Biology Commons^™

24andmore: Using Genomics To Improve Walleye (Sander Vitreus) Stocking In Iowa, Rachel Mcdonnell

Three Minute Thesis (3MT®) at UNI

Walleye, Sander vitreus, is one of the top gamefish in Iowa. Due to poor natural reproduction in many Iowa waterbodies, populations are managed with stocking. There are two strains of walleye used to stock Iowa’s inland waters: a river strain derived from the Mississippi River near Genoa, WI and a lake strain derived from Spirit Lake, IA. Each strain may have unique characteristics relative to their environment that could affect the fitness and success of fish stocked. The goal of this study is to understand the genetic diversity within and between each strain to offer stocking guidance to the Iowa …

Genetic Effect Of Long-Term Angling Pressure On Bluegill Populations In Small Impoundments In Kansas, Morganne Borsh

Three Minute Thesis (3MT®) at UNI

Bluegill (Lepomis macrochirus) is a versatile sport fish popularly fished across Kansas. Over the last decade, Bluegill catch rates have decreased, likely from high angler harvest rates of larger individuals. Large males that exhibit parental care have high growth rates and aggressively defend nests, making them vulnerable to angling. Males that display cuckoldry behavior reach maturity sooner, exhibit slower growth rates, and are generally smaller. The goal of this study is to determine if fisheries-induced evolution resulting from long-term harvest has led to a decline in the growth rate of Bluegill. A total of 100 individuals were sampled from ten …

The Ecological Role Of Cassiopea In Shallow Mangrove Habitats, David Marcel Durieux

USF Tampa Graduate Theses and Dissertations

Upside-down jellyfish, Cassiopea sp., can be locally abundant in shallow mangrove habitats throughout the tropics and subtropics. Unlike other jellyfish, Cassiopea sp. are epibenthic. Due to this unique lifestyle and their ability to achieve high population densities, an understanding is needed of their ecological impacts both individually and in aggregations, particularly given that Cassiopea sp. ranges are expanding poleward due to global climate change. We quantified the fluid flow produced by Cassiopea sp. feeding currents and found that an average-sized Cassiopea sp. can transport over 200 l/h of water in the vertical excurrent jet of their feeding current. Populations of …

Moving In Fluid: Exploring How Fishes Manipulate Water To Swim Efficiently, Nils B. Tack

USF Tampa Graduate Theses and Dissertations

Moving through a dense fluid such as water presents some unique challenges to minimizing energy use and maximizing performance (i.e., speed). Due to animal-fluid interactions during swimming (drag and thrust production) fish have evolved a variety of morphological structures and locomotor mechanisms. For instance, fish rely on body bending and/or fins to interact with the surrounding water such that energy can be transferred to generate thrust. Typically, this synergy promotes morphologies and behaviors aimed at enhancing propulsive efficiency and/or minimizing metabolic activity to lessen the cost of transport (COT). This work focuses on quantifying the energetic and hydromechanical benefits of …

Breathing Can Be Dangerous: Coccidioides And The Diverse Community Of The Lung Mycobiome, Paris S. Salazar-Hamm

Biology ETDs

Coccidioidomycosis, caused by soil-dwelling species of Coccidioides, is endemic to the Southwestern United States. It can present as a mild respiratory illness to life-threatening disseminated infections.Multi-gene phylogenetics and tracing patient histories revealed the presence of both Coccidioides species in New Mexico, and Native Americans may represent an unrecognized risk group. A PCR method developed distinguishes Coccidioides species by targeting regions of the mitochondrial genome. Recent advancements in molecular genetics solidifies lungs are not sterile. Illumina community data from 199 small mammals from Arizona, California, and New Mexico demonstrated a great diversity of fungi inhabiting lung tissues. One dominant order, Onygenales, …

Let It Rip: The Mechanics Of Self-Bisection In Asexual Planarians Determines Their Population Reproductive Strategies, T. Goel, Danielle Ireland, Vir Shetty , '22, Christina Rabeler, P. H. Diamond, Eva-Maria S. Collins

Biology Faculty Works

Asexual freshwater planarians reproduce by transverse bisection (binary fission) into two pieces. This process produces a head and a tail, which fully regenerate within 1–2 weeks. How planarians split into two offspring—using only their musculature and substrate traction—is a challenging biomechanics problem. We found that three different species, Dugesia japonica, Girardia tigrina and Schmidtea mediterranea, have evolved three different mechanical solutions to self-bisect. Using time lapse imaging of the fission process, we quantitatively characterize the main steps of division in the three species and extract the distinct and shared key features. Across the three species, planarians actively alter …

Unraveling The Role Of Novel G5 Peptidase Family Proteins In Virulence And Cell Envelope Biogenesis Of Staphylococcus Aureus, Stephanie M. Marroquin

USF Tampa Graduate Theses and Dissertations

Virulence factors and the bacterial cell envelope are two important components in S. aureus pathogenesis and survival. More importantly, understanding the regulation of these cellular processes is crucial to further understanding and combating this successful pathogen. To date, numerous factors have been identified as playing a role in the regulation of Agr activity in S. aureus, including transcription factors, antisense RNAs, and host elements. Herein we investigate the product of SAUSA300_1984 (termed MroQ), a transmembrane G5 peptidase family protein, as a novel effector of this system. Using a USA300 mroQ mutant we observed a drastic reduction in proteolysis, hemolysis, and …

A Sugarcane G-Protein-Coupled Receptor, Shgpcr1, Confers Tolerance To Multiple Abiotic Stresses, Manikandan Ramasamy, Mona B. Damaj, Carol Vargas-Bautista, Victoria Mora, Jiaxing Liu, Carmen S. Padilla, Sonia Irigoyen, Tripti Saini, Nirakar Sahoo, Jorge A. Dasilva, Kranthi K. Mandadi

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

Sugarcane (Saccharum spp.) is a prominent source of sugar and serves as bioenergy/biomass feedstock globally. Multiple biotic and abiotic stresses, including drought, salinity, and cold, adversely affect sugarcane yield. G-protein-coupled receptors (GPCRs) are components of G-protein-mediated signaling affecting plant growth, development, and stress responses. Here, we identified a GPCR-like protein (ShGPCR1) from sugarcane and energy cane (Saccharum spp. hybrids) and characterized its function in conferring tolerance to multiple abiotic stresses. ShGPCR1 protein sequence contained nine predicted transmembrane (TM) domains connected by four extracellular and four intracellular loops, which could interact with various ligands and heterotrimeric G …

Bio-Acoustic Tracking And Localization Using Heterogeneous, Scalable Microphone Arrays, Erik Verreycken, Ralph Simon, Brandt Quirk-Royal, Walter Daems, Jesse Barber, Jan Steckel

Biology Faculty Publications and Presentations

Microphone arrays are an essential tool in the field of bioacoustics as they provide a non-intrusive way to study animal vocalizations and monitor their movement and behavior. Microphone arrays can be used for passive localization and tracking of sound sources while analyzing beamforming or spatial filtering of the emitted sound. Studying free roaming animals usually requires setting up equipment over large areas and attaching a tracking device to the animal which may alter their behavior. However, monitoring vocalizing animals through arrays of microphones, spatially distributed over their habitat has the advantage that unrestricted/unmanipulated animals can be observed. Important insights have …

Panoramic Spatial Vision In The Bay Scallop Argopecten Irradians, Daniel R. Chappell, Tyler M. Horan, Daniel Isaac Speiser

Faculty Publications

We have a growing understanding of the light-sensing organs and light-influenced behaviours of animals with distributed visual systems, but we have yet to learn how these animals convert visual input into behavioural output. It has been suggested they consolidate visual information early in their sensory-motor pathways, resulting in them being able to detect visual cues (spatial resolution) without being able to locate them (spatial vision). To explore how an animal with dozens of eyes processes visual information, we analysed the responses of the bay scallop Argopecten irradians to both static and rotating visual stimuli. We found A. irradians distinguish between …

Who Are We? Highlighting Nuances In Asian American Experiences In Ecology And Evolutionary Biology, K. H. Nguyen, A. K. Akiona, C. C. Chang, V. B. Chaudhary, S. J. Cheng, S. M. Johnson, S. S. Kahanamoku, A. Lee, E. E. Deleon Sanchez, L. M. Segui, Richelle L. Tanner

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

"As ecologists and evolutionary biologists, it is important to recognize that issues surrounding AAPI do not exist in a vacuum and that these issues affect some of our students and colleagues in and outside of the classroom and lab. Recently, anti-Asian racism has been brought to the forefront of US society. Though media attention has primarily focused on how COVID-19 fears motivated both violent and nonviolent racist incidents against East Asians in 2020 (e.g., Chinese and Taiwanese Americans) (Tessler et al. 2020), attacks on other AAPI groups, such as South and Southeast Asians (e.g., Filipino, Pakistani, and Vietnamese Americans) (Truong …

Metastatic Mat Phenotype Driven By Noncanonical Epha2 Signaling In Melanoma, Chao Zhang

USF Tampa Graduate Theses and Dissertations

Acquired BRAF/MAPK/extracellular signal‒regulated kinase inhibitor resistance in melanoma results in a new transcriptional state associated with an increased risk of metastasis. In this study, we identified noncanonical ephrin receptor (Eph) EphA2 signaling as a driver of the resistance-associated metastatic state. We used mass spectrometry‒based proteomic and phenotypic assays to demonstrate that the expression of active noncanonical EphA2-S897E in melanoma cells led to a mesenchymal-to-amoeboid transition driven by Cdc42 activation. The induction of mesenchymal-to-amoeboid transition promoted melanoma cell invasion, survival under shear stress, adhesion to endothelial cells under continuous-flow conditions, increased permeability of endothelial cell monolayers, and stimulated melanoma transendothelial cell …

Ecology And Diversity Of Boletes Of The Southeastern United States, Arian Farid

USF Tampa Graduate Theses and Dissertations

The boletes are conspicuous stipito-pileate macrofungi that are generally defined by their tubulose hymenophores. Molecular phylogenetic analyses have informed extensive taxonomic revisions across the boletes. Despite this, the boletes in the southeastern USA have been largely absent from the literature. This dissertation seeks to understand the microbiome inhabiting the tuberculate ectomycorrhizae of the bolete Hemileccinum rubropunctum, and addresses taxonomic revisions of boletes found in the Boletaceae and Suillaceae. The introduction provides a brief background on boletes, as well as our understanding of tuberculate ectomycorrhizae. The second chapter seeks to understand the composition of the microbiome tuberculate ectomycorrhizae of H. rubropunctum …

The Dynamics Of Dominance: Open Questions, Challenges And Solutions, Eli D. Strauss, Daizaburo Shizuka

School of Biological Sciences: Faculty Publications

Although social hierarchies are recognized as dynamic systems, they are typically treated as static entities for practical reasons. Here, we ask what we can learn from a dynamical view of dominance, and provide a research agenda for the next decades. We identify five broad questions at the individual, dyadic and group levels, exploring the causes and consequences of individual changes in rank, the dynamics underlying dyadic dominance relationships, and the origins and impacts of social instability. Although challenges remain, we propose avenues for overcoming them. We suggest distinguishing between different types of social mobility to provide conceptual clarity about hierarchy …

Pi3k Pathway Inhibition With Nvp-Bez235 Hinders Glycolytic Metabolism In Glioblastoma Multiforme Cells, Shreya Udawant, Carl Litif, Alma Lopez, Bonnie Gunn, Erin Schuenzel, Megan Keniry

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

Glioblastoma (GBM) is the most lethal primary brain cancer that lacks effective molecular targeted therapies. The PI3K/AKT/mTOR pathway is activated in 90% of all Glioblastoma multiforme (GBM) tumors. To gain insight into the impact of the PI3K pathway on GBM metabolism, we treated U87MG GBM cells with NVP-BEZ235 (PI3K and mTOR a dual inhibitor) and identified differentially expressed genes with RNA-seq analysis. RNA-seq identified 7803 differentially regulated genes in response to NVP-BEZ235. Gene Set Enrichment Analysis (GSEA) identified two glycolysis-related gene sets that were significantly enriched (p < 0.05) in control samples compared to NVP-BEZ235-treated samples. We validated the inhibition of glycolytic genes by NVP-BEZ235 and examined the impact of the FOXO1 inhibitor (AS1842856) on these genes in a set of GBM cell lines. FOXO1 inhibition alone was associated with reduced LDHA expression, but not ENO1 or PKM2. Bioinformatics analyses revealed that PI3K-impacted glycolytic genes were over-expressed and co-expressed in GBM clinical samples. The elevated expression of PI3K-impacted glycolytic genes was associated with poor prognosis in GBM based on Kaplan–Meier survival analyses. Our results suggest novel insights into hallmark metabolic reprogramming associated with the PI3K-mTOR dual inhibition.

Complete Genome Sequence Of The Pantoea Phage Ah07, Gregory P. Krukonis, Sam J. Roth, Veronique A. Delesalle

Biology Faculty Publications

Bacteriophages of the phyllosphere have not been extensively described, despite their role in bacterial communities on this plant organ. Here, we describe a temperate Pantoea phage, AH07, that was isolated from the leaves of horse chestnut trees. The 37,859-bp linear double-stranded DNA genome contains 58 putative genes, including an integration cassette.

Complete Genome Sequences Of Four Phages Of The Horse Chestnut Phyllosphere, Gregory P. Krukonis, Sam J. Roth, Veronique A. Delesalle

Biology Faculty Publications

Bacteriophages play important roles in determining bacterial communities, including plant microbiota. Here, we describe four lytic phages, three Siphoviridae and one Podoviridae, isolated from four different bacterial species found on the leaves of horse chestnut trees. Their double-stranded DNA (dsDNA) genomes range from 39,095 to 46,062 bp and contain 51 to 70 genes.

Genome Sequences Of Erwinia Phyllophages Ah04 And Ah06, Gregory P. Krukonis, Sam J. Roth, Veronique A. Delesalle

Biology Faculty Publications

Although crucial in shaping bacterial communities, few bacteriophages of the phyllosphere have been described. We provide genome data for two Myoviridae phages, AH04 and AH06, isolated on Erwinia billingiae strains. AH04 shares limited genetic similarity with previously described phages, while AH06 shares over 75% similarity with various Erwinia phages.

Evolutionary Mechanisms For Host Resistance To Tumor Growth And Subsequent Cancer Cell Counter-Adaptations, Arig Ibrahim Hashim

USF Tampa Graduate Theses and Dissertations

Cancer is well-recognized as an evolutionary system, as first proposed by Cairns and Nowell more than 60 years ago. In an evolutionary context, cancers growing in vivo typically consist of heterogeneous subpopulations of cells that interact with each other and with host cells through selection forces operating at many temporal and spatial scales. Moreover, the tumor environment comprises more than just cancer cells; it includes a rich cancer stroma and cancer-driving molecules such as cytokines and metabolites. The tumor’s environment comprises intratumoral heterogeneity that often leads to therapy resistance attributed to the essential roles of many genetic and nongenetic mechanisms. …

High Rates Of Polygyny In Tropical Mexico Within The Native Range Of Vespula Squamosa., Alex K. Snyder, Kevin J. Loope

Honors College Theses

Polygyny, or the formation of colonies with multiple cooperating queens, has been observed in a variety of social Hymenoptera and likely exists as a convergent evolutionary strategy. Polygyne cooperation has been observed in several Vespula sp. and is correlated with a perennial social strategy. This perennial-polygyne behavior has been observed most commonly within the tropical and subtropical regions of the invasive Vespula pensylvanica and V. germanica, and rarely within their native temperate ranges. This phenomenon has been relatively undocumented within the tropical portions the V. squamosa native range, despite it being observed in their temperate ranges several times. We observed …

Morphological Characterization Of Trichomes Shows Enormous Variation In Shape, Density And Dimensions Across The Leaves Of 14 Solanum Species, Sakshi Watts, Rupesh R. Kariyat

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

Trichomes are the epidermal appendages commonly observed on plant surfaces including leaves, stem and fruits. Plant trichomes have been well studied as a structural plant defence designed to protect plants against abiotic and biotic stressors such as UV rays, temperature extremities and herbivores. Trichomes are primarily classified into glandular and non-glandular trichomes, based on the presence or absence of a glandular head. The plant genus Solanum is the largest genus of family Solanaceae that houses ~3500 species of ecological and economic importance have a diverse set of trichomes that vary in density and morphology. However, due to the incomplete and …

Reduced Toxicity Of Centruroides Vittatus (Say, 1821) May Result From Lowered Sodium Β Toxin Gene Expression And Toxin Protein Production, Aimee Bowman, Chloe Fitzgerald, Jeff F. Pummill, Douglas D. Rhoads, Tsunemi Yamashita

Faculty Publications - Biological Sciences

Body tissue and venom glands from an eastern population of the scorpion Centruroides vittatus (Say, 1821) were homogenized and molecular constituents removed to characterize putative sodium β toxin gene diversity, RT-qPCR, transcriptomic, and proteomic variation. We cloned sodium β toxins from genomic DNA, conducted RT-qPCR experiments with seven sodium β toxin variants, performed venom gland tissue RNA-seq, and isolated venom proteins for mass spectrophotometry. We identified greater than 70 putative novel sodium β toxin genes, 111 toxin gene transcripts, 24 different toxin proteins, and quantified sodium β toxin gene expression variation among individuals and between sexes. Our analyses contribute to …

Mapping The Hidden Diversity Of The Geophagus Sensu Stricto Species Group (Cichlidae: Geophagini) From The Amazon Basin, A. M. Ximenes, P. S. Bittencourt, V. N. Machado, Tomas Hrbek, I. P. Farias

Biology Faculty Research

South American freshwater ichthyofauna is taxonomically the most diverse on the planet, yet its diversity is still vastly underestimated. The Amazon basin alone holds more than half of this diversity. The evidence of this underestimation comes from the backlog of morphologically distinct, yet undescribed forms deposited in museum collections, and from DNA-based inventories which consistently identify large numbers of divergent lineages within even well-studied species groups. In the present study, we investigated lineage diversity within the Geophagus sensu stricto species group. To achieve these objectives, we analyzed 337 individuals sampled from 77 locations within and outside the Amazon basin representing …

Cetacean Acousticwelfare In Wild And Managed-Care Settings: Gaps And Opportunities, Paige E. Stevens, Heather Hill, Jason N. Bruck

Faculty Publications

Cetaceans are potentially at risk of poor welfare due to the animals’ natural reliance on sound and the persistent nature of anthropogenic noise, especially in the wild. Industrial, commercial, and recreational human activity has expanded across the seas, resulting in a propagation of sound with varying frequency characteristics. In many countries, current regulations are based on the potential to induce hearing loss; however, a more nuanced approach is needed when shaping regulations, due to other non-hearing loss effects including activation of the stress response, acoustic masking, frequency shifts, alterations in behavior, and decreased foraging. Cetaceans in managedcare settings share the …

On The Relationship Between Pain Variability And Relief In Randomized Clinical Trials, Siddharth Tiwari '22

Student Publications & Research

Previous research suggests greater baseline variability is associated with greater pain relief in those who receive a placebo. However, studies that evidence this association do not control for confounding effects (natural history and regression-to-the-mean); for this reason, we analyzed data from two randomized clinical trials (Placebo I and Placebo II, N = 134) while adjusting for confounding effects via a no-treatment group. Results agree between the two placebo groups: both placebo groups showed a negligible correlation between baseline variability and adjusted response (r sp (CI 95% ) = 0.13 (−0.09, 0.37) and 0.01 (−0.15, 0.20) for Placebo I and II, …

The Enigma Of Clinical Next Generation Sequencing (Ngs) Based Genetic Testing Variant Annotation Tools: A Performance Evaluation Study, Sachleen Tuteja '23

Student Publications & Research

As the scientific community continues to discover novel genetic variants associated with human constitutional disorders, there is a growing need for a standardized approach for reporting of genetic variants, as accurate variant identification is crucial for effective diagnosis and treatment. Robust identification and annotation of genetic variants relevant for human germline disorders is foundational for clinical Next Generation Sequencing (NGS) assays. Using a manually curated set of 296 variants, generated by targeted gene panel sequencing using the ~4700 gene medical exome panel on 105 patients, we evaluated the performance of two variant annotation tools (Variant Effect Predictor and Alamut Batch) …

Intraspecific Variation Mediates Density Dependence In A Genetically Diverse Plant Species, Andrii Zaiats, Matthew J. Germino, Marcelo D. Serpe, Bryce Richardson, T. Trevor Caughlin

Biology Faculty Publications and Presentations

Interactions between neighboring plants are critical for biodiversity maintenance in plant populations and communities. Intraspecific trait variation and genome duplication are common in plant species and can drive eco-evolutionary dynamics through genotype-mediated plant-plant interactions. However, few studies have examined how species-wide intraspecific variation may alter interactions between neighboring plants. We investigate how subspecies and ploidy variation in a genetically diverse species, big sagebrush (Artemisia tridentata), can alter the demographic outcomes of plant interactions. Using a replicated, long-term common garden experiment that represents range-wide diversity of A. tridentata, we ask how intraspecific variation, environment, and stand age mediate …

Golden Eagle Dietary Shifts Following Wildfire And Shrub Loss Have Negative Consequences For Nestling Survivorship, Julie A. Heath, Michael N. Kochert, Karen Steenhof

Biology Faculty Publications and Presentations

Wildfires and invasive species have caused widespread changes in western North America’s shrub-steppe landscapes. The bottom–up consequences of degraded shrublands on predator ecology and demography remain poorly understood. We used a before–after paired design to study whether Golden Eagle (Aquila chrysaetos) diet and nestling survivorship changed following wildfires in southwestern Idaho, USA. We assessed burn extents from 1981 to 2013 and vegetation changes between 1979 (pre-burn) and 2014 (post-burn) within 3 km of Golden Eagle nesting centroids. We measured the frequency and biomass of individual prey, calculated diet diversity indexes, and monitored nestling survivorship at 15 territories in …

A Draft Genome Provides Hypotheses On Drought Tolerance In A Keystone Plant Species In Western North America Threatened By Climate Change, Anthony E. Melton, James Beck, Stephanie J. Galla, Marcelo Serpe, Stephen Novak, Sven Buerki

Biology Faculty Publications and Presentations

Climate change presents distinct ecological and physiological challenges to plants as extreme climate events become more common. Understanding how species have adapted to drought, especially ecologically important nonmodel organisms, will be crucial to elucidate potential biological pathways for drought adaptation and inform conservation strategies. To aid in genome-to-phenome research, a draft genome was assembled for a diploid individual of Artemisia tridentata subsp. tridentata, a threatened keystone shrub in western North America. While this taxon has few genetic resources available and genetic/genomics work has proven difficult due to genetic heterozygosity in the past, a draft genome was successfully assembled. Aquaporin …

The Role Of Zingiberales Shared Evolutionary History And Leaf Traits In Structuring Rolled-Leaf Beetle Assemblages In A Tropical Forest, José Miguel Chaves Fallas

Dissertations

Understanding how local assemblages of plants and animals are structured is a central challenge for evolutionary ecology. Tropical assemblages are high in species numbers and in variety of ecological interactions, providing unique multispecies biological systems to test ecological and evolutionary hypotheses about community assembly. The objective of this dissertation was to understand the role of Zingiberales shared evolutionary history and plant traits for structuring the rolled-leaf beetle (Cephaloleia and Chelobasis, Chrysomelidae) assemblage in a lowland wet forest (La Selva Biological Station) of Costa Rica.

In chapter I studied the evolution of physical, nutritional, and chemical leaf traits, how …