Biology Commons^™

Procedures For Genetic Modification Of Miscanthus X Giganteus, A Biomass Crop, Anjali Arpan

Theses and Dissertations

Development of genetic improvement procedures for the bioenergy crop, Miscanthus × giganteus (M×g; triploid), are desired for trait improvement. Agrobacterium tumefaciens has been used in other Miscanthus spp. for genetic improvement, but not in M×g, nor have more than a few genes been introduced at a given time. Transformation procedures for M×g were developed; studies included use of A.tumefaciens (strain LBA4404) and A. rhizogenes (strain A4) for introduction of seven genes isolated (by other researchers) from Sorghum bicolor involved in sorgoleone biosynthesis (an allelopathic compound), and selectable marker gene neomycin phosphotransferase II. Procedural development included generation of …

Gene Expression Analysis Revealed The Activation Of Immune Responses During The Postnatal Development Of The Cerebellum In A Mouse Model Of Niemann-Pick Type C, Sierra Elizabeth Melli

Theses and Dissertations

Niemann-Pick Type C (NPC) is a recessive neurodegenerative lysosomal storage disorder that is caused by autosomal recessive mutations. The mutations result in the inactivation of NPC1 and NPC2 proteins. Inactivation of the NPC1 protein results in the accumulation of cholesterol within the endosomal and lysosomal compartments of cells including Cerebellar Purkinje cells. This accumulation of cholesterol leads to symptoms of dementia, neurodegeneration and potential of early childhood death in cases of early onset. In this study, we analyze the gene expression levels using the RNAseq technique in order to determine whether there is a significant difference between the expression of …

An Analysis Of The Effects Of Temperature And Other Environmental Factors On Microorganismal Productivity Within Aquatic Ecosystems Using Long-Term Data From Various Lter And Ilter Sites, Andrew Dorbu

Theses and Dissertations

Global climate change is a phenomenon resulting in more extreme weather patterns and species diversity loss. In this study, I explore the impacts of climate change on regional patterns of microbial productivity. Variation in microbial productivity was explained using temperature, salinity, and dissolved oxygen as predictors in regression models with data from the LTER and iLTER network of sites that ranged from the poles to the equator. I found a positive relationship between temperature and productivity. Antarctica and Arctic sites exhibited the strongest positive relationships supporting prior research demonstrating temperature as one of the driving forces of productivity change in …

The Potential Impact Of Climate Change On The Distributions Of Eleutherodactylus Cystignathoides And E. Planirostris (Anura: Eleutherodactylidae), Rebecca T. Chastain

Theses and Dissertations

Climate change is inducing changes in the distributions of many species, causing range shifts and habitat loss as well as facilitating invasions. It is a broad contributor to global amphibian decline, already causing mass extinctions and extirpations of amphibian populations, a phenomenon which is expected to continue. The understudied direct-developing frog Eleutherodactylus cystignathoides is a notable outlier, having rapidly expanded its distribution in recent years. This is of particular interest given that other eleutherodactylids, such as E. coqui and E. planirostris, have already shown propensity for rapid dispersal and invasion. Originally found in the southernmost tip of …

Effects Of Tributyltin Exposure On 8-Ohdg And Dsdna Expressions, Oxidative And Nitrative Stress In The American Oyster, Crassostrea Virginica, Mohan Kumar Dash

Theses and Dissertations

Environmental pollution increases due to anthropogenic activities. Different types of pollutants and/or chemicals impair growth, reproduction and development in aquatic organisms. Tributyltin (TBT, an organotin compound) is a tremendously toxic substance which widely uses as antifouling paints used in boats, hulls, and ships. The toxic effect of TBT is well documented in teleost species. The American oyster (Crassostrea virginica) is an ideal shellfish species to study on TBT exposure DNA lesion and oxidative/nitrative stress. In this study, the effects of TBT on 8’-hyrodxy-2’-deoxyguanosine (8-OHdG, a molecular marker), dsDNA, dinitrophenyl protein …

The Impacts Of Holocene Climate And Pre-Columbian Humans On Neotropical Andean Forests, Rachel Kathleen Sales

Theses and Dissertations

Humid montane forests in the tropical Andes form hotspots for biodiversity, endemism, and conservation. Threats to the forests from deforestation are amplified by ongoing climate change, which could further reduce available habitat area by about 57 – 80%. These forests are known to have withstood considerable climate change in the past, and an emerging view suggests that they have also been shaped by a long interaction with people. Although climate-driven species range shifts are broadly known, questions remain about how past climate change has affected the species composition of these forests. The interaction of people with forests on the eastern …

The Form And Function Of Cranial Spines In Fishes, Louis Michael Penrod

Theses and Dissertations

Despite the prevalence of fishes that express cranial spines, quantitative investigations into the function of these spines are rare. Function is often assumed with little or no evidence. Commonly, spine-like structures are considered to be used for defense despite spines potentially being used for other purposes. Here, I took a high-level approach to investigate the morphology and potential functions of cranial spines in over 2000 fishes. Identifying the function of cranial spines in fishes not only informs us as to how these fishes interact with conspecifics, with other species, and with their environment, but also may provide advances in human …

Removal Of Arsenic (Iii) And Arsenic (V) From Aqueous Solution Via Common Sunflower Helianthus Annuus By Phytoremediation, Irving A. Vazquez Hurtado

Theses and Dissertations

Phytoremediation provides a cost-effective, non-invasive technique to remove contaminants from the soil and groundwater. Sunflowers are fast growing and have a showed effective at removing various pollutants from soil, including lead and other heavy metals. Health issues related to arsenic are mainly attributed to exposure of arsenite, whereas arsenate is much less toxic. The common sunflower Helianthus annuus was the species used to remove both arsenic (III) and As(V) ions from hydroponics solutions. In the present study sunflower seeds were germinated for a week, placed under the sun for a day and subsequently placed in a nutrient solution to aid …

Metabolic Signatures Of Kin Recognition In The Model Angiosperm Arabidopsis Thaliana, Thiara Siqueira Bento

Theses and Dissertations

Many organisms have evolved to identify and respond to differences in genetic relatedness between conspecifics, allowing them to select between competitive and facilitative strategies to improve fitness. Due to their sessile nature, plants frequently draw from the same pool of nutrients, and the ability to limit competition between closely related conspecifics would be advantageous. Over the last 3 decades, significant evidence has accumulated in multiple species that such ‘kin recognition’ (KR) is indeed commonplace in plants. I propose that if KR has evolved, at least in part, as a plant-plant interaction to regulate nutrient uptake, then nutrients should modulate the …

Functional Facets Of Intergenic Hairpin Structures In Genus Caulobacter, Geetha Saarunya Clarke

Theses and Dissertations

DNA replication, recombination and repairs maintain bacterial genome stability. But these processes may also induce genome rearrangements leading to inter andintra chromosomal structural variations. Genus Caulobacter undergoes extensive genome rearrangements. Genomic studies in bacteria usually focus on the codingregions, but there is important information present in the intergenic DNA spaces inaddition to the regulatory elements involved in transcription. Recently, Ely published a new model for recombination in genus Caulobacter with simultaneousloss and gain of genes resulting from preferential recombination at non- homologous regions flanked by regions of homology. In my dissertation, I observedand catalogued hairpin structures at known sites of …

Defining Molecular And Morphological Phenotypes In Ash1l-Deficient Human Neurons, Foster D. Ritchie

Theses and Dissertations

Autism Spectrum Disorders (ASD) are highly heritable neurodevelopmental disorders characterized by social and verbal impairments as well as repetitive behaviors. Large human genetic studies showed that genes encoding chromatin and transcriptional regulatory proteins are among the most commonly mutated genes in ASD. Absent, Small, or Homeotic 1-like (ASH1L) is a histone methyltransferase that has previously been identified as a major genetic risk factor for ASD. ASH1L di-methylates Histone H3 on Lysine 36 (H3K36me2) and tri-methylates Histone H3 on Lysine 4 (H3K4me3), which mainly coincides with transcriptional activation. ASH1L is a Trithorax protein that is proposed to counteract the activity of …

Cryptic Cryptophytes: The Plasticity In How Cryptophytes Respond To Changes In Resource Availability, Rachel Ann-Marie Schomaker

Theses and Dissertations

Resource variability and availability often drives competition within ecosystems, which can lead to the diversification of organismal niches and physiological capabilities. In aquatic systems, common resources that photosynthetic organisms, such as algae, compete for are light and carbon. Both the spectral characteristics (color) and carbon concentrations of an aquatic system vary with time and space, which means that algae need to be able to respond to changes in resource availability to survive. Using a group of ubiquitous unicellular eukaryotes known as cryptophytes, we investigated both how cryptophytes respond to changes in the available light spectrum at a physiological and genetic …

The Comparative Neuroethology Of Distributed Visual Systems: Visual Neuroanatomy And Visually-Mediated Behaviors Of The Chiton Acanthopleura Granulata And The Bay Scallop Argopecten Irradians, Daniel Ritter Chappell

Theses and Dissertations

Vision is usually thought to be inextricably linked to cephalization; however, certain species of invertebrates deviate from this canonical association by having noncephalized visual systems that are composed of numerous photoreceptive organs distributed across their body paired with centralized, decentralized, or distributed neural architectures. In contrast to cephalized visual systems, we know comparatively little about the visual processing and visually-mediated behaviors of animals with distributed visual systems which are crucial towards understanding how and why these animals see with so many eyes. In this dissertation, we investigate the visual neuroanatomy and visually-mediated behaviors of two different marine molluscs with distributed …

Understanding The Genomic Influence And Virulence Capabilities Of Environmentally Isolated Vibrios, Shannon Elizabeth Pipes

Theses and Dissertations

The genus Vibrio consists of Gram-negative bacteria that possess a curved rod shape and are routinely isolated from estuarine and coastal salt water. Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus are the major three species that contribute to human disease worldwide, and a variety of other Vibrio species contribute to persistent problems in the aquaculture and fishing industries. The CDC estimates that vibrios cause 80,000 cases of disease each year in the United States alone, however, this number is thought to be underestimated, since some disease is only self-limiting, meaning patients may not seek medical treatment and have …

From Gene Expression To Physiology: A Study Of Chronic Thermal Tolerance In The Mytilus Edulis Species Complex, Lindsey Cate Schwartz

Theses and Dissertations

Rising ocean temperatures are a severe and ever-present threat to marine life. With environmental temperature having such a large impact on organismal performance, understanding the mechanisms which contribute to the ability to survive at higher temperatures is a crucial research focus. Significant progress has been made in discovering these mechanisms on the cellular, biochemical, and physiological levels, but is it much less common for those to be examined together. Using the Mytilus edulisspecies complex as a model system, this dissertation takes a closer look at how prolonged exposure to sub-lethal high temperatures impacts marine organisms on multiple levels of …

The Effects Of Ionizing Radiation On Domestic Dogs: Ancestry And Genetic Structure Of Free-Roaming Dog Populations In Chernobyl, Ukraine, Gabriella Jean Spatola

Theses and Dissertations

This thesis is concerned with the effects of ionizing radiation on domestic dogs (Canis lupus familiaris) which were commonly used as laboratory subjects during the era of atomic bomb testing (1950s - 1980s). Early laboratory studies on radiation effects in dogs provided important foundations of knowledge for research that has more recently shifted to natural populations exposed to ionizing radiation from nuclear accidents. A unique group of free-roaming dogs reside in an environment polluted by radioactive contamination deposited during the Chernobyl nuclear disaster of 1986, providing one such opportunity to study the effects of ionizing radiation on dogs …

Size Structure And Intraguild Interactions Between Two Ambystoma Species, Gwyneth Daunton

Theses and Dissertations

Intraguild interactions affect population and community structure through a combination of competition and predation. Changes in size structure influence intraguild interactions by affecting the strength and direction of these species’ interactions. I tested for size-structured intraguild interactions in temporary pond ecosystems between marbled salamanders (Ambystoma opacum) and tiger salamanders (Ambystoma tigrinum) using an outdoor mesocosm experiment. I hypothesized that 1) A. opacum survivorship and growth would be negatively impacted when both species start at a similar size because tiger salamanders grow faster and are more aggressive 2) A. tigrinum will grow slower and have lower survivorship …

The Effects Of Curricular Change On Student Learning And Well-Being In Biomedical And Clinical Education, Rachel Jalaire Tomco Novak

Theses and Dissertations

The implementation of curriculum change, and innovative pedagogical theory, can help educators and administrators in higher education further the learning gains of students in the sciences. But the introduction of new methods of teaching, or curricular restructuring, can be interpreted by students differently, potentially affecting students' emotional states as well as their relationships with peers. To support not only the learning of students, but also their emotional and social well-being, pedagogical and curricular theory should be enacted in ways that take into consideration the full scope of the student experience. In this dissertation, the implementation of curriculum and pedagogical theory, …

Taxonomic And Phylogenetic Diversity Of Pitcher Plant Bogs In Georgia's Coastal Plain, Melanie Flood

Theses and Dissertations

Diversity studies via floristic survey and taxonomic metrics have proven essential for discerning community composition and biodiversity, however, phylogenetic analyses are necessary to reveal underlying evolutionary change and potential community assembly patterns. Pitcher plant bogs are highly diverse, highly understudied habitats that contain numerous listed and at-risk plant and animal species of Georgia.

In this study I investigated the taxonomic and phylogenetic diversity of pitcher plant bogs by asking the following questions:

1) What is the taxonomic diversity of pitcher plant bogs,

2) What is the dispersion of phylogenetic diversity within bog habitats, and

3) Does taxonomic and phylogenetic diversity …

Molecular Characterization Of Antibiotic Resistant Shiga Toxin-Producing Escherichia Coli From Clinical And Food Samples, Khulud Alotaibi

Theses and Dissertations

Antimicrobial resistance (AMR) in foodborne pathogens can be a consequence of using antimicrobial drugs in food-producing animals. The emergence of antimicrobial resistance in foodborne pathogens is of great concern due to adverse patient health outcomes and the possibility of transferring genes encoding AMR to other clinically relevant pathogens. One of these bacteria is Shiga toxin-producing Escherichia coli (STEC), which can cause serious illness in humans for a haemolytic uremic syndrome (HUS). This study characterized and determined the mechanism of antibiotic resistance in 46 Shiga toxin-producing Escherichia coli strains collected by the U.S. Food and Drug Administration from food and clinical …

Design Of A Synthetic Temperature-Activated Epigenetic Biocontainment System, Owen Rivers Page

Theses and Dissertations

The need for an internal control to govern engineered strain survival is becoming apparent when considering the biosafety and ethics within biotechnological research. Using understudied regulatory elements known as RNA thermometers (RNATs) that can modulate protein translation based on temperature changes and a Type II restriction modification system, we posit the creation of a synthetic temperature-activated epigenetic biocontainment system, termed the ‘sentinel switch’. We have mined a wide variety of bacteria from Yersinia pestis to Synechocystis sp. looking for novel RNATs. A complementary synthetic biology approach based on library generation and screening of chimeric RNATs (ChRNATs) was also conducted. RNATs …

Human Otop1 Proton Channel Can Function As A Monomer, Gabriella Abigail Ulloa

Theses and Dissertations

Otopetrins (OTOP) represent a new family of eukaryotic proton channels that do not share structural similarities with other renowned ion channels. Otop1 was initially known for its involvement in vestibular function and its significance for otoconia formation before it was established as a bona fide sour taste receptor. The cryo-EM structures for several Otop channels have been determined and demonstrated Otop1 as a homodimer comprised of two subunits. Each subunit constitutes twelve transmembrane helices that can be further partitioned into two structurally similar six transmembrane domains designated as the N and C domains. Molecular dynamic simulations have also previously shown …

Regulation Of Interferon- Induced Interleukin-8 And Pd-L1 Expression In Ovarian Cancer Cells, Sveta Padmanabhan

Theses and Dissertations

Interferon-γ (IFNγ) is a pleiotropic cytokine that has a crucial role in immune response and tumor immunity. Because of its anti-tumor effects, IFNγ has been used in cancer treatment. However, IFNγ also has tumor-promoting functions that are less well understood. Here, I show that IFNγ induces expression of the pro-inflammatory and pro-angiogenic chemokine interleukin-8 (IL-8, CXCL8) in ovarian cancer (OC) cells. The IFNγ-induced IL-8 expression is dependent on JAK1, STAT1, and p65 NFκB, and is associated with an increased occupancy of K314/ 315 acetylated p65 NFκB and Ser-727 phosphorylated STAT1 at the IL-8 promoter. Neutralization of IL-8 using anti-IL-8 antibody …

Functional Modulation Of The Cav3.1 Calcium Channel By Alternative Splicing At The C-Terminus, Ruizhi Wang

Theses and Dissertations

The CACNA1G gene encodes for Cav3.1, the alpha-1G subunit of a low-voltage-activated T-type calcium channel, which plays crucial roles in cardiac and smooth muscle cells and neurons by influencing the transmembrane potentials and regulating intracellular Ca2+ signaling. Heterozygous missense mutations in the CACNA1G gene cause spinocerebellar ataxia-42 (SCA42), a heterogeneous group of neurodegenerative disorders characterized by brainstem and cerebellum degeneration, and mice that are null for this gene present severe motor coordination defects, abnormal electrical conductance in the heart, aberrant action potentials in the brain, disrupted sleeping patterns, and absence epilepsy. Different splice variants of Cav3.1 have been described, and …

Developmental Validation Of A Bacterial Signature-Based Identification Method Of Forensically Relevant Human Biological Samples, Denise M. Wohlfahrt

Theses and Dissertations

The confirmatory identification of body fluids is one of the most critical steps in criminal investigations, as it provides not only information on the source of the DNA, but it can corroborate evidence, aid in the reconstruction of a crime, and associate evidence with a person of interest. Current serological methods utilize biochemistry and immunology to identify biological evidence; however, these serological tests are mostly presumptive while only testing for one fluid at a time, potentially wasting precious evidence. More recently, forensic investigators have suggested the use of molecular methods such as mRNA, miRNA, or DNA methylation. While each of …

The Role Of Slu7 In Spliceosome Function In Saccharomyces Cerevisiae, Sovira A. Chaudhry

Theses and Dissertations

The removal of introns from pre-messenger RNA via splicing in the nucleus is an essential step in gene expression. In recent decades, significant effort has been made to understand the chemical mechanisms of splicing reactions and the composition of the spliceosome that catalyzes them. Yet very little is known about the exact function of many splicing factors and small proteins within the spliceosome. Slu7, a pre-mRNA splicing factor, is essential during the second catalytic step of splicing because it interacts with several proteins and stabilizes the active site conformation. It has been found that Slu7 is involved in 3' splice …

Chronic Adolescent Stress As A Predictive Factor For The Risk Of Developing Ptsd-Like Symptoms In Adulthood, Grace K. Young

Theses and Dissertations

Post-traumatic stress disorder is a stress and trauma based psychological disorder that is defined by the DSM-IV as an anxiety disorder that affects approximately 7.8% of people in the United States. PTSD is when those who suffer a traumatic event have intense and distressing feelings, emotions, and memories for a prolonged period of time after the event. A prominent feature of PTSD is the impaired ability to properly extinguish a fear response after a dangerous trigger or stressor is no longer present, also known as safety learning. Stressors are threats perceived within the environment that activate a response within the …

Biotic Characteristics Of Managed And Unmanaged Coastal Dunes In The Outer Banks, North Carolina, Andrew E. White

Theses and Dissertations

Under future climate change and sea level rise scenarios, Natural and Nature-Based Features (e.g., dunes) that protect coastal habitat and infrastructure will be exposed to increased wave energy and storm surge. Understanding how these forces will impact coastal dunes is necessary for their continued use as protective features. Coastal dunes develop through feedback between vegetation and sediment deposition, a process complicated by species-specific growth rates and responses to burial. Wave flume studies have tested the effects of dune vegetation on erosion and found multiple plant organs across several functional types to be important for resisting erosion. Although dune building and …

Coupled Structure-Function Responses To Disturbance: High Structural Complexity Resistance Supports Primary Production Resistance, Kerstin M. Niedermaier

Theses and Dissertations

The capacity of forests to resist structural change and retain material legacies–the biotic and abiotic resources that persist through disturbance–is crucial to sustaining ecosystem functioning after disturbance. However, the role of forest structure as both a material legacy and feature supporting carbon (C) cycling stability following disturbance has not been widely investigated. We used a large-scale disturbance manipulation to ask whether LiDAR-derived canopy structures as material legacies drive 3-year responses of NPP to a range of disturbance severity levels. As part of the Forest Resilience Threshold Experiment (FoRTE) in northern Michigan, USA we simulated phloem-disrupting disturbances at a range of …

Advancing Forest Structure-Function Relationships: Linking Above- And Belowground Structure To Soil Respiration, Laura J. Hickey

Theses and Dissertations

Variation in the soil-to-atmosphere C flux, or soil respiration (Rs), is influenced by a suite of biotic and abiotic factors, including soil temperature, soil moisture, and root biomass. However, whether canopy structure is tied to soil respiration through its simultaneous influence over these drivers is not known. We assessed relationships between measures of above- and belowground vegetation density and complexity, and evaluated whether Rs is linked to remotely sensed canopy structure through pathways mediated by established biotic and abiotic mechanisms. Our results revealed that, at stand-scale, canopy rugosity–a measure of complexity–and vegetation area index were coupled to soil respiration through …