Biology Commons^™

Seeing Eye To Eye? Comparing Faculty And Student Perceptions Of Biomolecular Visualization Assessments, Josh T. Beckham, Daniel R. Dries, Bonnie L. Hall, Rarchel M. Mitton-Fry, Shelly Engelman, Charmita Burch, Roderico Acevedo, Pamela S. Mertz, Didem Vardar-Ulu, Swati Agrawal, Kristin M. Fox, Shane Austin, Margaret A. Franzen, Henry V. Jakubowski, Walter R. P. Novak, Rebecca Roberts, Alberto I. Roca, Kristen Procko

Chemistry Faculty Publications

While visual literacy has been identified as a foundational skill in life science education, there are many challenges in teaching and assessing biomolecular visualization skills. Among these are the lack of consensus about what constitutes competence and limited understanding of student and instructor perceptions of visual literacy tasks. In this study, we administered a set of biomolecular visualization assessments, developed as part of the BioMolViz project, to both students and instructors at multiple institutions and compared their perceptions of task difficulty. We then analyzed our findings using a mixed-methods approach. Quantitative analysis was used to answer the following research questions: …

Dynamics Of Soil Microbial Communities Involved In Carbon Cycling Along Three Successional Forests In Southern China, Minghui Hu, Shuyidan Zhou, Xin Xiong, Xuan Wang, Yu Sun, Ze Meng, Dafeng Hui, Jianling Li, Deqiang Zhang, Qi Deng

Biology Faculty Research

Dynamics of plant communities during forest succession have been received great attention in the past decades, yet information about soil microbial communities that are involved in carbon cycling remains limited. Here we investigated soil microbial community composition and carbohydrate degradation potential using metagenomic analysis and examined their influencing factors in three successional subtropical forests in southern China. Results showed that the abundances of soil bacteria and fungi increased (p ≤ 0.05 for both) with forest succession in relation to both soil and litter characteristics, whereas the bacterial diversity did not change (p > 0.05) and the fungal diversity of Shannon-Wiener index …

Trade-Offs In Rooting Strategy Dimensions Along An Edaphic Gradient In A Grassland Ecosystem, Yuguo Yang, Sabrina E. Russo

School of Biological Sciences: Faculty Publications

1. Roots are essential to the diversity and functioning of plant communities, but trade-offs in rooting strategies are still poorly understood.
2. We evaluated existing frameworks of rooting strategy trade-offs and tested their underlying assumptions, guided by the hypothesis that community-level rooting strategies are best described by a combination of variation in organ-level traits, plant-level root:shoot allocation and symbiosis-level mycorrhizal dependency. We tested this hypothesis using data on plant community structure, above-and below-ground biomass, eight root traits including mycorrhizal colonisation and soil properties from an edaphic gradient driven by elevation and water availability in sandhills prairie, Nebraska, USA.
3. We found multidimensional trade-offs …

A Test Of The Pioneer Factor Hypothesis For Silent Gene Activation, Jeffrey Hansen

Arts & Sciences Graduate Student Theses and Dissertations

Transcription factors (TFs) activate silent genes by binding to and opening heterochromatic instances of their motifs. While we rely on this process for cellular reprogramming, we have an incomplete understanding of which TFs are capable of recognizing inaccessible instance of their motifs and what parameters are important for this activity. My thesis work aimed to address these two questions. The leading model for silent gene activation is the pioneer factor hypothesis (PFH). The PFH states that pioneer factors (PFs) are qualitatively unique TFs that can bind to and open DNA and subsequently recruit non-pioneer factors (nonPFs) to activate expression. We …

Treatment Of Oil Refinery Wastewater Polluted By Heavy Metal Ions Via Adsorption Technique Using Non-Valuable Media: Cadmium Ions And Buckthorn Leaves As A Study Case, Salem Jawad Alhamd, Mohammed Nsaif Abbas, Mehrdad Manteghian, Thekra Atta Ibrahim, Karar Dawood Salman Jarmondi

Karbala International Journal of Modern Science

This study focuses on the removal of cadmium ions generated by oil refinery wastewater, employing an agricultural by-product. Buckthorn leaves, sourced from Baghdad and Diyala provinces, underwent preparation, including washing, drying, crushing, and sieving before being utilized in experiments. Batch experiments were conducted using simulated solutions to assess the impact of six key adsorption design parameters: pH, cadmium concentration, agitation speed, contact time, adsorbent dosage, and temperature. The highest adsorption efficiency, reaching 94.4367%, was directly correlated with contact time, adsorbent dosage, pH value, and agitation speed, and inversely related to other variables. Morphological studies on the treated adsorbent, indicated structural …

Turtle Species And Ecology Drive Carapace Microbiome Diversity In Three Seasonally Interconnected Wetland Habitats, Matthew Parks, Jun Sheng Lee, Kassandra Camua, Ethan Hollender

Biological Sciences Faculty Publications and Presentations

Different species of freshwater turtles exhibit primary behaviours ranging from aerial basking to benthic bottom-walking, cycle between wet and dry conditions at different time intervals, and undertake short-distance overland movements between aquatic habitats. These behaviours in turn may impact the accumulation of microbes on external shell surfaces of turtles and provide novel niches for differentiation of microbial communities. We assessed microbial diversity using 16S and 18S rRNA metabarcoding on carapace surfaces of six species of freshwater turtles residing in three adjacent and seasonally interconnected wetland habitats in southeast Oklahoma (United States). Communities were highly diverse, with nearly 4200 prokaryotic and …

Applications Of Bioinformatics For Exploring The Genomic Landscape Of Cancer And Characterizing Treatment Response For Precision Oncology, Sharon Freshour

Arts & Sciences Graduate Student Theses and Dissertations

While the integration of next-generation sequencing and bioinformatics into cancer research has been immeasurably useful for advancing the field, there are still many gaps in understanding the genomic landscape of cancer due to the complexity of cancer development and evolution. Likewise, there are still many challenges for identifying and applying effective therapeutics for cancer treatment. Thus, there remains a need to continue characterizing the genomic landscape of cancer, to explore the evolution of cancer, and to understand how tumors respond to treatment. The projects described in this dissertation cover several applications of next-generation sequencing, bioinformatic analysis, and database resources for …

The Macrophage Autophagy-Lysosome System In Atherosclerosis Pathogenesis, Astrid Carolina Rodriguez Velez

Arts & Sciences Graduate Student Theses and Dissertations

Cardiovascular diseases, particularly atherosclerosis, pose significant health concerns, necessitating a comprehensive understanding of underlying mechanisms for effective therapeutic interventions. In this dissertation, I studied diverse topics, ranging from dietary impacts to intracellular processes, shedding light on novel avenues for atherosclerosis research. It is divided in 4 core projects. In Chapter 2) I studied how dietary protein drives atherosclerosis and lesion complexity. We found that protein ingestion acutely elevates amino acid levels in blood and atherosclerotic plaques, stimulating macrophage mTOR signaling. This is causal in plaque progression as the effects are abrogated in macrophage-specific Raptor-null mice. Mechanistically, we find amino acids …

Vibroscape Analysis Reveals Acoustic Niche Overlap And Plastic Alteration Of Vibratory Courtship Signals In Ground-Dwelling Wolf Spiders, Noori Choi, Pat Miller, Eileen A. Hebets

School of Biological Sciences: Faculty Publications

To expand the scope of soundscape ecology to encompass substrate-borne vibrations (i.e. vibroscapes), we analyzed the vibroscape of a deciduous forest floor using contact microphone arrays followed by automated processing of large audio datasets. We then focused on vibratory signaling of ground-dwelling Schizocosa wolf spiders to test for (i) acoustic niche partitioning and (ii) plastic behavioral responses that might reduce the risk of signal interference from substrate-borne noise and conspecific/heterospecific signaling. Two closely related species - S. stridulans and S. uetzi - showed high acoustic niche overlap across space, time, and dominant frequency. Both species show plastic behavioral …

Headstarting Eastern Box Turtles In Southwest Michigan: Implications For Growth, Survival, And Spatial Ecology, Faith C. Kuzma

Masters Theses

Turtles and tortoises are one of the most endangered groups of animals in the world as anthropogenic activities like overexploitation, collection for the pet trade, and habitat loss and fragmentation have caused dramatic population declines in recent years. As a result, proactive conservation techniques are being increasingly implemented to facilitate population recovery. Headstarting is a popular chelonian conservation technique that aims to reduce vulnerability and increase survival of juvenile turtles. While headstarting has been a valuable tool for many species, there is increasing evidence that species-specific influences impact its success. In this study, we headstarted four annual cohorts of eastern …

Microhabitat Selection Of Adult Female Eastern Diamondback Rattlesnakes (Crotalus Adamanteus) In The Carolinas, Matthew Gacheny

Theses, Dissertations and Capstones

Reptiles rely on environmental conditions to regulate body temperature using behavioral strategies to meet basic life history needs. Viviparous squamates use thermoregulatory behaviors to meet energetic requirements for vitellogenesis and gestation, which carry considerable energetic costs and must balance with maintenance and survival. Embryonic development is often optimized in a narrower temperature range than the mother’s preferred temperature, creating an intergenerational conflict that should be addressed with maternal microhabitat selection. Field-based studies are needed to understand the link between the thermal biology of reptiles, their reproduction, and implications for population viability. With a use-availability logistic regression framework, I examined thermal …

Symbiosis Under Stress: Unraveling The Interplay Of Ocean Acidification And Rising Temperatures On Acropora Samoensis (Staghorn Coral), Jerald William Smolkin

Theses and Dissertations

This experiment explores the response of marine organisms to the combined challenges of ocean acidification and rising temperatures, with a focus on coral reef ecosystems. As global climate change threatens profound declines in coral reefs, understanding the multifaceted impacts of these stressors becomes crucial. The study observes cellular changes in A. samoensis tissues in four different groups, including control, Temp, pH, and Temp and pH. Results indicate significant breakdown of membrane compartmentalization and cell junctions, with notable degradation and calcium carbonate crystallization in pH-stressed samples. Additionally, chlorophyll extraction data support coral bleaching due to the expulsion of zooxanthellae. These findings …

Mercury Bioaccumulation In Top-Level Predatory Fishes From Marine And Freshwater Environments, David L. Taylor, Jillian Haudenshield, Johnathan Serbst, Jim Lake, Alan Libby

Student Research Symposium

Mercury is a widespread environmental contaminant that poses a threat to human and wildlife health. Mercury concentrations ([Hg]) may be elevated in fish tissues due to individual bioaccumulation and biomagnification in the food web. This study examined Hg bioaccumulation rates in striped bass (SB) and largemouth bass (LMB): top-level predatory fishes in marine and freshwater environments. SB, LMB, and their prey were collected in Rhode Island waters from 2006 to 2023 using rod & reel, electrofishing, and trawling methods. Age (yr) was determined for each fish based on measurements of total lengths (TL; cm) in the laboratory (LMB: 15-57 cm, …

Factors Associated With Acoustic Bat Presence During Spring Emergence In The Appalachian Mountains Of Western Virginia, Emily Kirk Pody

Theses, Dissertations and Capstones

Studies of threats that bats face during hibernation have increased in response to white-nose syndrome (WNS), a fungal disease that has ravaged North American bat populations. However, impacts of WNS on bat ecology during spring emergence, when bats are potentially recovering from infection and allocating resources for reproduction, is relatively understudied. As more bat species become listed at the federal and state level, the need to understand the factors associated with spring emergence is critical for improving conservation guidelines and habitat management practices. Acoustic monitoring is an efficient method for monitoring bat presence for prolonged periods of time, giving biologists …

Three Fundamental Challenges To The Advancement Of Stemflow Research And Its Integration Into Natural Science, John T. Van Stan Ii, Juan Pinos

Biological, Geological, and Environmental Faculty Publications

Plant canopies divert a portion of precipitation to the base of their stems through "stemflow", a phenomenon that influences the canopy water balance, soil microbial ecology, and intrasystem nutrient cycling. However, a comprehensive integration of stemflow into theoretical and numerical models in natural science remains limited. This perspective examines three unresolved, fundamental questions hindering this integration, spanning the canopy to the soil. First, the precise source area within the canopy that generates stemflow is undefined. Thus, we asked, "whence stemflow?" Current common assumptions equate it to the entire tree canopy, a potentially misleading simplification that could affect our interpretation of …

Entomologists Require Ethical Guidance For Compassionate Management Of Delusional Parasitosis Cases, Kathleen Murphy-Hollies, Michael Skvarla, Robin M. Verble

Biological Sciences Faculty Research & Creative Works

No abstract provided.

Comparison Of Energy Budget Of Cockroach Nymph (Hemimetabolous) And Hornworm (Holometabolous) Under Food Restriction, Charles J. Green, Chen Hou

Biological Sciences Faculty Research & Creative Works

Animals with different life histories budget their intake energy differently when food availability is low. It has been shown previously that hornworm (larva of Manduca sexta), a holometabolous insect species with a short development stage, prioritizes growth at the price of metabolism under food restriction, but it is unclear how hemimetabolous insect species with a relatively long development period budget their intake energy under food scarcity. Here, we use orange head cockroaches (Eublaberus posticus) to investigate this question. We found that for both species under food restriction, rates of metabolism and growth were suppressed, but the degree of reduction was …

Do Nest Box Temperatures Affect Nest Success And Nestlings Growth For Eastern Bluebirds?, Mathew Gordon, Katie Stumpf

Graduate Research Showcase

Rising global temperatures due to climate change have caused declines in many species. For birds, temperature is a primary factor in nest site selection and nest success, so successful management will require temperature mitigation techniques. Secondary cavity nesting birds such as the Eastern Bluebird are particularly vulnerable as common occupants of nest boxes, which are often warmer inside than the outside ambient temperature. Temperatures exceeding 42°C can have numerous negative consequences for Bluebirds, including reducing hatching success and nestling growth. We monitored 50 Eastern Bluebird nest boxes (25 are painted white and 25 are unpainted) at Panola Mountain State Park …

The Comparison Of Different Wetland Fish Assemblages Over Time, Robert Edward Adelstein

Theses, Dissertations and Capstones

Wetlands provide essential ecosystem services. Historically, we have drained and filled 73% of wetlands for agricultural use throughout the United States from the 1780s to the 1980s (Dahl, 1990). A nationwide focus on restoring wetlands has since occurred. Literature on restored/mitigated wetlands is rife with examples that do and do not support the same ecosystem services as natural wetlands (Langston, 1997; Meil, 2014). Restoration of wetlands occurred at the Green Bottom Wildlife Management Area (GBWMA) over several decades. Various sections of the wetland were classified by age, water depth, and vegetation. One hypothesis was that differences in fish assemblage would …

Late Summer Plankton Community Variation In Near Shore Environments, Aidan Jacobs-Walker

Copley Library Undergraduate Research Awards

Phytoplankton communities have profound impacts on ecosystem health and function. In the Southern California Bight, hydrographic conditions play a key role in determining the composition of phytoplankton communities. This study conducted hydrographic and plankton community analyses of the nearshore environment off Dana Point, California, during late September. Similar to other studies in the SCB during fall, we observed weakly stratified, oligotrophic waters dominated by dinoflagellates under 10 μm. However, the recorded plankton abundances onshore vs. offshore deviated from the “green ribbon” typical of the SCB, in which phytoplankton are much more abundant onshore than offshore. Additionally, while the onshore community …

The E-Liquid Flavorings Cinnamaldehyde, Vanillin, And Ethyl Vanillin Induce Cellular Stress Responses In Human Proximal Tubule (Hk-2) Epithelial Cells, Ashley J. Cox

Theses, Dissertations and Capstones

The use of electronic nicotine delivery systems (ENDS) has become popular in recent years as an alternative to traditional cigarettes. These devices heat and subsequently vaporize e-liquids for inhalation by the user, which allows for the delivery of ingredients such as flavorings, nicotine, and solvents through the vapor. Flavorings used in e-liquids are “generally recognized as safe” (GRAS) for consumption by the Food and Drug Administration (FDA), however there are currently no recommendations on safety regarding the inhalation of flavoring agents. While research characterizing effects of e-liquids and their flavorings is abundant in lung and respiratory tract models, few studies …

Female Biology, Jennifer Dever

All USF Faculty Authored Books

Over twenty years ago I developed a course for the upper- level biology major at the University of San Francisco called

Female Biology. This was from what I perceived as a gap in the undergraduate biology curriculum- students were not learning about the evolutionary aspects of being female and studying the specific health-related issues unique to women. The information in the most widely used general biology textbooks written from a male perspective, focuses on research gained from male models by work conducted in male-led laboratories. There still exists a problem with a lack of adequate representation of women in biomedical …

Prevalence Of Insecticide Resistance Gene In Aedes Albopictus Population In Illinois Regions, Merylann Ochieng

2024 Awards for Excellence in Student Research and Creative Activity - Documents

Mosquitoes are vectors known to transmit many pathogens and parasites that cause serious human diseases such as Malaria, Dengue, Yellow and Chikungunya fever, Encephalitis, and Filariasis (Becker et al., 2010) (Franklinos et al., 2019). Aedes albopictus specie transmits Zika, Chikungunya, yellow Fever and Rift valley fever viruses (Leta et al., 2018). Aedes species are geographically invading new areas due to globalization and environmental changes (Lwande et al., 2020). Temperature increase, severe rainfall, and high humidity encourage diseases to spread to new areas where new vectors may act as carriers (Näslund et al., 2021). Aedes albopictus are expanding further along the …

Thymidine Phosphorylase Is A Promising Target In Sars-Cov-2 Spike Protein-Enhanced Thrombosis, Renat Roytenberg

Theses, Dissertations and Capstones

Thrombosis, as an underlying mechanism in cardiovascular diseases, is the leading global cause of death in the 21st century. Infection is a risk factor for thrombosis, and the coronavirus disease 2019 (COVID-19) pandemic has led to a rise in the incidence of thrombosis, thereby increasing mortality. In comparison to previous severe coronavirus outbreaks, rates of thrombosis in COVID-19 have been unprecedented. COVID-19 is caused by the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 spike protein (SP), the key used to enter host cells, is implicated in thrombosis pathology, though mechanisms are not fully understood. The SARS-CoV-2 …

Differential Tail Autotomy Between Two Genetic Clades Of A Woodland Salamander, Plethodon Cinereus, Ryan Mayer

Masters Theses

Following the retreat of glaciers in North America, a wide diversity of organisms rapidly migrated into previously uninhabited regions, including animals with limited dispersal abilities such as amphibians. I wanted to better understand the strategies that salamanders use to aid in their dispersal abilities and to understand if patterns of post-glacial range expansion affect phenotypic traits such as anti-predator strategies. In this study, I used existing phylogeographic evidence of clade membership as a framework to examine whether red-backed salamanders (Plethodon cinereus) differed in tail autotomy behavior at the range edge versus the range core, and across the geographic range of …

Examining Quantitative Honest Signaling In Aposematic Traits Of The Green And Black Poison Frog Dendrobates Auratus From Costa Rica, Katherine Porras-Brenes

Masters Theses

No abstract provided.

A Global Synthesis Of The Relative Impacts Of Habitat Amount, Fragmentation, And Matrix Quality On Forest Biodiversity, Antoinette Esposito

Masters Theses

Aim To assess the relative impact of different landscape variables on species richness and to determine whether species richness declines more rapidly below an extinction threshold of remaining habitat. The results of this study will help to better inform future conservation strategies. Location Global Time period 1997 – 2013 Major taxa studied Amphibians, birds, invertebrates, mammals, and reptiles Methods Data from 71 studies published in the global BioFrag database were used to determine species richness across multiple landscapes and biomes. The Hansen dataset was used to collect data on habitat amount (forest area), fragmentation (patch density), and matrix quality (mean …

Development Of A Novel Edna Sampling Method For Macroinvertebrate Species Of Greatest Conservation Need (Sgcn) In Texas, James York

Biology Theses

Environmental DNA (eDNA) sampling is a new sampling technique that allows for non-invasive sampling of target species or the characterization of entire communities based on barcoding genes. The goal of this study was to sequence common barcoding genes such as 28S rRNA and Cytochrome C Oxidase I (COI), and then develop species-specific primers for eight macroinvertebrates listed as Species of Greatest Conservation Need (SGCN) in Texas. After sampling for the target species, five were not found, all of which were in the Order Trichoptera (caddisflies). A sixth target species, Isoperla sagittata, was found to have only one gap and …

Investigating Scube3 Nuclear Localization In Presence Of Doxorubicin Treatment In Triple Negative Breast Cancer Cells, Lillian Ergle

Merge

Signal peptide-CUB-EGF-like domain-containing protein 3 (SCUBE3) is a glycosylated secreted protein. Prior to its secretion, SCUBE3 localizes in the cytoplasm. We observed that SCUBE3 protein trans-localized to the nucleus following Doxorubicin (DOX) treatment. DOX is one of the strongest chemotherapeutic agents and the first-line drug used in breast cancer treatment. SCUBE3 structural analysis showed that it lacks a DNA binding domain. Based on this observation and other preliminary data, we hypothesized that nuclear SCUBE3 protein promotes the survival of cells against Doxorubicin treatment. To investigate this hypothesis, we made a wild-type construct and three constructs with mutated nuclear localization sequences …

Documentation Of Hadrosaurid Humeri From The Liscomb Bonebed, North Slope, Alaska Prior To Histological Sectioning, Makenna Galvin

Student Research Poster Presentations 2024

Proper documentation of research specimens is a crucial component that must be completed prior to histological sectioning. Since specimens are unique and irreplaceable, documentation provides information that may later be unobtainable after sectioning, due to the inherent nature of the technique having to permanently alter the specimen. The hadrosaurid dinosaur, the Edmontosaurus, has an abundant fossil record, which can be partly attributed to being gregarious, and therefore preserves multiple monodominant bonebeds and several dozen associated skeletons across North America. This makes Edmontosaurus an ideal taxon to use for life history studies. However, previous Edmontosaurus bonebeds have only preserved specimens of …