Digital Commons Network^™

Entap: Software To Improve The Quality And Functional Annotation Of De Novo Assembled Non Model Eukaryotic Transcriptomes, Alexander Hart

Master's Theses

EnTAP (Eukaryotic Non-Model Transcriptome Annotation Pipeline) was designed to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model Eukaryotes. This software package addresses the fragmentation and related assembly issues that result in inflated transcript estimates and poor annotation rates. Following filters applied through assessment of true expression and frame selection, open-source tools are leveraged to functionally annotate the translated proteins. Downstream features include fast similarity search across three repositories, protein domain assignment, orthologous gene family assessment, and Gene Ontology term assignment. The final annotation integrates across multiple databases and selects an optimal …

Kinetics Of Copper Uptake In Periphyton Under Natural Stream And Wastewater Effluent Exposures, Katelyn Turpin-Nagel

Master's Theses

The aim of the present study was to examine the uptake kinetics of copper to periphyton, a biofilm community of heterotrophic and autotrophic species, under freshwater and wastewater effluent exposure conditions. Copper uptake kinetic experiments were run using a constructed trickle apparatus, where short-term exposures were completed using environmentally relevant total copper concentrations. The differences in periphyton surface bound copper and intracellular uptake kinetics were observed and modeled by examining periphyton copper content, periphyton cellular binding parameters, and metal speciation based on dissolved organic matter (DOM) characteristics. First-order rate kinetics were used to analyze the differences in initial uptake rates …

The Role Of Bmp Signaling In Mediating Stimulatory Effects Of Fgf-Fgfr Signaling On Odontoblast Differentiation In Dental Pulp, Karen Sagomonyants

Master's Theses

Odontoblast differentiation is dependent on multiple signaling molecules, including growth factors stored in the extracellular dentin matrix. Our previous studies have demonstrated that Fibroblast Growth Factor 2 (FGF2) exerted stage-specific effects on odontoblast differentiation in primary dental pulp cultures. FGF2 stimulated differentiation of functional odontoblasts expressing high levels of Dmp1 from early progenitors but inhibited the terminal differentiation of functional odontoblasts to fully differentiated odontoblasts expressing high levels of Dspp. These stimulatory effects involved activation of FGFR and ERK1/2, and increased levels of expression of Bmp2, Runx2, and Osx (components of BMP signaling) suggesting the involvement of …

Development Of An In-Situ Passive Sampling Device For Munitions Compounds And Sulfate, Joseph K Warren

Master's Theses

Passive sampling is a novel method of analyte concentration from the environment that strives to bring greater ease to field sampling regimes than traditional liquid-solid phase extractions (SPE). It is easier to deploy than a Niskin bottle or CTD rosette, and easier to recover than hoisting up dozens of liters of water. Passive sampling also offers the opportunity for wider exploratory studies, as compounds can be selectively extracted back in lab, rather than having to select a particular phase SPE and follow phase-specific elution methods. In this study, Ethylene Vinyl Acetate copolymer (EVA) was used as a marine sorption and …

Role Of Nrf2 In The Regulation Of Ppar Expression In Mice, Fabio Carvalho

Master's Theses

The peroxisome-proliferator activated receptors (Ppars) are a family of ligand-dependent nuclear receptors, which promote transcriptional activation of target genes. Pparα regulates genes involved in hepatic fatty acid transport, uptake and metabolism. Several of these target genes are upregulated by hypolipidemic fibrate-type drugs. Clofibrate (CFB) is a prototype for this class, and a well-known Pparα activator. CFB treatment also prevents liver injury by acetaminophen (APAP) in a Pparα-dependent manner. Similarly, nuclear factor erythroid 2-related factor 2 (Nrf2) is an important genetic determinant of susceptibility to APAP hepatotoxicity. The purpose of this study was to analyze the potential interaction between Pparα and …

Force-System Generated By Rigid Archwires With V-Bends: A 3-D Analysis Of Varying Activations, Meenakshi Vishwanath

Master's Theses

No abstract provided.

Regulation Of Proliferation, Apoptosis, And Metastasis In Prostate Cancer Cells By Dax-1 (Nr0b1)- An Androgen-Induced Orphan Nuclear Receptor, Roxxana Valeria Beltran Valencia

Master's Theses

DAX-1 (Dosage-sensitive sex reversal, adrenal hypoplasia congenita, critical region on the X-chromosome, gene 1) is an unusual member of the Nuclear Hormone Receptor superfamily that has the ability to interact with other Nuclear Receptors (NRs) and transcriptional co-repressors and co-activators. While DAX-1 plays an important role in adrenal and gonadal development, recent studies have elucidated the role DAX-1 plays as a transcriptional repressor and its influence on the progression of different types of cancers. The primary aim of this thesis research project is to investigate the role of non-aromatizable androgens in inducing DAX-1 expression and to determine how DAX-1 influences …

Rank Aggregation Of Feature Scoring Methods For Unsupervised Learning, Tara N. Yankee

Master's Theses

The ability to collect and store large amounts of data is transforming data-driven discovery; recent technological advances in biology allow systematic data production and storage at a previously unattainable scale. It is common for biological Big Data to have an order of magnitude or more features than samples. Feature scoring with selection is therefore an essential pre-processing step to finding meaningful clusters in these data. Many feature scoring algorithms have been proposed; they are based on dramatically different ideas about what constitutes a “good” or “important” feature. Motivated by studies in data classification, we use a rank aggregation (RANKAGG) method …

Impacts Of De-Icing Salt Contamination Of Groundwater In A Shallow Urban Aquifer, Lukas Mcnaboe

Master's Theses

No abstract provided.

Conformation Of Transmembrane Segments Of A Protein By A Coarse Grain Model, Sunita Subedi Paudel

Master's Theses

The human voltage-gated proton channels (hH_V1) are critical in many physiological functions and control proton conduction in the cell. This process is governed by the cooperative response of different transmembrane segments of the protein. It is believed that the two subunits of the C-terminal dimer provide independent proton channel pathways through the membrane where the conformations of both monomers and dimer are key for selective proton transport. Conformational response of these transmembrane segments of the protein hH_V1 is studied by a coarse-grained model as a function of temperature where structural detail of a residue is ignored …

Exploitation Of Land And Labor In Appalachia: The Manipulation Of Men In Ann Pancake's Strange As This Weather Has Been, Britani W. Baker

Master's Theses

Ecofeminism is traditionally interested in the relationship between patriarchal domination of women and nature. Ann Pancake’s novel Strange As this Weather Has Been critiques the way the coal mining industry has affected the Appalachian people and land. The novel reflects natural ecofeminism, which views the connection between women and nature in essentialist terms. This outdated mode of ecofeminism leads to a reinforcement of gender stereotypes and a misrepresentation of the relationship between gender, nature, and culture. This study of Pancake’s novel employs a material ecofeminist approach to both critique and develop the novel’s gender politics. Material ecofeminism, even as it …

Sedimentary Characteristics And Nutrient Sequestration Of Embanked Floodplains Along The Lower Mississippi River, Mississippi And Louisiana, R M Malitha Rathnayake

Master's Theses

The Mississippi River Basin is the largest river basin in North America and the third largest river basin in the world. Most of the corn, soybeans, wheat, cattle, and hogs harvested in the United States come from the Mississippi River Basin and about 58% of the entire drainage basin is croplands. Runoff from these lands carries sediments and nutrients, and the Mississippi River transports these downstream and ultimately deposits them in the Gulf of Mexico. The northern Gulf of Mexico is one of largest human-caused hypoxic zones in the world. Hypoxia is the phenomena where the dissolved oxygen level decreases …

Effects Of A Function-Based Peer Management Intervention With Middle-School Students With Adhd, Kate A. Helbig

Master's Theses

Attention Deficit/Hyperactivity Disorder (ADHD) is characterized by impairment in functioning due to inattention, hyperactivity, or impulsivity, as well as difficulties in school with social rejection and academic underachievement (American Psychiatric Association, 2013). The purpose of this study was to investigate the effectiveness of a peer-mediated non-contingent reinforcement (NCR) intervention informed by functional assessment data to decrease disruptive behavior for students with a special education classification of OHI-ADHD. Participants included three student dyads in a middle school setting located in the Southeastern United States. An A/B/A/B withdrawal design was used to evaluate the effectiveness of this intervention. The primary dependent variables …

Effects Of Wave Action On The Structure Of Fish Assemblages Across An Exposure Gradient, Lauren Liddon

Master's Theses

Disturbance affects the function and diversity of ecosystems. Increased wave exposure to salt marsh can disturb sediments and cause a loss of habitat. The purpose of this study was to explore the effects of increased wave exposure on diversity, abundance, and functional ecology of estuarine fishes. If increased wave exposure is acting as a disturbance to these habitats, ecological theory (Intermediate Disturbance Hypothesis) predicts that diversity will peak at intermediate frequencies and intensities of disturbance. Fish were sampled from 10 sites monthly for 6 years. The sites were assigned to different exposure categories (Open, Intermediate, and Sheltered) using an exposure …

Solitary And Social Object Play In The Bottlenose Dolphin (Tursiops Truncatus), Briana M. Cappiello

Master's Theses

Many comparative studies have focused on the emergence of solitary and social play in early development. However, few consider observer and parallel forms of solitary play. In this study, use of video analysis revealed that there is a significant difference between the frequency of solitary, observer, parallel, and social object play states, in calf, juvenile, subadult, and adult bottlenose dolphins (Tursiops truncatus). While juveniles engaged in solitary play significantly more than any other age group, both juveniles and calves engaged in observer and social play significantly more than adults and subadults. Within their own age group, calves, juveniles, …

Environmentally-Driven Variation In The Population Dynamics Of Gulf Menhaden (Brevoortia Patronus), Grant D. Adams

Master's Theses

Gulf Menhaden (Brevoortia patronus) is an abundant forage fish distributed throughout the Northern Gulf of Mexico (NGOM). Gulf Menhaden support the second largest fishery, by weight, in the United States and represent a key linkage between upper and lower trophic levels. Variation in the population dynamics can, therefore, pose consequences for the ecology and economy in the NGOM. Here we aim to understand variation in the individual and population dynamics of Gulf Menhaden throughout ontogeny and how such variation relates to environmental processes. We utilized a suite of fishery-dependent and –independent, remote sensing, modeled, and in situ data …

Biodiversity And Phenology Of The Epibenthic Macroinvertebrate Fauna In A First Order Mississippi Stream, Jamaal Bankhead

Master's Theses

I used Hester-Dendy multiplate samplers and stick and leaf samples to collect the aquatic insects of Granny Creek, a first-order perennial stream in southern Mississippi, on twelve sampling dates from March 2014 to June 2015. The dominant insect/invertebrate group in Granny Creek was the dipteran family Chironomidae. Forty-two distinct taxa of chironomid larvae were collected over the duration of my study. Two of the dominant chironomid subfamilies in my samples, the Orthocladiinae and the Chironominae, displayed a phenological pattern in which the Orthocladiinae were more prevalent, both in terms of number of species and in abundance of individuals, in the …

Black And Blue: Competing Social Constructions Of Police On Instagram And Twitter, Mary Frances Thornhill

Master's Theses

Mass media outlets newspapers and television were traditionally where individuals gathered their news information; however, with the growth of new media platforms like Twitter, Facebook, and Instagram, individuals are now co-producers of the content that is seen by the public. Previous research indicated that media-generated images of the police influence public perception and that new media outlets are becoming increasingly influential, particularly in regards to social and political conflicts. This means that research on the role of new media outlets in socially constructing reality is essential, though not much of this research has yet been completed. This current analysis fills …

Evidence Of Multidecadal Recruitment In The Ocean Quahog, Arctica Islandica In The Western Atlantic Ocean, Sara M. Pace

Master's Theses

Ocean quahogs (Arctica islandica) are the longest-lived, non-colonial animals known today, with a maximum life span exceeding 500 years. Limited information is available regarding recruitment, making the sustainable management of this valuable fishery a challenge. The objective of this research was to describe the age structure and growth rates for four populations of ocean quahogs from the mid-Atlantic stock to evaluate long-term recruitment trends. Clams were sectioned for age estimation to develop population age frequencies. Initial colonization began approximately 175-250 years ago depending upon site. All sites experienced an increase in recruitment beginning in the late 1800’s to …

Eignefunctions For Partial Differential Equations On Two-Dimensional Domains With Piecewise Constant Coefficients, Abdullah Muheel Momit Aurko

Master's Theses

In this thesis, we develop a highly accurate and efficient algorithm for computing the solution of a partial differential equation defined on a two-dimensional domain with discontinuous coefficients. An example of such a problem is for modeling the diffusion of heat energy in two space dimensions, in the case where the spatial domain represents a medium consisting of two different but homogeneous materials, with periodic boundary conditions.

Since diffusivity changes based on the material, it will be represented using a piecewise constant function, and this results in the formation of a complicated mathematical model. Such a model is impossible to …

The Differential Expression Of Gene Cohorts Over The Course Of Development In Type I And Type Ii Layer V Pyramidal Neurons Of The Mouse Medial Prefrontal And Primary Somatosensory Cortex, Ryan Shaun Pevey

Master's Theses

Two of the most challenging problems in neuroscience may be the characterization of different neuron types and determining the various decision points over the course of development that defines those different cell types. Part of the problem is that for the clear majority of neuron types, no single gene so far has been shown to act as a type marker. Instead it seems that signatures involving multiple genes are necessary to define each type. The identity of the genes in these signatures remains an important gap in our knowledge. However, recent developments in bioinformatics have produced population level transcript sequencing …

How Did We Get Here? An Inquiry Into Pop Culture, Pop Culture Icons, And America's Support Of The Degradation Of Humanity Through Mass Media Consumption, Thomas Steele

Master's Theses

This thesis focuses on the contemporary human condition associated with the consumption of current entertainment media. Sampling on modes of thought from anthropological, biological, psychological, sociological, and biographical points of view I sought to define what it means to be uniquely human. Furthermore, I sought to compare and contrast contemporary human interactions as described through research studies associated with tabloid news sources, and the entertainment industry. The results of this study were then articulated through four works of art that visually describe that which was found amongst a variety of resources. They describe the rise and fall of the careers …

Investigation Of Ammonia And Nitrate Removal From Municipal Wastewater Using Biowish, Emily Holland

Master's Theses

This research entails investigation of ammonia, nitrate, and nitrite removal from wastewater using a proprietary blend of bacteria known as BiOWiSH^TM. The degradation rates of ammonia, nitrate, and nitrite for Aqua were determined using wastewater at the San Luis Obispo Water Resource Recovery Facility (SLO WRRF). Laboratory and field experiments were conducted to test how Aqua compared with natural bacteria for removal of nitrogen compounds. Preliminary data suggested that Aqua performed nitrate removal best in SLO WRRF wastewater at the secondary clarifier. Aqua could perform anoxic and aerobic denitrification in secondary clarifier wastewater. In mineral media, Aqua removed …

Removal Of Nitrates From Stormwater Using Nanoclays, Rubia Siddiqi

Master's Theses

Creeks and rivers are often polluted as a result of stormwater runoff that carries various contaminants in to open water bodies, causing adverse environmental and health effects. Low impact development (LID) techniques are currently employed to treat this runoff prior to discharge. Nitrate, however, is not consistently removed by these LID techniques. This study analyzed the ability of several nanoclays to remove nitrate in runoff and determined the feasibility of using them as a soil supplement for LID implementation. Six different nanoclays and HCl-treated clays were compared (pre-modified trimethyl stearyl ammonium nanoclay, pre-modified dimethyl dialkyl amine nanoclay, unmodified hydrophilic bentonite, …

Investigating The Potential Of Plant-Derived Antimicrobials And Probiotic Bacteria For Improving The Microbiological Safety Of Dry Pet Food, Chi-Hung Chen

Master's Theses

No abstract provided.

Comparison Of White Spot Lesions Among Clear Aligners, Self-Ligating Brackets And Conventional Brackets - A Randomized Controlled Clinical Trial, Hussin Alshatti

Master's Theses

No abstract provided.

Force And Fatigue Development Following Electrical Stimulation: The Effect Of Frequency And Fiber Type, Maria Vromans

Master's Theses

Functional electrical stimulation (FES) has been used broadly during rehabilitation and sport injuries to expedite tissue and muscle recovery. More recently, attention has been given to the use of electrical stimulation at the cellular level for muscle regeneration. One of the challenges, however, is understanding the optimal FES characteristics to stimulate a muscle without causing fatigue or adverse injury to the muscle. The purpose of this research is to evaluate the effect of different FES frequencies (10, 35, and 50Hz) on the onset of skeletal muscle fatigue, defined by a drop in muscle force. Further, to evaluate the electrical activity …

Advantages And Limitations Of Different Resolution Force Fields To Study Membrane Active Peptides, Michael Ward

Master's Theses

No abstract provided.

Using Stable Isotope Analysis To Infer Breeding Latitude And Migratory Timing Of Juvenile Pacific-Slope Flycatchers (Empidonax Difficilis), Emily Bailey Moffitt

Master's Theses

Effective conservation of migratory species is hindered by a lack of knowledge of population links between breeding, wintering and stopover habitats. The Pacific-slope flycatcher (Empidonax difficilis) is one of the many Neotropical migratory songbirds whose populations are steadily declining throughout western North America. This research contributed to the assessment of connectivity in this species by inferring relative breeding origins and habitat selection of juvenile birds that migrate along the Pacific Flyway to the South San Francisco Bay Area in the fall. Feather data collected from July 20 to October 12, 2014 were analyzed for three stable isotopes (δ2H, δ13C, δ15N). …

Temporal And Spatial Impacts Of Water Control Structures On The Benthic Infaunal Community Of A Tidally Restricted Wetland In Elkhorn Slough, Ca, Christine Marie Mann

Master's Theses

North Azevedo Pond in Elkhorn Slough, CA is a partially tidally restricted wetland that underwent an experimental ponding manipulation which increased inundation and tidal mixing within the system. This wetland has two spatially significant infaunal microsystems, south and north. Benthic cores taken before and after the manipulation showed that both the south and north infaunal communities remained dominated by the same major taxa, respectively. Both systems, however, experienced species shifts following the ponding manipulation. In the South, the non-native bivalve, Gemma gemma, declined from an average of 19,103 to 385 individuals (m2)-1 whereas the native clam, Nutricola tantilla, increased from …