Biology Commons^™

A Comparison Of Natural, Living, And Hardened Shorelines Ability To Prevent Coastal Erosion And Maintain A Healthy Ecosystem, Gabrielle Spellmann

Master's Theses

It is important to find a suitable method to protect the U.S. Gulf Coast shoreline, since its’ low elevation and the Loop current make it vulnerable to sea level rise. I focused on two manmade methods, hardened, and living shorelines, of coastal protection for when the natural marsh suffers excess erosion rates. Living shorelines are a suite of shoreline conservation and restoration techniques that usually involve some sort of hardened structure that dampens wave energy so that the native vegetation behind it can take root and stabilize the shoreline. This study looked at six different sites, all containing a natural, …

Ocean Quahog (Arctica Islandica) Population Dynamics: Sex-Based Demographics And Regional Comparisons In The Northwest Atlantic, Kathleen M. Hemeon

Dissertations

Arctica islandica (ocean quahog) is the longest-lived bivalve on Earth. Individuals on the deep continental shelf of the Mid-Atlantic (US) can survive for centuries, and when found in the colder, boreal waters of Iceland, ages over 500 years can be reached. The ocean quahog is important in the US, yet very little is known about the resiliency of the ocean quahog stock to fishing activity, and ocean quahog recruitment patterns over time. To quantify and constrain age-reader error prior to age analysis, a triple-method error protocol was developed for A. islandica that included age-reader bias, precision, and error frequency. The …

High-Frequency Accelerometer Recording Of Key Predatory Behaviors In Vipers: Validation And Case Study With Timber Rattlesnakes (Crotalus Horridus), Morgan L. Thompson, Richard H. Adams, Anna Tipton, Dominic L. Desantis

Graduate Research Showcase

High-frequency accelerometer recording of key predatory behaviors in vipers: validation and case study with Timber Rattlesnakes (Crotalus horridus)

Morgan Thompson, Richard H. Adams, Anna F. Tipton, and Dominic L. DeSantis

Tri-axial accelerometers (ACTs) are becoming increasingly common in studies of animal behavior wherein direct observation of subjects in nature is constrained or impossible. ACTs are small (< 1 g) piezo-electric (spring-like) sensors that measure three-dimensional acceleration (upward, downward, and side-to-side) derived from subject motion. When leveraged with advanced machine learning techniques, these data can enable precise automated classification of a wide range of movement-mediated behaviors. Until recently, ACTs were largely reserved for larger-bodied organisms or those most amenable to the temporary external attachment of devices. Ongoing ACT miniaturization has now expanded the breadth of organisms amenable to these methods. This project aims to expand on a recently developed framework for ACT monitoring in wild-ranging snakes, a group that has been mostly overlooked in biologging applications. We are currently conducting extensive captive validation trials for robust model training and testing to enable classification of predatory behaviors, including striking and ingestion of prey items, in Timber Rattlesnakes (Crotalus horridus). Following captive validation, we will translate this method to the field with a population of C. horridus in the lower Piedmont of middle Georgia to evaluate the efficacy of externally attached ACTs for remote and continuous monitoring of …

Human Adaptation And Morphological Variation: Expanding Diversity In Anatomy Curriculum, Jordan Cass, Cooker Storm

Seaver College Research And Scholarly Achievement Symposium

Introduction: The recent upturn in our nation’s socio-political conversation has fueled interest in ensuring that college curricula is diverse and inclusive. Because human anatomy is ubiquitous across colleges, it may be a valuable avenue to purposefully incorporate topics of diversity in a way that positively impacts our socio-cultural relationships. Providing students with a scientific understanding of our visible differences may mitigate subconscious bias when we see others who have different features. Purpose: We investigated the biogeographical factors that contribute to the morphological variability of the face, hair, and body size; with the secondary aim of developing diverse and …

Endogenous Cftr Expression In Human Epithelial Cell Lines, Zithlaly Amezquita

Undergraduate Research Conference

CFTR (Cystic Fibrosis Transmembrane-conductance Regulator) is a plasma membrane protein that functions as a chloride ion channel on many epithelial cells. There are over 1000 mutations that affect the function of this protein; however, the most common mutation is DF508. CFTR mutations target many secretory organs like pancreas and lungs causing the genetic disease cystic fibrosis (CF), common among Caucasians of northern European origin. Detection of endogenous CFTR expression is possible by a difficult and costly immunoprecipitation method but not by the most used western blotting method. Therefore, the goal of this project was to detect the endogenous CFTR expression …

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 …

Rethinking Public Health Risk Mitigation Strategies: Recognizing The Biosocial Nature Of Covid-19, Grace Savard

CSB and SJU Distinguished Thesis

The SARS-CoV-2 virus has rippled throughout every aspect of society and influenced how we live, breathe, and interact with one another. The purpose of this thesis is to explore the interdisciplinary biosocial impacts of the SARS-CoV-2 virus and the resulting disease, COVID-19. In order to understand the complexities of caregiving during COVID-19, we conducted 75 semi-structured interviews with 55 healthcare providers across 18 states over a span of two years. This research assesses how COVID-19 risk mitigation strategies were designed with the primary intention to stop the spread of the virus rather than account for the longer-term social and biological …

Using Quantitative Imaging For Personalized Medicine In Pancreatic Cancer: A Review Of Radiomics And Deep Learning Applications, Kiersten Preuss, Nate Thach, Xiaoying Liang, Michael Baine, Justin Chen, Chi Zhang, Huijing Du, Hongfeng Yu, Chi Lin, Michael A. Hollingsworth, Dandan Zheng

School of Biological Sciences: Faculty Publications

As the most lethal major cancer, pancreatic cancer is a global healthcare challenge. Personalized medicine utilizing cutting-edge multi-omics data holds potential for major breakthroughs in tackling this critical problem. Radiomics and deep learning, two trendy quantitative imaging methods that take advantage of data science and modern medical imaging, have shown increasing promise in advancing the precision management of pancreatic cancer via diagnosing of precursor diseases, early detection, accurate diagnosis, and treatment personalization and optimization. Radiomics employs manually-crafted features, while deep learning applies computer-generated automatic features. These two methods aim to mine hidden information in medical images that is missed by …

Microbiological Contamination Associated With The Proximity Of A Refuse Dumpsite To A River Situated In Okada, Edo State, Nigeria, Ebere J. Okafor-Elenwo, Odaro S. Imade, Osazee E. Izevbuwa

Journal of Bioresource Management

This study was performed to evaluate the potential contamination of the Okponha river situated near a dumpsite in Okada, Edo State, Nigeria. Water samples were collected and analyzed for bacteriological and parasitological quality using standard procedures. Isolation and enumeration of bacterial colonies were performed by pour plate technique and the isolated bacteria were identified by standard phenotypic tests. Helminths and protozoa were screened by the direct smear technique. The values of HPC (3.79 ± 0.12 log₁₀ CFU/ml) and TCC (2.20 ± 0.14 log₁₀ CFU/ml) obtained from the river water samples exceeded WHO and NAFDAC recommended limits (≤ 2 …

Rapid Pivot Of Cure Wet Lab To Online With The Help Of Instructor Communities, Enid T. González-Orta, Deborah Tobiason, Brittany J. Gasper, Aarti Raja, Sarah Miller

Biology Faculty Articles

The pivot to remote and hybrid learning during the Covid-19 pandemic presented a challenge for many in academia. Most institutions were not prepared to support this rapid change, and instructors were left with the burden of converting a traditional face-to-face course into multiple modalities with very limited preparation time. When institutional support is lacking, we posit that instructor communities of practice can help provide the resources needed to meet the instructional demands. Tiny Earth, a course-based-undergraduate research experience (CURE) and international network of instructors and students, responded to the instructional challenges of the pandemic by leveraging its large community of …

The Gut Microbiome Of Exudivorous Marmosets In The Wild And Captivity, Joanna Malukiewicz, Reed Cartwright, Jorge A. Dergam, Claudia S. Igayara, Sharon E. Kessler, Silvia B. Moreira, Leanne T. Nash, Patricia A. Nicola, Luiz C. M. Pereira, Alcides Pissinatti, Carlos R. Ruiz-Miranda, Andrew T. Ozga, Adriana A. Quirino, Christian Roos, Daniel L. Silva, Anne C. Stone, Adriana D. Grativol

Biology Faculty Articles

Mammalian captive dietary specialists like folivores are prone to gastrointestinal distress and primate dietary specialists suffer the greatest gut microbiome diversity losses in captivity compared to the wild. Marmosets represent another group of dietary specialists, exudivores that eat plant exudates, but whose microbiome remains relatively less studied. The common occurrence of gastrointestinal distress in captive marmosets prompted us to study the Callithrix gut microbiome composition and predictive function through bacterial 16S ribosomal RNA V4 region sequencing. We sampled 59 wild and captive Callithrix across four species and their hybrids. Host environment had a stronger effect on the gut microbiome than …

Dissecting Mutational Allosteric Effects In Alkaline Phosphatases Associated With Different Hypophosphatasia Phenotypes: An Integrative Computational Investigation, Fei Xiao, Ziyun Zhou, Xingyu Song, Mi Gan, Jie Long, Gennady M. Verkhivker, Guang Hu

Mathematics, Physics, and Computer Science Faculty Articles and Research

Hypophosphatasia (HPP) is a rare inherited disorder characterized by defective bone mineralization and is highly variable in its clinical phenotype. The disease occurs due to various loss-of-function mutations in ALPL, the gene encoding tissue-nonspecific alkaline phosphatase (TNSALP). In this work, a data-driven and biophysics-based approach is proposed for the large-scale analysis of ALPL mutations-from nonpathogenic to severe HPPs. By using a pipeline of synergistic approaches including sequence-structure analysis, network modeling, elastic network models and atomistic simulations, we characterized allosteric signatures and effects of the ALPL mutations on protein dynamics and function. Statistical analysis of molecular features computed for the …

Empirically Derived Thermal Thresholds Of Four Coral Species Along The Red Sea Using A Portable And Standardized Experimental Approach, Nicolas R. Evensen, Christian R. Voolstra, Maoz Fine, Gabriela Perna, Carol Buitrago-López, Anny Cárdenas, Guilhem Banc-Prandi, Katherine Rowe, Daniel J. Barshis

Biological Sciences Faculty Publications

Global warming is causing an unprecedented loss of species and habitats worldwide. This is particularly apparent for tropical coral reefs, with an increasing number of reefs experiencing mass bleaching and mortality on an annual basis. As such, there is a growing need for a standardized experimental approach to rapidly assess the thermal limits of corals and predict the survival of coral species across reefs and regions. Using a portable experimental system, the Coral Bleaching Automated Stress System (CBASS), we conducted standardized 18 h acute thermal stress assays to quantitively determine the upper thermal limits of four coral species across the …

Editorial: Pathways And Processes Underpinning Axonal Biology And Pathobiology, Pabitra K. Sahoo, Dianna E. Willis, James N. Sleigh

Faculty Publications

No abstract provided.

Research On Characteristics, Development Trend And Funding Countermeasures Of Biology, Jie Chen, Jing Qu, Zhiyong Lou, Bing Zhu, Le Kang

Bulletin of Chinese Academy of Sciences (Chinese Version)

Strengthening the research in biology aimed at national strategic needs and major scientific frontier issues is conducive to giving full play to the strategic supporting role of biological research for national economic development and the promotion of international competitiveness. This article combs the basic characteristics and development trend of biology, summarizes the practical experience of international biological research funding, and analyzes the outstanding problems in biological research in China, such as incomplete layout, lack of sustainable and stable support, and insufficient funding for top talents and teams. By referring to the international practical experience, it puts forward policy suggestions to …

Embryological Development And Mortality Of Danio Rerio In Long Term Exposure To 17Α-Ethynylestradiol, Seong A. Jeon

University Honors Theses

Synthetic estrogens as well as other chemicals have become an increasing issue in the impact they have on marine species particularly those sensitive to the environment. A broadly used synthetic estrogen, 17α-ethynylestradiol, has become more widely known to become a growing problem to the ecology of marine wildlife due to increased usage and lack of removal in municipal sewage treatment facilities. This study observes the impact of low level EE2 in embryos following generational exposure. Zebrafish embryos, following three generations of exposure, were observed in rate of mortality, lethality, and hatch success. Concentrations as low as 1ng/L of EE2 has …

Centralized Project-Specific Metadata Platforms: Toolkit Provides New Perspectives On Open Data Management Within Multi-Institution And Multidisciplinary Research Projects, Andrew Wright Child, Jennifer Hinds, Lucas Sheneman, Sven Buerki

Biology Faculty Publications and Presentations

Open science and open data within scholarly research programs are growing both in popularity and by requirement from grant funding agencies and journal publishers. A central component of open data management, especially on collaborative, multidisciplinary, and multi-institutional science projects, is documentation of complete and accurate metadata, workflow, and source code in addition to access to raw data and data products to uphold FAIR (Findable, Accessible, Interoperable, Reusable) principles. Although best practice in data/metadata management is to use established internationally accepted metadata schemata, many of these standards are discipline-specific making it difficult to catalog multidisciplinary data and data products in a …

The Life History Of Drosophila Sperm Involves Molecular Continuity Between Male And Female Reproductive Tracts, Erin L. Mccullough, Emma Whittington, Akanksha Singh, Scott Pitnick, Mariana F. Wolfner, Steve Dorus

Biology

Interactions between sperm and the female reproductive tract (FRT) are critical to reproductive success and yet are poorly understood. Because sperm complete their functional maturation within the FRT, the life history of sperm is likely to include a molecular “hand-off” from males to females. Although such intersexual molecular continuity is likely to be widespread among all internally fertilizing species, the identity and extent of female contributions are largely unknown. We combined semiquantitative proteomics with sex-specific isotopic labeling to catalog the posttesticular life history of the sperm proteome and determine the extent of molecular continuity between male and FRTs. We show …

Identification And Characterization Of A Stem Canker And Twig Dieback Disease Of Pear Caused By Neofusicoccum Parvum In Chinese Mainland, Feng He, Jie Yang, Yancun Zhao, Pedro Laborda, Yifan Jia, Asma Safdar, Alex Machio Kange, Bingxin Li, Lan Zhou, Quan Zeng, Sally Brown, Zheng Qing Fu, Fengquan Liu

Faculty Publications

Pear (Pyrus spp.) is one of the most consumed fruits in China, but the pear production has to confront the growing threat from fatal diseases. In this study, we report two incidences of stem canker and twig dieback disease on pear plants, which led to death of pear seedlings (approximately 10% of total plants) in Guangxi and Jiangsu provinces. Using a combination of morphological and molecular diagnoses, along with pathogenicity test, the causal agent of the disease in these two locations was identified to be the fungus Neofusicoccum parvum. However, the isolates were divided into two clades: CY-2 …

Determinants Of Food Selection By Bivalve Larvae, Maria Rosa, Diane K. Padilla

Biology Faculty Publications

Selection of food particles for consumption by larvae impacts nutritional gain needed for growth, development, and metamorphosis. Past work has suggested that molluscan larvae are capable of collecting food within a narrow size range. Recent studies have found evidence of size-independent food selection in molluscan larvae, but relatively little is known about the characteristics of particles that larvae preferentially capture. Therefore, we conducted experiments with the larvae of two mussels, Mytilus trossulus and Mytilus edulis, to determine whether they are selective feeders, and if so, whether we could determine the characteristics of particles selected as food. We fed larvae microalgae …

The Role Of Chemical Cues In Host Susceptibility To Fish-Parasitic Gnathiid Isopods., Clayton M. Vondriska

Student Theses and Dissertations

Parasitism is one of the most common lifestyle strategies. Ectoparasites must navigate complex environments to find their host and many rely heavily on chemical cues to do so. Gnathiid isopods are common parasites that use chemical cues to find their marine fish hosts. While gnathiids are considered host-generalists, hosts vary in their susceptibility to infestation. However, the mechanisms that mediate differential susceptibility are unknown. Here I used field and laboratory experiments to investigate if the chemo-attractiveness of hosts explains differences in susceptibility of Caribbean reef fishes to infestation by a common Caribbean gnathiid isopod, Gnathia marleyi. While G. marleyi can …

Source Of Off-Type Frequencies In Winter Wheat Varieties, Michaela Benes

Honors Program: Senior Projects (Public)

The enzyme polyphenol oxidase (PPO) is undesirable in most wheat products due to the discoloration it causes. Purifying wheat varieties through selective breeding is the best way at getting rid of PPO in a variety. The variety NW15443 was planted in both a field in McCook, NE, and in a greenhouse in Lincoln, NE. Individual heads were snapped from the field and the greenhouse seed was harvested in bulk. After completing a PPO test of the seed, it was determined that the percentages of off-type frequencies from the field seed and the greenhouse seed were 11% and 3.6%, respectively. Using …

Health Risk From Toxic Metals In Wild Rice Grown In Copper Mining-Impacted Sediments, Rohan Deep Sarkar, Zhiming Zhang, Manas Warke, Rupali Datta

Michigan Tech Publications, Part 1

Northern wild rice is of great dietary and cultural importance to the Native American population in the Upper Peninsula of Michigan. Millions of tons of mine tailings were discharged into Lake Superior and other inland lakes during the copper mining boom in the early 20th century in this area. This includes L’Anse Bay, located within the Keweenaw Bay Indian Community (KBIC) reservation. Since wild rice restoration is being encouraged by the KBIC, we investigated the distribution of toxic metals in sediments, water, and wild rice and their potential impact on human health from two locations. Sand Point sloughs on L’Anse …

The Ability To Classify Patients Based On Gene-Expression Data Varies By Algorithm And Performance Metric, Stephen Piccolo, Avery Mecham, Nathan P. Golightly, Jérémie L. Johnson, Dustin B. Miller

Faculty Publications

By classifying patients into subgroups, clinicians can provide more effective care than using a uniform approach for all patients. Such subgroups might include patients with a particular disease subtype, patients with a good (or poor) prognosis, or patients most (or least) likely to respond to a particular therapy. Transcriptomic measurements reflect the downstream effects of genomic and epigenomic variations. However, high-throughput technologies generate thousands of measurements per patient, and complex dependencies exist among genes, so it may be infeasible to classify patients using traditional statistical models. Machine-learning classification algorithms can help with this problem. However, hundreds of classification algorithms exist—and …

Nonhistone Lysine Methylation As A Protein Degradation Signal, Nicholas A. Lehning, Brad E. Morrison

Biology Faculty Publications and Presentations

Protein degradation is a fundamental feature of cellular life, and malfunction of this process is implicated in human disease. Ubiquitin tagging is the best characterized mechanism of targeting a protein for degradation; however, there are a growing number of distinct mechanisms which have also been identified that carry out this essential function. For example, covalent tagging of proteins with sequestosome-1 targets them for selective autophagy. Degradation signals are not exclusively polypeptides such as ubiquitin, NEDD8, and sequestosome-1. Phosphorylation, acetylation, and methylation are small covalent additions that can also direct protein degradation. The diversity of substrate sequences and overlap with other …

Genetic Variation Of The Mitochondrial Dna Control Region Across Plains Bison Herds In Usa And Canada, Gaimi Davies, Blake Mccann, Lee Jones, Stefano Liccioli, Maria Cecilia Penedo, Igor V. Ovtchinnikov

Biology Faculty Publications

Once numbering in the tens of millions, bison (Bison bison) have faced a broad range of challenges over the past century, including genetic impacts from the population bottleneck in the 1800s, and significant loss and fragmentation of habitat resulting in little opportunity for population growth on remaining small, geographically isolated reserves. To identify best practices for bison stewardship against this backdrop, managers must understand the genetic composition of existing conservation herds. This study characterized 14 plains bison (Bison bison bison) herds managed by the U.S. Department of Interior and Parks Canada Agency based on complete mtDNA …

Bumble Bees Exhibit Body Size Clines Across An Urban Gradient Despite Low Genetic Differentiation, Matthew W. Austin, Amber D. Tripodi, James P. Strange, Aimee S. Dunlap

Educator Preparation & Leadership Faculty Works

Environmental heterogeneity resulting from human-modified landscapes can increase intraspecific trait variation. However, less known is whether such phenotypic variation is driven by plastic or adaptive responses to local environments. Here, we study five bumble bee (Apidae: Bombus) species across an urban gradient in the greater Saint Louis, Missouri region in the North American Midwest and ask: (1) Can urban environments induce intraspecific spatial structuring of body size, an ecologically consequential functional trait? And, if so, (2) is this body size structure the result of plasticity or adaptation? We additionally estimate genetic diversity, inbreeding, and colony density of these species—three …

Quantitative Assessment Of The Trophic Ecology Of The Oceanic Ctenophore, Bolinopsis Infundibulum, In Monterey Bay, California, Victoria C. Scriven

USF Tampa Graduate Theses and Dissertations

Bolinopsis infundibulum is a wide-ranging, ubiquitous ctenophore whose fragile nature makes the collection of specimens and quantification of key predator-prey activities in controlled laboratory experiments, challenging. Thus, in situ methods often represent the best means for data collection. However, while present in surface waters, these animals can also be abundant at depths well beyond those attainable by divers. As a result, very little empirical data exist over the depth range of their natural habitats which limits our ability to assess key predator-prey interactions needed to assess their ecological role in midwater food webs. Working in Monterey Bay, California, remotely operated …

Characterization Of SccMec Instability In Methicillin-Resistant Staphylococcus Aureus Affecting Adjacent Chromosomal Regions, Including The Gene For Staphylococcal Protein A (Spa), Isabella A. Tickler, Fred C. Tenover, C. R. Scharn, R. V. Goering

Biology Faculty Publications

Staphylococcal cassette chromosome mec (SCCmec) represents a sequence of clear clinical and diagnostic importance in staphylococci. At a minimum the chromosomal cassette contains the mecA gene encoding PBP2a but frequently also includes additional antibiotic resistance genes (e.g., ermA and aadC; macrolide and aminoglycoside resistance, respectively). Certain regions within SCCmec elements are hot spots for sequence instability due to cassette-specific recombinases and a variety of internal mobile elements. SCCmec changes may affect not only cassette stability but the integrity of adjacent chromosomal sequences (e.g., the staphylococcal protein A gene; spa). We investigated SCCmec stability …

Selection On Dispersal Drives Evolution Of Metabolic Capacities For Energy Production In Female Wing-Polymorphic Sand Field Crickets, Gryllus Firmus, Lisa A. Treidel, Gessen S. Quintanilla Ramirez, Dillon J. Chung, Michael Menze, Jose P. Vazquez-Medina, Caroline M. Williams

Faculty and Staff Scholarship

Life history and metabolism covary, but the mechanisms and individual traits responsible for these linkages remain unresolved. Dispersal capability is a critical component of life histories that is constrained by metabolic capacities for energy production. Conflicting relationships between metabolism and life histories may be explained by accounting for variation in dispersal and maximal metabolic rates. We used female wing-polymorphic sand field crickets, Gryllus firmus, selected either for long wings (LW) and flight-capability or short wings (SW) and high early lifetime fecundity to test the hypothesis that selection on dispersal capability drives the evolution of metabolic capacities. While resting metabolic …