Biology Commons^™

Volume 08, Meghan Enzinna, Casey Dawn Gailey, Raven Collins, Chiara Enriquez, Amelia Mcconnell, Alexander Morton, Emma Beckett, Leah G. Parr, Briana Adhikusuma, Taylor Embrey, Rowan Davis, Danielle Sisson, Bianca Cherry, Melissa Cacho, Chloe Woodward, Catherine Rollins, Carson Reeher, Landon Cooper, Haley Vasquez, Marlisha Stewart, Eric Whitehead, Sabrina Walker, James Bates

Incite: The Journal of Undergraduate Scholarship

Introduction from Interim Dean Dr. Jennifer Apperson

Indigenous Peoples and the Modern Era by Meghan Enzinna

"Who Says": How Selena Gomez and the Scene Attempt to Subvert the Popular Standards of Beauty by Casey Dawn Gailey

Art by Raven Collins

Meltdown on Social Media: Amy's Baking Company Meets Kitchen Nightmares by Nathena Haddrill

Art by Chiara Enriquez

Design by Amelia Mcconnell

Worth More Than a Thousand Words: A Visual Rhetorical Discussion of Virtual Reality by Examining "Clouds Over Sidra" by Alexander Morton

Design by Emma Beckett

The Sonata: An Analysis of Piano Sonata No. 14 in C Minor, K. …

Is Metabolism Goal-Directed? Investigating The Validity Of Modeling Biological Systems With Cybernetic Control Via Omic Data, Frank T. Devilbiss

Open Access Dissertations

Cybernetic models are uniquely juxtaposed to other metabolic modeling frameworks in that they describe the time-dependent regulation of cellular reactions in terms of dynamic "metabolic goals." This approach contrasts starkly with purely mechanistic descriptions of metabolic regulation which seek to explain metabolic processes in high resolution — a clearly daunting undertaking. Over a span of three decades, cybernetic models have been used to predict metabolic phenomena ranging from resource consumption in mixed-substrate environments to intracellular reaction fluxes of intricate metabolic networks. While the cybernetic approach has been validated in its utility for the prediction of metabolic phenomena, its central feature, …

Judging Adaptive Management Practices Of U.S. Agencies, Robert L. Fischman, J. B. Ruhl

Articles by Maurer Faculty

All U.S. federal agencies administering environmental laws purport to practice adaptive management (AM), but little is known about how they actually implement this conservation tool. A gap between the theory and practice of AM is revealed in judicial decisions reviewing agency adaptive management plans. We analyzed all U.S. federal court opinions published through 1 January 2015 to identify the agency AM practices courts found most deficient. The shortcomings included lack of clear objectives and processes, monitoring thresholds, and defined actions triggered by thresholds. This trio of agency shortcuts around critical, iterative steps characterizes what we call AM-lite. Passive AM differs …

Case-Oriented Pathways Analysis In Pancreatic Adenocarcinoma Using Data From A Sleeping Beauty Transposon Mutagenesis Screen, Yen Yi Ho, Timothy K. Starr, Rebecca S. Larue, David A. Largaespada

Faculty Publications

Background: Mutation studies of pancreatic ductal adenocarcinoma (PDA) have revealed complicated heterogeneous genomic landscapes of the disease. These studies cataloged a number of genes mutated at high frequencies, but also report a very large number of genes mutated in lower percentages of tumors. Taking advantage of a well-established forward genetic screening technique, with the Sleeping Beauty (SB) transposon, several studies produced PDA and discovered a number of common insertion sites (CIS) and associated genes that are recurrently mutated at high frequencies. As with human mutation studies, a very large number of genes were found to be altered by transposon insertion …

Characterization Of Soundscapes In Shallow Water Habitats Of The Florida Keys (Usa) And Their Influence On The Settlement Of Larval Fish And Invertebrates, John R. Butler

Biological Sciences Theses & Dissertations

In recent decades, changes in climate and water quality in Florida Bay and the Florida Keys (FL, USA) caused expansive cyanobacteria blooms that in turn precipitated massive sponge die-offs that drastically altered sponge-dominated hard-bottom communities in south-central Florida Bay. This area served as a model system to explore the effect of ecosystem change and habitat restoration on underwater soundscapes and larval recruitment. I had four main objectives: (1) characterize the underwater soundscapes of three near-shore, benthic habitats: mangrove islands, seagrass meadows, and hard-bottom (Chapter 2); (2) quantify larval settlement within healthy, degraded, and restored hard-bottom areas to test whether habitat …

Naturalization Of Salt Marsh Restoration Sites In The Elizabeth River, Virginia, Assessed By Feeding Activity And Trophic Level Of Mummichogs (Fundulus Heteroclitus), Moriah Anne Good

Biological Sciences Theses & Dissertations

Recent efforts to mitigate environmental issues within the Southern Branch of the Elizabeth River, Virginia, designated a “Region of Concern” by the Chesapeake Bay Program, include several salt marsh restorations. By examining gut contents and stable isotopes values (δ13C and δ15N) from mummichogs (Fundulus heteroclitus), the functional equivalency of restored salt marshes compared to natural marshes was measured. In July 2013 I collected mummichogs from three restored and three reference salt marshes in the Southern Branch. Fish were collected for gut content analysis and were analyzed for stable isotopes (δ13C and δ15N).

I removed gut contents from 16 fish per …

Xenoestrogens From Household Plastics Bind Estrogen Receptors And Affect Cell Proliferation, Susan G. Hurley, Brett R. Lackey, Patricia L. Tate, Sandra L. Gray

Journal of the South Carolina Academy of Science

Xenoestrogens are “foreign” chemicals or compounds that interact with estrogen receptors as either agonists or antagonists to interfere with endocrine system function. Xenoestrogens include phytoestrogens, pesticides, industrial by- products and synthetic estrogens. In this study, consumer plasticware, including baby bottles and food storage containers, were found to release xenoestrogenic compounds that bound to ERα and ERβ and affected cell proliferation.

Mechanisms Of Methane Transport Through Populus Trichocarpa, Ellynne Marie Kutschera, M. A. K. Khalil, Andrew Rice, Todd Rosenstiel

Physics Faculty Publications and Presentations

Although the dynamics of methane (CH4) emission from croplands and wetlands have been fairly well investigated, the contribution of trees to global CH4 emission and the mechanisms of tree transport are relatively unknown. CH4 emissions from the common wetland tree species Populus trichocarpa (black cottonwood) native to the Pacific Northwest were measured under hydroponic conditions in order to separate plant transport mechanisms from the influence of soil processes. Roots were exposed to CH4 enriched water and canopy emissions of CH4 were measured. The average flux for 34 trials (at temperatures ranging from 17 to 25 °C) was 2.8 ± 2.2 …

Predicting Dissolved Lignin Phenol Concentrations In The Coastal Ocean From Chromophoric Dissolved Organic Matter (Cdom) Absorption Coefficients, Cédric G. Fichot, Ronald Benner, Karl Kaiser, Yuan Shen, Rainer M. W. Amon, Hiroshi Ogawa, Chua-Jung Lu

Faculty Publications

Dissolved lignin is a well-established biomarker of terrigenous dissolved organic matter (DOM) in the ocean, and a chromophoric component of DOM. Although evidence suggests there is a strong linkage between lignin concentrations and chromophoric dissolved organic matter (CDOM) absorption coefficients in coastal waters, the characteristics of this linkage and the existence of a relationship that is applicable across coastal oceans remain unclear. Here, 421 paired measurements of dissolved lignin concentrations (sum of nine lignin phenols) and CDOM absorption coefficients [ag(λ)] were used to examine their relationship along the river-ocean continuum (0–37 salinity) and across contrasting coastal oceans (sub-tropical, temperate, high-latitude). …

Rab8 Directs Furrow Ingression And Membrane Addition During Epithelial Formation In Drosophila Melanogaster, Lauren M. Mavor, Hui Miao, Zhongyuan Zuo, Ryan M. Holly, Yi Xie, Dinah Loerke, J Todd Blankenship

Biological Sciences: Faculty Scholarship

One of the most fundamental changes in cell morphology is the ingression of a plasma membrane furrow. The Drosophila embryo undergoes several cycles of rapid furrow ingression during early development that culminate in the formation of an epithelial sheet. Previous studies have demonstrated the requirement for intracellular trafficking pathways in furrow ingression; however, the pathways that link compartmental behaviors with cortical furrow ingression events are unclear. Here, we show that Rab8 has striking dynamic behaviors in vivo. As furrows ingress, cytoplasmic Rab8 puncta are depleted and Rab8 accumulates at the plasma membrane in a location that coincides with known regions …

Effects Of A Pyrrole-Based, Microtubule-Depolymerizing Compound On Raw 264.7 Macrophages, John A. Ciemnieckia, Clarke P. Lewis, John T. Gupton, Krista J. Stenger

Biology Faculty Publications

RAW 264.7 murine macrophages were exposed to the pyrrole-based compound 3,5-Dibromo-4-(3,4-dimethoxyphenyl)-1H-pyrrole-2-carboxylic acid ethyl ester (JG-03-14), which is a known microtubule depolymerizing agent with antitumor activity [1,2,3]. In this study exposure to JG-03-14 reduced the production of pro-inflammatory molecules by macrophages activated with lipopolysaccharide (LPS). Treatment with the pyrrole-based compound decreased the concentration of tumor necrosis factor-α (TNF-α) and nitric oxide (NO) released from the macrophages. Exposure to JG-03-14 also decreased TNF-α mRNA expression levels and the protein expression levels of inducible nitric oxide synthase (iNOS), the enzyme responsible for NO production in the activated macrophages. Furthermore, JG-03-14 treatment significantly changed …

Ex-Situ Conservation Programs: Worthwhile?, Nicolette Sliwa, Aaron Sieve

Biology: Student Scholarship & Creative Works

The effectiveness of conservation programs was researched, specifically within zoos, and their attempts to repopulate areas with captive-born individuals of endangered species. There are major biological and economic concerns with these programs focused on, including potential genetic adaptation to captivity, effects of inbreeding, and if this is a truly worthwhile use of funds to restore a species. Looking at the black-footed ferret, the whooping crane, and other supposed successful captive-breeding programs, it is explored whether reintroduced individuals thrive in their new habitats sufficiently enough to contribute to the restoration of the species, and more broadly, their ecosystems.

A Revision Of Megalocraerus Lewis, 1902 (Coleoptera, Histeridae: Exosternini), Michael S. Caterino, Alexey K. Tishechkin

Publications

The formely monotypic Neotropical genus Megalocraerus Lewis is revised to include five species, known from southeastern Brazil to Costa Rica: M. rubricatus Lewis, M. mandibularis sp. n., M. chico sp. n., M. madrededios sp. n., and M. tiputini sp. n. We describe the species, map their distributions, and provide a key for their identification. Their subcylindrical body form and emarginate mesosternum have previously hindered placement to tribe, although their curent assignment to Exosternini now appears well supported by morphological evidence. Nothing is known of the natural history of the species.

Spatial Distribution Of Earthworms In An East Texas Forest Ecosystem, Melissa A. Bozarth, Kenneth W. Farrish, George A. Damoff, James Van Kley, J. Leon Young

Faculty Publications

Earthworms were collected and identified in different ecological habitats of the Stephen F. Austin Experimental Forest (SFAEF) in the Piney Woods Ecoregion (PWE) of Texas. Earthworm spatial distribution data were collected over four distinct ecological habitats with a range of soil conditions and vegetative cover. A total of 128 sampling plots were surveyed in two different, broadly defined locations (mesic slope = 68 plots, dry-mesic upland = 60 plots). Using multivariate classification/ordination (TWINSPAN) and detrended correspondence analysis (DCA) of overstory vegetation data, these two locations were further divided into four distinct habitats: dry-mesic mixed upland, transitional zone, mesic slope and …

Dentine Oxygn Isotopes (Δ18o) As A Proxy For Odontocete Distributions And Movements., Cory J.D. Matthews, Fred J. Longstaffe, Steven H. Fergispm

Earth Sciences Publications

Spatial variation in marine oxygen isotope ratios ( δ¹⁸O) resulting from differential evaporation rates and precipitation inputs is potentially useful for characterizing marine mammal distributions and tracking movements across δ¹⁸O gradients. Dentine hydroxyapatite contains carbonate and phosphate that precipitate in oxygen isotopic equilibrium with body water, which in odontocetes closely tracks the isotopic composition of ambient water. To test whether dentine oxygen isotope composition reliably records that of ambient water and can therefore serve as a proxy for odontocete distribution and movement patterns, we measured δ¹⁸O values of dentine structural carbonate (δ^{18 …}

Unraveling The Consequences Of The Terminal Pleistocene Megafauna Extinction On Mammal Community Assembly, Felisa A. Smith, Catalina P. Tomé, Emma A. Elliott Smith, S. Kathleen Lyons, Seth D. Newsome, Thomas W. Stafford

School of Biological Sciences: Faculty Publications

Recent studies connecting the decline of large predators and consumers with the disintegration of ecosystems often overlook that this natural experiment already occurred. As recently as 14 ka, tens of millions of large-bodied mammals were widespread across the American continents. Within 1000 yr of the arrival of humans, ∼80% were extinct including all > 600 kg. While the cause of the late Pleistocene (LP) extinction remains contentious, largely overlooked are the ecological consequences of the loss of millions of large-bodied animals. Here, we examine the influence of the LP extinction on a local mammal community. Our study site is Hall’s Cave …

Effects Of Nutrient Supplementation On Host-Pathogen Dynamics Of The Amphibian Chytrid Fungus: A Community Approach, Julia C. Buck, Jason R. Rohr, Andrew R. Blaustein

Integrative Biology Faculty and Staff Publications

1. Anthropogenic stressors may influence hosts and their pathogens directly or may alter host–pathogen dynamics indirectly through interactions with other species. For example, in aquatic ecosystems, eutrophication may be associated with increased or decreased disease risk. Conversely, pathogens can influence community structure and function and are increasingly recognised as important members of the ecological communities in which they exist.
2. In outdoor mesocosms, we experimentally manipulated nutrients (nitrogen and phosphorus) and the presence of a fungal pathogen, Batrachochytrium dendrobatidis (Bd), and examined the effects on Bd abundance on larval amphibian hosts (Pseudacris regilla: Hylidae), amphibian traits and community dynamics. We …

To Jump Or Not To Jump: Mule Deer (Odocoileus Hemionus) And White-Tailed Deer (Odocoileus Virginianus) Crossing Decisions, Emily N. Burkholder

Undergraduate Theses, Professional Papers, and Capstone Artifacts

There have been recent efforts to enhance ungulate movement through modified fencing structures. Ungulates such as mule deer (Odocoileus hemionus) and white-tailed deer (Odocoileus virginianus) typically negotiate fences by either jumping over fencing or going under. Here we examine crossing success and crossing decisions of mule deer and white-tailed deer and determine factors that influence crossing success and the impending decision to jump over or crawl underneath fencing. Using a BACI (Before-After-Control-Impact) design, we deployed remote cameras along fence lines in three study areas; Canadian Forces Base (CFB) Suffield and OneFour research center in Southeastern Alberta, …

Assessing Accuracies And Improving Efficiency For Segmentation-Based Rna Secondary Structure Prediction Methods, Gerardo A. Cardenas

Open Access Theses & Dissertations

RNA secondary structure prediction has become an important area of interest in biology and medicine because it helps in understanding the mechanisms of many biological processes such as gene regulation and viral replication, and in designing RNA-based therapies to treat various diseases such as cancers and AIDS. Different thermodynamics-based computational algorithms for RNA structure prediction exist, and have been used to help understand the disease mechanisms and design treatments. However, most of these computational tools that can predict complex pseudoknot structures have a sequence length limitation of few hundred nucleotide bases due to their high demands of computer resources. Yet, …

Modeled Inflow Validation & Nutrient Loading Estimation In Two Subwatersheds Of The Lower Laguna Madre, Hudson R. Deyoe, Warren Pulich, Nelun Fernando

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

University of Texas Rio Grande Valley will characterize nutrient loading rates into the Lower Laguna Madre for subwatersheds by monitoring stream flow and water quality (particularly total nitrogen and phosphorus). This information will be used to evaluate Texas Rainfall-Runoff model performance in estimating ungaged inflows and to establish a relationship between ungaged inflows and nutrient loading regimes to the Lower Laguna Madre. View on Map

Biolabeling Through The Use Of Water-Soluble Colloidal Quantum Dots, Cody Stombaugh

Honors Projects

Nanomaterials continues to be a growing field of study due to their wide range of potential applications. Quantum dots are artificially synthesized crystalline clusters of atoms able to confine electron motion as a result of their incredibly small size. Recently, medical applications of nanomaterials have expanded greatly. Quantum dots are ideal for biolabeling due to their rather narrow photoluminescence emission peaks. By synthesizing quantum dots of a specific diameter, it is possible to predetermine the peak photoluminescence wavelength of a sample. Through ligand exchange and immunoconjugation of the quantum dots with proteins, it is possible to use the quantum dots …

Development Of A Dreissena Bioassay To Assess The Toxicity Of Contaminants Across Two Life-History Stages, Caroline Joyce Addis

Wayne State University Theses

Dreissenid mussels (Dreissena polymorpha and D. bugensis) have rapidly become widespread and ubiquitous in North America since their introduction into the Great Lakes in the 1980s. The resulting environmental and economic impacts of their invasion have been extensive, negatively affecting biodiversity and costing millions of dollars in control efforts and damage to power generation and water treatment facilities. Although dreissenids are often associated with negative impacts, they may present a practical tool for toxicology studies. The typically sessile behavior of the benthic adults coupled with the planktonic nature of the veligers allow for a more complete evaluation of water quality …

Novel Cell Penetrating Peptide-Adaptors Effect Intracellular Delivery And Endosomal Escape Of Protein Cargos, John C. Salerno, Verra M. Ngwa, Scott J. Nowak, Carol A. Chrestensen, Allison N. Healey, Jonathan L. Mcmurry

Faculty Articles

The use of cell penetrating peptides (CPPs) as biomolecular delivery vehicles holds great promise for therapeutic and other applications, but development has been stymied by poor delivery and lack of endosomal escape. We have developed a CPP-adaptor system capable of efficient intracellular delivery and endosomal escape of user-defined protein cargos. The cell penetrating sequence of HIV transactivator of transcription was fused to calmodulin, which binds with subnanomolar affinity to proteins containing a calmodulin binding site. Our strategy has tremendous advantage over prior CPP technologies because it utilizes high affinity noncovalent, but reversible coupling between CPP and cargo. Three different cargo …

Phytoforensics Tools: The Degradation And Detection Of Chlorinated Solvents In Integrated Systems, Tommy J. Goodwin Jr.

Masters Theses

"Due to decades of mismanaged pollutants entering groundwater, subsurface pollution of various compounds has become a widespread challenge. Chlorinated solvents are the most common groundwater contaminants that persist in aquifers, and remediation of these wide-spread plumes is difficult. Bioremediation, permeable reactive barriers, and phytoremediation are remedial technologies that have been developed and applied to chlorinated solvents in groundwater systems. This study integrates these technologies in different combinations to demonstrate the remediation potential of this approach. Zerovalent iron (ZVI) and bioaugmentation with a Dehalococcoides sp. (DHC) culture were applied separately and in combination for degradation of perchloroethene (PCE). Salix pentandra were …

Assessing The Use Of Food Waste Biochar As A Biodynamic Plant Fertilizer, Rachel Mazac

Departmental Honors Projects

Biochar is a charcoal-like substance produced from plant material such as food waste. Converting food waste into a useful product would mitigate environmental damage through reduced landfill inputs, reduced greenhouse gas production, and increased benefits to soils. I asked (1) if biochar improved plant growth and (2) if the effects of biochar varied among different samples of mixed food waste (batches) and between different biochar preparation times (treatments). Four independent batches of biochar were prepared with assorted, uncooked food waste collected from a university dining facility. Each batch was dried then placed in a covered ceramic pot at 260℃ for …

Analyzing Urine In Mice With Tyrosinemia Type 1 Using Nmr Spectroscopy, Emily Olsen

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

Powerful Association Test Combining Rare Variant And Gene Expression Using Family Data From Genetic Analysis Workshop 19, Yen Yi Ho, Weihua Guan, Michael O'Connell, Saonli Basu

Faculty Publications

Background: Genetic association studies aim to test for disease or trait association with genetic variants, either throughout the human genome or in regions of interest. However, for most diseases and traits, the combined effects of associated genetic variants explain only a small proportion of the genetic variation. This "missing heritability" may be a result of the small effects of common variants considered in the genetic association studies. Rare variants may also play an important role in understanding the missing heritability of complex traits. Method: We propose a novel weight-adjustment approach to combine gene expression into rare variant analysis. Results from …

Altitudinal Shifts Of The Native And Introduced Flora Of California In The Context Of 20th-Century Warming, A. Wolf, Naupaka B. Zimmerman, W. R. Anderegg, P. E. Busby, J. Christensen

Biology Faculty Publications

Aim: The differential responses of plant species to climate change are of great interest and grave concern for scientists and conservationists. One underexploited resource for better understanding these changes are the records held by herbaria. Using these records to assess the responses of different groups of species across the entire flora of California, we sought to quantify the magnitude of species elevational shifts, to measure differences in shifts among functional groups and between native and introduced species, and to evaluate whether these shifts were related to the conservation of thermal niches.

Location: California.

Methods: To characterize these shifts in California, …

Identification And Quantification Of Zooplankton In Ne Ohio Drinking Water Reservoirs, Michael Vigorito

Williams Honors College, Honors Research Projects

Cyanobacteria, or blue-green algae, are present in most freshwater ecosystems and are usually harmless. When these algae swell in numbers, they release harmful toxins that can be detrimental to animal and human health, and can destroy ecosystems. For this reason, many scientists and engineers have studied these harmful algal blooms in an attempt to predict, prevent, or control them to keep people and ecosystems safe. One of the variables in this investigation is the presence and quantity of zooplankton. These animals could play an important role in the prevalence of cyanobacteria, but more information is needed to determine what that …

Three Simple Experiments To Examine The Effect Of Sediment Pollution On Algae-Based Food Webs In Streams, Patrick M. Edwards, Rodney Shroufe

Environmental Science and Management Faculty Publications and Presentations

Streams and stream macroinvertebrates are ideal natural systems for ecological inquiry. We present three simple experiments that students can use to conduct field-based investigations which illustrate the importance of algae-based food webs in streams and measure the effects of sediment pollution (scour and deposition) on stream ecological processes. Over the past 5 years, we have conducted these experiments 19 times with our students. We report on the results and reliability of these experiments and make suggestions for other educators who may want to conduct them.