Life Sciences Commons^™

Population Genetics And Morphometrics Of Overwintering Swamp Sparrows (Melospiza Georgiana) At Panola Mountain State Park, Ashley Mcmahon

Graduate Research Showcase

Grassland birds are facing the greatest decline of any bird guild in North America due to widespread loss of grassland habitats. Conservation efforts tend to focus on birds that breed in grasslands, but grassland habitat loss will also negatively affect populations that overwinter in grasslands. Three Swamp Sparrow subspecies (Melospiza georgiana georgiana, M. g. ericrypta, M. g. nigrescens) segregate on at least some of their breeding grounds but may mix on wintering grounds, which often includes grasslands. Philopatric passerines often also segregate by sex on wintering grounds. Thus, loss of overwintering grasslands may disproportionately impact both subspecies and sex, leading …

Preliminary Analysis Of Landscape Associations For Virginia Opossum Roadkills, Lucy Beck

Graduate Research Showcase

Methods for mitigating wildlife-vehicle collisions are important for the health of local wildlife populations and for driver safety. A variety of spatial, temporal, and biological factors are known to influence these collisions, and the combination of these factors varies for any given road. Therefore, understanding the spatial distribution of roadkill on the local landscape scale is required for effective mitigation planning. Furthermore, the distribution of roadkill on a local scale aids in our understanding of species’ ranges and the environmental factors associated with habitat use. A total of 620 Virginia Opossums (Didelphis virginiana) roadkills were recorded during a 10-year period …

Fluorescent Analysis Of Protein Localization In Saccharomyces Cerevisiae, Lewis Barr, Ellen France Phd

Graduate Research Showcase

A principal objective of cellular biology is to identify the function of proteins as they interact with their environment. Cellular localization provides context for the function and interactions of proteins. In this study, we seek to identify the localization of three proteins within Saccharomyces cerevisiae through C-terminal green fluorescent protein epitope tagging and subsequent fluorescent microscopy. As 75% of the yeast proteome has been classified, this project seeks to fill the remaining gap in unidentified cellular localization by investigating the proteins fsh3, gid10, and ade13. The analysis of high-resolution localization and comparative phylogenetic data reveals potential cellular environments and protein …

Emerging Vibrio Harveyi And Vibrio Campbellii Pathogens In Georgia Waters, Cameron Brown

Graduate Research Showcase

In the face of global warming and ocean acidification, waterborne pathogens are geographically expanding and rapidly evolving. The Vibrio genus contains a number of pathogens of humans and aquatic animals, many of which benefit from elevated temperatures and low pH conditions. Vibrio harveyi and Vibrio campbellii belong to the Harveyi clade and are barely distinguishable upon their genetic make-up. Natively found in warm waters of Asia and South America, these species are well-established pathogens that infect fish, shrimp, and mollusks. Due to climate change, the Southeastern United States is potentially becoming an accommodating environment for these pathogens, however this has …

The Effect Of Callery Pear (Pyrus Calleryana) On Soil Macrofauna (Diplopoda And Oligochaeta), Joseph M. Mcgee, Bruce Snyder

Graduate Research Showcase

Callery pear (Pyrus calleryana) is a relatively recent invader of North America. Its ecological effects are still being explored, including those affecting soil macrofauna such as millipedes (Diplopoda) and earthworms (Clitellata: Oligochaeta). These animals play important roles in many soil processes so understanding how they respond to invasive species is vital to soil health. A previous study exploring potential herbicide control was completed in 2019, however as of 2022 there are still treatment zones with little to no Callery pear alongside fully invaded plots, providing an optimal habitat mosaic for comparison. This allowed us to pursue two research goals: To …

Effects Of Roadways On Seasonal Movement Strategies And Mate Location Success In An Imperiled Pit Viper (Crotalus Horridus), Elizabeth J. Noble

Graduate Research Showcase

Understanding animal movement behavior is fundamental to effective conservation and management. Within populations, various movement strategies can be displayed in search of critical resources, and these strategies are influenced by multiple factors related to individuals and the environment. Mating partners are one critical resource that affect movement during mating seasons. For many large-bodied snakes, male mate-searching movements are the primary determinant of mate location success, however, males incur significant risks associated with elevated movement. In an increasingly human-modified world, this often includes increased interactions with anthropogenic landscape features. A recent range-wide status assessment for Timber Rattlesnakes (Crotalus horridus) identified roadways …

Comparison Of Avian And Non-Avian Reptile Digestion On Small Mammal Remains And The Implications For Palaeoecological Interpretations., Todd B. Bennett*

Graduate Research Showcase

Small mammals are a uniquely important group in understanding paleoecology due to their restricted habitat and sensitivity to changing environments. The use of small mammal fossils has been widely documented in taphonomical and paleontological research, mainly in the form of owl pellet analysis. However, few studies have focused on other animal clades, though a small number have examined digestive damage due to mammals and reptiles. Research presented here examines digestive modification of small mammals caused by various species of snakes, a previously unresearched taxa, compared to previous work done on owl pellets. This study lays out a systematic approach for …

The Mindful Athlete Program, Joanne Bullard, Sojung Kim

Rita & Larry Salva School of Nursing and Health Professions Departmental Research

According to the spring 2020 NCAA Well-Being Study, collegiate student-athletes reported experiencing mental health concerns due to the impact of the COVID-19 pandemic. The data indicated that student-athletes were experiencing mental health concerns 150%-250% higher than historically reported (NCAA, 2020). These concerns were prevalent among all divisions. For Division III student-athletes, mental health concerns experienced during the COVID-19 pandemic included “feeling overwhelmed by all they had to do, sleep difficulties, feeling mentally exhausted, feeling very lonely, feeling a sense of loss, and feeling very lonely and sad” (NCAA, 2020). This study indicated desired resources of Division III student-athletes included elements …

Mechanism Of Sphingolipid Homeostasis Revealed By Structural Analysis Of Arabidopsis Spt-Orm1 Complex, Peng Liu, Tian Xie, Xinyue Wu, Gongshe Han, Sita D. Gupta, Zike Zhang, Jian Yue, Feitong Dong, Kenneth Gable, Somashekarappa Niranjanakumari, Wanyuan Li, Lin Wang, Wenchen Liu, Ruifeng Yao, Edgar B. Cahoon, Teresa M. Dunn, Xin Gong

Center for Plant Science Innovation: Faculty Publications

The serine palmitoyltransferase (SPT) complex catalyzes the first and rate-limiting step in sphingolipid biosynthesis in all eukaryotes. ORM/ORMDL proteins are negative regulators of SPT that respond to cellular sphingolipid levels. However, the molecular basis underlying ORM/ORMDL-dependent homeostatic regulation of SPT is not well understood.We determined the cryo–electron microscopy structure of Arabidopsis SPT-ORM1 complex, composed of LCB1, LCB2a, SPTssa, and ORM1, in an inhibited state. A ceramide molecule is sandwiched between ORM1 and LCB2a in the cytosolic membrane leaflet. Ceramide binding is critical for the ORM1-dependent SPT repression, and dihydroceramides and phytoceramides differentially affect this repression. A hybrid β sheet, formed …

Stabilizing G-Quadruplex Dna And Rna Structures With Ionic Liquids, Timothy Vaden

College of Science & Mathematics Departmental Research

Stabilizing DNA and RNA for long-term room-temperature storage is important for many biotechnological applications including oncology pharmaceuticals and mRNA-based vaccines (e.g. Covid vaccines). This poster shows that ionic liquids can improve the thermal stability of G-quadruplex DNA and RNA structures, and motivates further studies of ionic liquid-based materials for DNA / RNA stabilization.

2023 Nebraska Women In Agriculture Conference, Jessica Groskopf, Katie Hothem

Cornhusker Economics

Includes a recap of the 38th Nebraska Women in Agriculture Conference held in February 2023 in Kearney, Nebraska.

Protocol To Identify The Core Gene Supported By An Essential Gene In E. Coli Bacteria Using A Genome-Wide Suppressor Screen, Isao Masuda, Ya-Ming Hou

Department of Biochemistry and Molecular Biology Faculty Papers

We describe here a genome-wide screening approach to identify the most critical core reaction among a network of many that are supported by an essential gene to establish cell viability. We describe steps for maintenance plasmid construction, knockout cell construction, and phenotype validation. We then detail isolation of suppressors, whole-genome sequencing analysis, and reconstruction of CRISPR mutants. We focus on E. coli trmD, which encodes an essential methyl transferase that synthesizes m1G37 on the 3'-side of the tRNA anticodon. For complete details on the use and execution of this protocol, please refer to Masuda et al. (2022).

Developing Tools For Introducing Modifications Into The Chicken Genome, Zachary Eldon Olsen

Theses and Dissertations

The chicken is a classic model organism that has provided key insights into embryonic development. Chicken embryos can be directly manipulated and observed during development while retaining the potential to reach adulthood. Despite this benefit, the utility of the chicken in studying development has been limited by the difficulty of introducing genetic changes to the genome. The recent development of cell culture conditions for chicken primordial germ cells (cPGC) has made it feasible to produce transgenic chickens, but there is still a lack of tools for introducing genetic modifications into cPGCs. Recombinase Mediated Cassette Exchange (RMCE) is a technique that …

Surveillance And Stewardship: Where Infection Prevention And Antimicrobial Stewardship Intersect, Fred C. Tenover, Debra A. Goff

Biology Faculty Publications

Colonization with multidrug-resistant organisms (MDROs) is a risk factor for subsequent infection. Surveillance for MDROs, including methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, extended-spectrum beta-lactamase-producing Enterobacterales, and carbapenemase-producing organisms, is commonly conducted in hospitals to prevent spread of MDROs, in part to reduce the potential for additional infections. Although colonization is a risk factor for infection, data on colonization with various MDROs are often not considered when selecting anti-infective therapy. There are conflicting data on the strength of the positive and negative predictive values of the colonization test results to guide therapeutic strategies. Defining therapeutic strategies for patients with complicated or …

Statistical Analysis Of Ribonucleotide Incorporation In Human Cells, Tejasvi Channagiri

USF Tampa Graduate Theses and Dissertations

During the DNA replication process, ribonucleotides, the building blocks of RNA, may be occasionally incorporated in the newly synthesized DNA. DNA is primarily composed of deoxyribonucleotides and there exist cellular mechanisms for removing ribonucleotides from DNA, which may point towards ribonucleotide incorporation being a replication error. Further, an excess of these ribonucleotides in the genome has been known to lead to genomic instability and has been implicated in human diseases. However, there are also hypotheses that suggest that ribonucleotides may be beneficial in certain circumstances. In this study we examine ribonucleotide incorporation in the human genome in several human cell …

Partial Characterization Of Plasmodium Falciparum Genes Implicated In Altered Artemisinin Stress Response, Caroline F. Simmons

USF Tampa Graduate Theses and Dissertations

Malaria is a parasitic illness caused by the Plasmodium spp., with an estimated 247 million malaria cases reported in 2021 across 84 endemic countries. Treatment of the deadliest malaria parasite, P. falciparum, relies on artemisinin combination therapies (ACTs). However, while ACTs have greatly decreased malaria mortality, this progress is threatened due to artemisinin (ART) partial resistance and ACT failure in Southeast Asia and Sub-Saharan Africa. SNPs to the Kelch13 (K13) gene are a well-characterized marker for ART resistance. However, increasing evidence that resistance to ART mediated by genes not related to K13 SNPs prompts the need to characterize other novel …

How Some Arboreal Salamanders (Genus Aneides) Jump, Glide, And Generate Lift, Christian E. Brown

USF Tampa Graduate Theses and Dissertations

The jumping and subsequent aerial behaviors of arboreal lungless salamanders (genus Aneides) had never been investigated or described. The aims of this research were to (1) compare jumping performance within the family Plethodontidae with a special focus on arboreal species from genus Aneides, (2) describe the biomechanics and kinematics of aerial behaviors after a jump or extended fall, and (3) model airflow over the morphology of the most aerially adept salamanders to investigate if they are capable of generating lift. First, I recorded salamanders jumping, locomoting vertically, dropping, and flying in a vertical wind tunnel. Then, I laser-scanned and reconstructed …

Design, Biological Evaluation, And Computer-Aided Analysis Of Dihydrothiazepines As Selective Antichlamydial Agents, Luana Janaína De Campos, Mohamed A. Seleem, Jiachen Feng, Kelly Mari Pires De Oliveira, João Víctor De Andrade Dos Santos, Shivdeep Hayer, Jonathan B. Clayton, Sharvath Kathi, Derek J. Fisher, Scot P. Ouellette, Martin Conda-Sheridan

Department of Food Science and Technology: Faculty Publications

Chlamydia trachomatis (CT) causes the most prevalent sexually transmitted bacterial disease in the United States. The lack of drug selectivity is one of the main challenges of the current antichlamydial pharmacotherapy. The metabolic needs of CT are controlled, among others, by cylindrical proteases and their chaperones (e.g., ClpX). It has been shown that dihydrothiazepines can disrupt CT-ClpXP. Based on this precedent, we synthesized a dihydrothiazepine library and characterized its antichlamydial activity using a modified semi-high-throughput screening assay. Then, we demonstrated their ability to inhibit ClpX ATPase activity in vitro, supporting ClpX as a target. Further, our lead …

The Influence Of Gmos On The Composition Of The Gut Microbiome, Shawnia Rakhshani, Hailey Wight

Celebrating Scholarship and Creativity Day (2018-)

Genetically modified organisms have been used for decades in agriculture across the world. The use of GMOs has been advertised as a solution to many agricultural issues. However, people have raised concerns about GMOs reshaping human health, and more importantly, the composition of the gut microbiome. The gut microbiome has a vital role in human health through digestion, immune abilities, and protection against disease-causing bacteria. If any disturbances occur in the microbiome, it can have negative effects on an individual’s overall health and wellbeing. Our paper investigates the pros and cons of ingesting GMOs in relation to our human gut …

Inferring Gene Regulatory Networks From Rna-Seq Data Using Kernel Classification, Dirar Homouz

Faculty, Staff and Student Publications

Gene expression profiling is one of the most recognized techniques for inferring gene regulators and their potential targets in gene regulatory networks (GRN). The purpose of this study is to build a regulatory network for the budding yeast Saccharomyces cerevisiae genome by incorporating the use of RNA-seq and microarray data represented by a wide range of experimental conditions. We introduce a pipeline for data analysis, data preparation, and training models. Several kernel classification models; including one-class, two-class, and rare event classification methods, are used to categorize genes. We test the impact of the normalization techniques on the overall performance of …

Predicting Site‑Specific Economic Optimal Nitrogen Rate Using Machine Learning Methods And On‑Farm Precision Experimentation, Alfonso De Lara, Taro Mieno, Joe D. Luck, Laila A. Puntel

Department of Agronomy and Horticulture: Faculty Publications

Applying at the economic optimal nitrogen rate (EONR) has the potential to increase nitrogen (N) fertilization efficiency and profits while reducing negative environmental impacts. On-farm precision experimentation (OFPE) provides the opportunity to collect large amounts of data to estimate the EONR. Machine learning (ML) methods such as generalized additive models (GAM) and random forest (RF) are promising methods for estimating yields and EONR. Twenty OFPE N trials in wheat and barley were conducted and analyzed with soil, terrain and remote-sensed variables to address the following objectives: (1) to quantify the spatial variability of winter crops yield and the yield response …

Morphological Characterization Of Intraspecific Variation For Trichome Traits In Tomato (Solanum Lycopersicum), Satinderpal Kaur, Neetu Khanal, Robert K. Dearth, Rupesh R. Kariyat

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

Trichomes, the hairlike protuberances in plants, have been well known to act as the first line of defense against herbivores, and abiotic stresses, along with other structural defenses such as spines, thorns, and waxes. We previously reported the tremendous variation in trichome traits among different wild and cultivated Solanum species and demonstrated that trichomes types and density are traditionally miscalculated and often misnamed. However, intraspecific variation in trichome traits is poorly understood, although this has implications for stress tolerance and resistance breeding programs in economically important crop species and can also mediate ecological interactions at multiple trophic levels in their …

Rare Variant Enrichment Analysis Supports Greb1l As A Contributory Driver Gene In The Etiology Of Mayer-Rokitansky-Küster-Hauser Syndrome, Angad Jolly, Haowei Du, Christelle Borel, Na Chen, Sen Zhao, Ruizhi Duan, Moez Dawood, Sejal Salvi, Shalini N Jhangiani, Donna M Muzny, André Koch, Konstantinos Rouskas, Stavros Glentis, Efthymios Deligeoroglou, Flora Bacopoulou, Carol A Wise, Jennifer E Dietrich, Ignatia B Van Den Veyver, Antigone S Dimas, Sara Brucker, V Reid Sutton, Richard A Gibbs, Stylianos E Antonarakis, Nan Wu, Zeynep H Coban-Akdemir, Lan Zhu, Jennifer E Posey, James R Lupski

Faculty, Staff and Student Publications

Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is characterized by aplasia of the female reproductive tract; the syndrome can include renal anomalies, absence or dysgenesis, and skeletal anomalies. While functional models have elucidated several candidate genes, only WNT4 (MIM: 603490) variants have been definitively associated with a subtype of MRKH with hyperandrogenism (MIM: 158330). DNA from 148 clinically diagnosed MRKH probands across 144 unrelated families and available family members from North America, Europe, and South America were exome sequenced (ES) and by family-based genomics analyzed for rare likely deleterious variants. A replication cohort consisting of 442 Han Chinese individuals with MRKH was …

Hpv-Related Anal Cancer Is Associated With Changes In The Anorectal Microbiome During Cancer Development, Jacob H Elnaggar, Victoria O Huynh, Daniel Lin, R Tyler Hillman, Chike O Abana, Katarina C Tomasic, Ramez Kouzy, Jae L Phan, Jennifer Wargo, Emma B Holliday, Prajnan Das, Melissa P Mezzari, Nadim J Ajami, Erica J Lynn, Bruce D Minsky, Van K Morris, Andrea Milbourne, Craig A Messick, Ann H Klopp, P Andrew Futreal, Cullen M Taniguchi, Kathleen M Schmeler, Lauren E Colbert

Faculty, Staff and Student Publications

BACKGROUND: Squamous cell carcinoma of the anus (SCCA) is a rare gastrointestinal cancer. Factors associated with progression of HPV infection to anal dysplasia and cancer are unclear and screening guidelines and approaches for anal dysplasia are less clear than for cervical dysplasia. One potential contributing factor is the anorectal microbiome. In this study, we aimed to identify differences in anal microbiome composition in the settings of HPV infection, anal dysplasia, and anal cancer in this rare disease.

METHODS: Patients were enrolled in two prospective studies. Patients with anal dysplasia were part of a cross-sectional cohort that enrolled women with high-grade …

Effects Of Equine Interaction On Mutual Autonomic Nervous System Responses And Interoception In A Learning Program For Older Adults, Ann L. Baldwin, Lisa Walters, Barbara K. Rector, Ann C. Alden

People and Animals: The International Journal of Research and Practice

Equine-assisted learning (EAL) may improve the health of older adults, but scientific data are sparse. This study investigated whether people aged 55 and older show increased heart rate variability (HRV) during EAL and awareness of bodily sensations that are overall pleasant. Subjects (n = 24) participated in mindful grooming during which they slowed their breathing and brushed a horse while noticing sensations in their body and watching the horse’s reactions. The subject’s and horse’s HRV were recorded simultaneously before, during, and after mindful grooming. For control, the same subjects performed mindful grooming with a plush simulation horse. During exit …

Performance Evaluation Of Wastewater Treatment Plant, Vidyaranyapuram, Mysuru, Snehalatha B, Sahana K S, Chaitra M, Mounikasree M, Sulochanadevi B Chakrashali, Madhu B, Jamunabai A, Balasubramanian S

International Journal of Health and Allied Sciences

Background: The primary goal of sewage water treatment is to eliminate or bring down the number of pollutants in the sewage water. This study was needed to assess the efficacy of a sewage treatment plant in reducing contaminants levels to comply with government environmental standards. The wastewater re-use for irrigation approaches must be in compliance with the guidelines and indicators must be tracked and impended consistently, it is therefore essential to give top priority to requirements at the stage of evaluating and development to protect land and water supplies as well as public health. Methods: Chemical and biological approaches were …

Development Of A Novel Cox Ii Mitochondrial Dna Marker For Rat Fecal Contamination.**, A'Aden Redhead

Graduate Research Showcase

Rodent feces can contain dangerous human microbial pathogens that are a serious health hazard to the human population. Currently, there is no known rapid assay to detect rodent fecal contamination. In this study, a rapid PCR-based mitochondrial DNA primer pair was constructed as it enabled the detection of rodent fecal pollution in environmental samples. Environmental samples were all tested using end-point PCR after filtration and then extraction of DNA using the DNeasy Powersoil pro kit. These primers were designed to specifically detect rodent feces that belong to the Rattus Sp. taxonomic group. Rodent samples from various counties in Georgia were …

Damped Oscillating Phosphoryl Transfer Reaction In The Cyanobacterial Circadian Clock, Hye In Jang, Pyonghwa Kim, Yongick Kim

Chemistry Faculty Research

Most organisms have circadian clocks to ensure the metabolic cycle to resonate with the rhythmic environmental changes without “damping,” or losing robustness. Cyanobacteria is the oldest and simplest form of life that is known to harbor this biological intricacy. Its KaiABC-based central oscillator proteins can be reconstituted inside a test tube, and the post-translational modification cycle occurs with 24 h periodicity. KaiC’s two major phosphorylation sites, Ser-431 and Thr-432, become phosphorylated and dephosphorylated by interacting with KaiA and KaiB, respectively. Here, we mutate Thr-432 into Ser to find the oscillatory phosphoryl transfer reaction damps. Previously, this mutant KaiC was reported …

Diverse Portfolios: Investing In Tributaries For Restoration Of Large River Fishes In The Anthropocene, Kristen L. Bouska, Brian D. Healy, Michael J. Moore, Corey G. Dunn, Jonathan J. Spurgeon, Craig P. Paukert

Nebraska Cooperative Fish and Wildlife Research Unit: Staff Publications

Rehabilitation of large Anthropocene rivers requires engagement of diverse stakeholders across a broad range of sociopolitical boundaries. Competing objectives often constrain options for ecological restoration of large rivers whereas fewer competing objectives may exist in a subset of tributaries. Further, tributaries contribute toward building a “portfolio” of river ecosystem assets through physical and biological processes that may present opportunities to enhance the resilience of large river fishes. Our goal is to review roles of tributaries in enhancing mainstem large river fish populations. We present case histories from two greatly altered and distinct large-river tributary systems that highlight how tributaries contribute …

Less Fuel For The Next Fire? Short-Interval Fire Delays Forest Recovery And Interacting Drivers Amplify Effects, Kristin H. Braziunas, Nathan G. Kiel, Monica G. Turner

Aspen Bibliography

As 21st-century climate and disturbance dynamics depart from historic baselines, ecosystem resilience is uncertain. Multiple drivers are changing simultaneously, and interactions among drivers could amplify ecosystem vulnerability to change. Subalpine forests in Greater Yellowstone (Northern Rocky Mountains, USA) were historically resilient to infrequent (100–300 year), severe fire. We sampled paired short-interval (<30-year) and long-interval (>125-year) post-fire plots most recently burned between 1988 and 2018 to address two questions: (1) How do short-interval fire, climate, topography, and distance to unburned live forest edge interact to affect post-fire forest regeneration? (2) How do forest biomass and fuels vary following short-interval versus long-interval severe fires? …