigs to investigate the additivity of AID or SID of CP and AA in mixed …

The Effects Of Dietary Probiotic Inclusion On Skeletal Health Of Poultry And Its Possible Mechanisms, Feifei Yan

Open Access Dissertations

Probiotics are live microorganisms which may confer health benefits on the host when administered in appropriate amounts. Numerous studies have shown that probiotics improve bone health in humans and rodents with less information available on the skeletal health of avians given probiotics. The objective of this study was to determine the effects of probiotic supplementation on bone health of egg-laying and meat-type chickens. Dietary supplementation of a multi-species based probiotic reduced the percentage of shell-less eggs beginning at 4 wk following treatment and increased tibial and femoral bone mineral density in egg-laying hens at 7 wk post-treatment. Similarly, bone mineralization …

Synthesis And Performance Of Novel Supramolecular Tools For Single-Particle Cryogenic Electron Microscopy And Drug And Gene Delivery, Kyle J. Wright

Open Access Dissertations

High-resolution biomacromolecular structure elucidation is fundamentally important to structure-based drug design and basic research into complex biochemical processes. Cryo-EM is an emerging alternative to XRD and NMR that is complementary in many ways relative to XRD and NMR. Materials approaches to cryo-EM are anticipated to greatly facilitate the cryo-EM process, allowing progress toward a more high-throughput application of cryo-EM to address challenges in structural biology. ^ Various affinity-based approaches inspired by approaches previously introduced for 2D crystallization were developed for facilitation of cryo-EM. A library of affinity lipopolymer constructs were synthesized consisting of lipopolymers of various PEG molecular weights conjugated …

Complex Glycan Utilization Preferences Of Human Gut Bacteria, Yunus Emre Tuncil

Open Access Dissertations

Complex glycans, making up dietary fiber, have gained significance in recent years as they are the main energy source for the colonic microbiota which are physiologically important for the host health. Understanding glycan utilization strategies of the members of this community is essential to maximize beneficial health outcomes obtained from them. In order to investigate how the members of our gut microbiota utilize glycans and activate their respective polysaccharide utilization loci (PULs), we performed a series of time-course assays in which two model organisms, Bacteroides thetaiotamicron (Bt) and B. ovatus (Bo), were individually grown in a medium containing carbohydrates utilized …

Prevalence And Antimicrobial Resistance Patterns Of Salmonella Isolated From Poultry Farms, Carmen G. Velasquez Moreno

Open Access Theses

Antimicrobial agents are used in human medicine to treat infections by inhibiting the growth of bacteria. The same or similar drugs are used in in food-producing animals for therapeutic and sub-therapeutic purposes. Antimicrobial resistant bacteria that develop on farms are a public health risk as these organisms may contribute to treatment failures in infected humans. The main objective of this study was to determine the prevalence of Salmonella isolated from poultry farms in two different seasons to evaluate the effect of recommended biosecurity practices. Specifically, we identified Salmonella serotypes, measured antimicrobial resistance (AMR), and characterized AMR patterns. We hypothesized that …

Billbug (Sphenophorus Spp.) Chemical Ecology And Seasonal Biology In Indiana Turfgrass, Alexandra G. Duffy

Open Access Theses

Billbugs (Coleoptera: Curculionoidea: Sphenophorus) are serious pests of managed turfgrass across North America. Damage symptoms are most visible during stressful periods of the growing season and are commonly confused with disease, drought, or nutrient deficiency. Billbugs are frequently a perennial problem and when misdiagnosed, damage often results in seriously degraded stands of turfgrass that are easily encroached by weeds. Presently, management of billbugs relies heavily on chemical insecticides. Even then, the nationwide assemblage of multiple sympatric billbug species and the cryptic nature of the damaging larval stage makes management of these insects challenging. A better understanding of billbug biology …

Sugarcane Bagasse Hydrolysis Enhancement Using Bsa, Antonio Carlos Freitas Dos Santos

Open Access Theses

Lignocellulose is composed of polysaccharides linked to lignin and other aromatic compounds, making the sugars not readily available to fermentation. This entails that biomass must go through the unit operations of pretreatment and enzyme hydrolysis. Pretreatment opens the structure to allow the enzymes to act on and hydrolyze cellulose and hemicellulose to glucose and/or xylose which in turn are fermented to ethanol. Concomitantly, the enzymes interact with soluble phenols and insoluble solids derived from lignin that inhibit hydrolysis. This leads to high enzyme loadings and higher production costs. Soluble phenols can be eliminated through washing. Insoluble lignin, however, demands another …

Design And Plan Of A Modified Hydroponic Shipping Container For Research, John A. Houtman

Open Access Theses

As the world’s population continues to increase, food production will need to increase in order to meet the predicted rise in food demand. However, with increased pressure on cropland available from environmental effects and urbanization, new innovative methods of crop production need to be researched in order to increase agricultural production with limited land. This research focuses on the design of a single form of urban agriculture that is considered Zfarming and has the potential to produce quality urban agricultural produce through ground-based measures. This project produced detailed step-by-step analysis of the design process, develop variability within the modified hydroponic …

Lower Food Web Dynamics In Lakes Michigan And Huron: Spatial And Temporal Responses To Recent Oligotrophication, Margaret Hutton Stadig

Open Access Theses

Nutrient abatement programs, originally enacted to counter eutrophication have successfully suppressed nutrient loads and relative primary production in marine and freshwater systems. Recently, the additive impacts of invasive filter feeders have further reduced offshore primary production in several aquatic systems throughout the world. It has been hypothesized that the biological activity of these invasive species may sequester nutrients within the nearshore benthic environment, creating steep gradients in primary production between nearshore and offshore habitats. In the Laurentian Great Lakes, past studies of oligotrophication have primarily focused on food web responses in offshore habitats. Organisms at higher trophic levels have been …

A Comparison Of The Efficacy Of Radiant And Immersion Frying Using Hash Brown Patties As A Model Food Matrix, Kaitlin R. Kaczay

Open Access Theses

Radiant frying is an alternative technique to traditional immersion frying. While enjoyed by consumers, immersion fried foods are typically high in fat. Radiant frying uses infrared energy to produce finished products with similar sensory characteristics to traditional frying, but with significantly less fat. This research compared the efficacy of radiant and immersion frying using hash brown patties as a model food matrix by measuring temperature profiles, heat flux profiles, moisture and oil contents, peak shear force, color, mottling, and crust thickness as well as executing semi-trained and untrained sensory evaluations. The FryLess 100K Radiant Fryer was used for all experimentation. …

The Impact Of Tickling Rats On Human-Animal Interactions And Rat Welfare, Megan Renee Lafollette

Open Access Theses

Rats initially fear humans which can lead to negative affect, poor welfare, and difficult handling. Also, modeling and measuring positive affect states in rats can pose an additional challenge. Heterospecific play, or “tickling,” is a handling habituation technique that mimics rat rough-and-tumble play that is being used to study positive affect. It can also be used to reduce fear of human, improve welfare, and elicit a positive affect state. However, current studies implementing the technique in laboratory rats use a wide variety of protocols to achieve differential results. Unlike in laboratory environment, pet store rats experience high levels of novelty …

Evaluation Of A Cool-Season Grass-White Clover Mixture For Low-Nitrogen Input Lawns, Gabriel Adam Macke

Open Access Theses

Turfgrass lawns require supplemental nitrogen (N) to maintain green color and seasonal shoot density. Improper lawn fertilization with excess N or phosphorus has the potential to contaminate both surface and groundwater. Thus, to reduce the reliance on supplemental N fertilization, alternative strategies or novel turf systems like grass-legume mixtures need explored. White clover ( Trifolium repens L.) is a stoloniferous legume that biologically fixes N from the atmosphere and adds N into the soil via mineralization. The objective of this field study was to evaluate the persistence and feasibility of a cool-season grass-clover lawn mixture. A lawn grass mixture with …

Mathematical Analysis Of Feedback Targets Of Bmp Signaling In Drosophila Embryonic Development, Yan Luo

Open Access Theses

Bone morphogenetic proteins (BMPs) drive a range of cellular processes especially in the early stages of embryonic development. This family of proteins acts as one of the most important extracellular signals in development pattern formation across the animal kingdom. Cells in embryos differentiate into different cell types in response to the concentration level of BMP. This complex process is regulated by multiple regulators that serve to tune the signal response.

Extensive experimental and computational research has been performed to analyze BMP regulation in Drosophila, a widely studied model organism, and has advanced our understanding of animal development. Because of …

Residual Effects Of Nitrogen Fertilization On Soil Nitrogen Pools And Corn Growth, Meghan E. Moser

Open Access Theses

Given the dynamic nature of soil nitrogen (N), inorganic N fertilization to corn (Zea mays L.) has potential to alter N pool balance by creating an accumulation or depletion of soil N. Current corn N recommendations in the common corn-soybean rotation of Indiana strive to find the best N rate that maximizes producer profit. Increasing our understanding of soil N will inform producers if they should adjust fertilizer rates for corn to influence maintenance of organic N and Carbon. Our objective was to determine residual N effects from fertilized corn in a corn-soybean rotation by measuring (1) soil N …

Dopamine D1 Receptor Activity In The Basolateral Amygdala Is Important For Mediating Fear, Reward And Safety Discrimination Learning, Ka Ho Ng

Open Access Theses

Post traumatic stress disorder (PTSD) patients frequently show impairment in safety learning (Jovanovic, Kazama, Bachevalier, & Davis, 2012). Since the amygdala is known to be critical for emotional processing(Wassum & Izquierdo, 2015) and dopamine signaling in the amygdala is important for mediating both fear and reward learning, current experiments examined the role of dopamine signaling in the BLA in mediating both safety learning and reward seeking. We manipulated dopamine D1 receptor activity with a D1 receptor agonist (SKF 38393) or D1 receptor antagonist (SCH23390) either systemically or infused directly into the BLA 20 minutes prior to training rats in a …

Modeling Relative Habitat Suitability And Movement Behavior Of Invasive Burmese Pythons In Southern Florida, Holly E. Mutascio

Open Access Theses

Invasive Burmese pythons are established in the Everglades and are altering the ecology of southern Florida. Their distribution in Florida is expanding northward into more urbanized and fragmented habitats. An understanding of the suitability of habitat throughout southern Florida for Burmese pythons and their interaction with Florida’s landscapes through movement behavior is vital for predicting the python’s ability to persist in habitats outside of the Everglades. In this thesis, we use ecological modeling to predict habitat suitability and to investigate personality-dependent dispersal.

First, we used presence-only ecological niche modeling with correction for sampling bias to identify the key landscape variables …

Evaluation Of Thermal Process Lethality In Meat For Non-Pathogenic Escherichia Coli As A Surrogate For Salmonella, Morgan Alyse Redemann

Open Access Theses

Non-typhoidal Salmonella is the leading cause of foodborne illness in the United States, resulting in about 20,000 hospitalizations and nearly 380 deaths annually. The meat processing industry has been especially plagued by Salmonella, from meat-inherent sources and more alarmingly, cross-contamination. For ready-to-eat (RTE) meat products specifically, this can cause significant problems in processing facilities ensuring safe product for consumption, resulting in foodborne illness.

The development of standard lethality compliance guidelines by the United States Department of Agriculture Food Safety and Inspection Service (USDA-FSIS) within Appendix A assists processors in confirming that Salmonella is inactivated in RTE beef and poultry products, …

Cereal Rye Cover Crop Effects On Soil Physical And Chemical Properties In Southeastern Indiana, Joseph D. Rorick

Open Access Theses

Cover crops are growing in popularity in the Midwest, although questions remain about how to include them most effectively in a corn-soybean ( Zea mays L. - Glycine max L.) rotation. This study was conducted to determine the effects of cereal rye ( Secale cereale L.) on soil bulk density and water retention, soil organic carbon, soil nitrogen, and water stable aggregate mean weight diameter after four years of cover crop growth and the effects on soil moisture over a five year period. The study was conducted at the Southeast Purdue Agricultural Center (SEPAC) on silt loam soils. A 14 …

The Impact Of Sleep Disruption On Mouse Physiology, Behavior, And Welfare, Amanda L. Robinson-Junker

Open Access Theses

Laboratory mice are nocturnal, spending most of their daylight hours asleep. But they live in the diurnal world of human investigators and husbandry staff, who primarily work during this rest period. In humans, lack of sleep or sleep that occurs outside the normal circadian sleep period (as in shift work) has adverse effects. These include increased risk of cardiovascular disease, cancer, metabolic disorder, mood disorders, type II diabetes, and obesity. However, it is unknown if mice experience sleep disruption due to these human activities, and, if so, what the adverse effects may be. This is an important question, not only …

Investigations On The Vampire Moth Genus Calyptra Ochsenheimer, Incorporating Taxonomy, Life History, And Bioinformatics (Lepidoptera: Erebidae: Calpinae), Julia L. Snyder

Open Access Theses

The seventeen species and two subspecies described in the genus Calyptra are known to be obligate fruit piercers, with some species being of economic importance. Males within the genus have not only been observed piercing their fruit hosts, but have also been documented to occasionally feed on mammalian blood. The genetic and ecological mechanisms contributing to host preference for either plant or vertebrate hosts in this lineage are unknown. Thus, the focus of this study was to investigate the chemosensory systems between and among Calyptra species exhibiting differential feeding strategies. Before investigating the chemosensory systems within Calyptra, the taxonomy …

Forest Industry Byproducts Improve Soil Quality And Increase Pepper Growth In Three Soils Infested With Phythophthora Blight, Xiaojun Zhao

Open Access Theses

Phytophthora blight is a serious threat to the Midwest vegetable industry, because the oomycete pathogen responsible for this disease, Phytophthora capsici, has a wide host range, can spread quickly in fields, and produces resilient oospores that can survive in soil for years. Phytophthora capsici has become resistant to commonly used fungicides and resistant crop varieties are rare. Amending soil with complex organic substrates has potential to improve soil quality and suppress soil-borne pathogens including P. capsici. Indiana has a significant forest industry with many residual products that could be used as locally available amendments to meet this goal. …

Genomic And Transcriptomic Analysis Of Biofilm Formation In Persistent And Transient L. Monocytogenes, Clara Assisi

Open Access Theses

The Next Generation Sequencing (NGS) has been popularized and aid in the advancement of many fields of science. The other field of science that is being revolutionized is food science and technology, especially food safety. NGS application in food safety, especially the whole genome sequencing analysis (WGS), has been widely used for tracing back the source of outbreaks. The other application of NGS that is also being developed is the analysis of global transcriptomic or RNA-sequencing (RNA-Seq). In this research, we utilize NGS (Ilumina MiSeq Sequencing platform) to perform sequence comparison and identify single nucleotide polymorphisms (SNPs) and observe the …