Biology Commons^™

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 …

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 …

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 …

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 …

The Role Of The Dna Helicase Rrm3 Under Replication Stress, Julius Muellner

USF Tampa Graduate Theses and Dissertations

DNA replication needs to be strictly monitored to ensure proper duplication of the genome. During DNA synthesis, the DNA replication machinery encounters multiple obstacles such as incorrect dNTP incorporation, RNA-DNA hybrids, modification of DNA nucleobases, collision with the transcription-replication machinery. These endogenous and exogenous sources of DNA damage may result in single-strand breaks (SSBs) and double-strand DNA breaks (DSBs), thereby impeding fork progression. To prevent stalling of DNA synthesis a multitude of DNA repair pathways are specifically designed to deal with these kinds of blockages. One of the proteins involved in ensuring DNA replication fork progression is the DNA helicase …

Body Dimension And Length-Weigh Relationships Of Invasive Exotic Earthworm Species In Huron Mountains Forests, Paula Arroyo, Xiaoyong Chen, Timothy Gsell, John A. Yunger, Mary E. Carrington

Research Days

Invasive exotic earthworms have undesired ecological effects on structure, function, and biodiversity of forest ecosystems in the Great Lakes region. Biological parameters including body length, weight, growth rate, and regeneration patterns of earthworms are necessary to understand their life cycle and impacts on ecological processes such as nutrient biogeochemistry cycling and carbon sequestration in the forests, as well as for forest management practices. In this work, earthworms were surveyed in main forest types of the Huron Mountains Preserve of Michigan, Upper Peninsula during the period of May 2021 to October 2022. Earthworms were captured from established sampling quadrates using a …

Role Of Nod2 Receptor In Immune Response To Staphylococcus Aureus, Precious Mckenzie, Aparna Palakodeti Ph.D

Research Days

Staphylococcus aureus, a gram-positive, commensal bacterium, causes several opportunistic diseases and infections in humans. Furthermore, some strains of S.aureus have developed resistance to antibiotics such as methicillin and pose a health risk. Pattern Recognition Receptors (PRRs) on host immune cells recognize specific components of S.aureus cell wall and mount an immune response against the bacteria. One such PRR is the Nuclear Oligomerization Domain 2 (NOD2) receptor which is present in the cytosol of host immune cells. NOD2 recognizes Muramyl-Dipeptide (MDP), a component of the peptidoglycan cell wall of several bacteria including S. aureus. The binding of MDP to NOD2 allows …

College Students' Relationship With Attention Deficit Hyperactivity Disorder And Learning Accommodations At The University Of Nebraska-Lincoln, Brianna Danehey, Kim Hansen Dr., Chelsea Witt Dr.

Honors Program: Senior Projects (Public)

Attention deficit hyperactivity disorder (ADHD) can provide many challenges for college students due to difficulties focusing, multi-tasking, and staying organized. Colleges are required to offer academic accommodations to students with disabilities in an attempt to provide students with an equitable learning environment. However, accommodations may be ineffective if they are highly unattainable, unused by the student once granted, or hindered by university faculty.

The objective of this study was to identify barriers to receiving effective and beneficial academic accommodations for individuals with ADHD at the University level and to provide insight into college students' knowledge and relationships relating to the …

Margalefidinium Polykrikoides Cyst Resuspension In The Lafayette River, A Sub-Tributary Of The Chesapeake Bay, Gabrielle Greaney, Eduardo Perez Vega, Katherine Crider, Dreux Chappell, Kimberly Powell, Richard Hale, Peter Bernhardt, Margaret Mulholland

Undergraduate Research Symposium

Harmful Algal Blooms are a collection of algae in a body of water that can cause serious environmental issues and health problems in both people and aquatic organisms. Dinoflagellates are microscopic, unicellular, and eukaryotic organisms that are well known for forming harmful algal blooms because of eutrophication. Coastal Virginia suffers from HABs in the Chesapeake Bay and its tributaries. A common species of dinoflagellate, known as Margalefidinium polykrikoides exists in the Chesapeake Bay. The purpose of this study is to determine if sediment resuspension produced by wind generated surface gravity waves cause cysts (dinoflagellate resting stages) to be suspended into …

Histone Deacetylase 8 Is A Novel Therapeutic Target For Mantle Cell Lymphoma And Preserves Natural Killer Cell Cytotoxic Function, January M. Watters

USF Tampa Graduate Theses and Dissertations

This study demonstrates for the first time that HDAC8 function is critical for MCL survival, and abrogating its activity in human primary NK cells does not interfere with NK IgG antibody directed ADCC therapies ex vivo. Human NK cells, isolated from healthy donors, are highly resistant to HDAC8 inhibitor treatment with PCI-34051. Even at the highest concentration, 20uM, no toxicity was observed. Conversely, MCL cell lines representative of the aggressive MCL subtype, classical MCL, were especially sensitive to PCI-34051, an HDAC8 selective inhibitor, treatment. Blocking HDAC8 activity and/or abrogating expression through shRNA silencing induced significant DNA damage, hyperacetylation of SMC3, …

Deep Learning Can Be Used To Classify And Segment Plant Cell Types In Xylem Tissue, Sean Wu, Reem Al Dabagh, Fabien Scalzo, Helen Irene Holmlund

Seaver College Research And Scholarly Achievement Symposium

Studies of plant anatomical traits are essential for understanding plant physiological adaptations to stressful environments. For example, shrubs in the chaparral ecosystem of southern California have adapted various xylem anatomical traits that help them survive drought and freezing. Previous studies have shown that xylem conduits with a narrow diameter allows certain chaparral shrub species to survive temperatures as low as -12 C. Other studies have shown that increased cell wall thickness of fibers surrounding xylem vessels improves resistance to water stress-induced embolism formation. Historically, these studies on xylem anatomical traits have relied on hand measurements of cells in light micrographs, …

Nutrient Resorption And Stoichiometric Characteristics Of Wuyi Rock Tea Cultivars, Dehuang Zhu, Suhong Peng, Wenzhen Liu, Shengjie Yu, Dafeng Hui

Biology Faculty Research

Nutrient resorption is an important strategy for plants to retain critical nutrients from senesced leaves and plays important roles in nutrient cycling and ecosystem productivity. As a main economic crop and soil and water conservation species, Wuyi Rock tea has been widely planted in Fujian Province, China. However, foliar nutrient resorptions of Wuyi Rock tea cultivars have not been well quantified. In this study, three Wuyi Rock tea cultivars (Wuyi Jingui, Wuyi Rougui, and Wuyi Shuixian) were selected in the Wuyishan National Soil and Water Conservation, Science and Technology Demonstration Park. Resorption efficiencies of nitrogen (NRE), phosphorus (PRE), and potassium …

Small Rnas >26 Nt In Length Associate With Ago1 And Are Upregulated By Nutrient Deprivation In The Alga Chlamydomonas, Yingshan Li, Eun-Jeong Kim, Adam Voshall, Etsuko Moriyama, Heriberto D. Cerutti

School of Biological Sciences: Faculty Publications

Small RNAs (sRNAs) associate with ARGONAUTE (AGO) proteins forming effector complexes with key roles in gene regulation and defense responses against molecular parasites. In multicellular eukaryotes, extensive duplication and diversification of RNA interference (RNAi) components have resulted in intricate pathways for epigenetic control of gene expression. The unicellular alga Chlamydomonas reinhardtii also has a complex RNAi machinery, including 3 AGOs and 3 DICER-like proteins. However, little is known about the biogenesis and function of most endogenous sRNAs. We demonstrate here that Chlamydomonas contains uncommonly long (>26 nt) sRNAs that associate preferentially with AGO1. Somewhat reminiscent of animal PIWI-interacting RNAs, …

Rna Virus-Mediated Changes In Organismal Oxygen Consumption Rate In Young And Old Drosophila Melanogaster Males, Eli Hagedorn, Dean Bunnell, Beate Henschel, Daniel Smith Jr, Stephanie Dickinson, Andrew Brown, Maria De Luca, Ashley Turner, Stanislava Chtarbanova

Research, Publications & Creative Work

Aging is accompanied by increased susceptibility to infections including with viral pathogens resulting in higher morbidity and mortality among the elderly. Significant changes in host metabolism can take place following virus infection. Efficient immune responses are energetically costly, and viruses divert host molecular resources to promote their own replication. Virus-induced metabolic reprogramming could impact infection outcomes, however, how this is affected by aging and impacts organismal survival remains poorly understood. RNA virus infection of Drosophila melanogaster with Flock House virus (FHV) is an effective model to study antiviral responses with age, where older flies die faster than younger flies due …

Thymic Stromal Lymphopoietin Participates In The Host Response To Intra-Amniotic Inflammation Leading To Preterm Labor And Birth, Tomi Kanninen, Li Tao, Roberto Romero, Yi Xu, Marcia Arenas-Hernandez, Jose Galaz, Zhenjie Liu, Derek Miller, Dustyn Levenson, Jonathan M. Greenberg, Jonathan Panzer, Justin Padron, Kevin Theis, Nardhy Gomez-Lopez Phd

Medical Student Research Symposium

Objective: To determine if bacteria (Ureaplasma parvum and Sneathia spp.) associated with intra-amniotic infection can trigger the induction of cytokine Thymic stromal lymphopoietin (TSLP) in human amnion epithelial cells (hAECs) in vitro.

Material or subjects: Amniotic fluid and chorioamniotic membrane (CAM) were collected from women with sPTL who delivered at term (n=30) or preterm without intra-amniotic inflammation (n=34), with sterile intra-amniotic inflammation (SIAI, n=27), or with intra-amniotic infection (IAI, n=17). Amnion epithelial cells (AECs), Ureaplasma parvum, and Sneathia spp. were also utilized.

Methods: The expression of TSLP, TSLPR, and IL-7Rα was evaluated in amniotic fluid or CAM by …

The Effects Of Chronic Hypercarbia On Morphological And Ventilatory Development In Crayfish, Cassandra Poeppelman, Josh Hivner, Lynn K. Hartzler

Festival of Research

Instances of abnormally high CO2 levels are becoming increasingly common in freshwater ecosystems undergoing eutrophication. Chronic hypercarbia (long-term elevation of the partial pressure of carbon dioxide (Pco2)) is pervasive in these eutrophic ecosystems. Elevated Pco2 increases the ventilation and metabolism of some tadpoles and aquatic frogs and hinders their morphological development23. We expect that chronic hypercarbia will affect most aquatic organisms in the same way, but it remains to be verified that chronic hypercarbic conditions also alter aquatic organisms similarly to intermittent and acute hypercarbic challenges.

Comparing Mortality In Response To Simulated Climate Change In The Harvester Ant, Pogonomyrmex Badius, And The Fire Ant, Solenopsis Invicta, Haley Depner

USF Tampa Graduate Theses and Dissertations

With the rapid transport of plants, produce, and goods out of its South American home, the fire ant, Solenopsis invicta, has invaded continents on a global scale. In the United States alone, S. invicta is responsible for an estimated $1 billion in damages annually. In contrast to the invasive fire ant, Florida’s native harvester ant, Pogonomyrmex badius, is a keystone seed disperser, providing seed relocation benefits to Florida’s sandhill wildfire-adapted habitats. Seed relocation reduces seedling competition for nutrients with the parent plant, reduces predation of seeds by rodents, increases nutrient loads associated with ant mound soils, and protects seeds from …

Bats And Bridges: What You Need To Know, Rusty Yeager, Jason Dupont

Purdue Road School

Bats’ use of bridges is well documented. With more bat species being added to the endangered species list, this is a significant issue for maintenance, rehabilitation, and replacement. From defining bat species using specific bridges to monitoring bat use through in-depth analysis, several techniques can facilitate USFWS coordination and ensure negative impacts to endangered species are avoided or minimized throughout transportation improvements. This session will detail these techniques and approaches and educate transportation planners on best practices.

Morphological And Transcriptional Effects Of Crude Oil And Dispersant Exposure On The Marine Sponge Cinachyrella Alloclada, Yvain Desplat, Jacob F. Warner, Emily J. Blake, Nidhi Vijayan, Marie Cuvelier, Patricia Blackwelder, Jose V. Lopez

Biology Faculty Articles

Marine sponges play important roles in benthic ecosystems. More than providing shelter and food to other species, they help maintain water quality by regulating nitrogen and ammonium levels in the water, and bioaccumulate heavy metals. This system, however, is particularly sensitive to sudden environmental changes including catastrophic pollution event such as oil spills. Hundreds of oil platforms are currently actively extracting oil and gas in the Gulf of Mexico. To test the vulnerability of the benthic ecosystems to oil spills, we utilized the Caribbean reef sponge, Cinachyrella alloclada, as a novel experimental indicator. We have exposed organisms to crude …

Dwarfism And Gigantism Drive Human-Mediated Extinctions On Islands, Roberto Rozzi, Mark V. Lomolino, Alexandra A.E. Van Der Geer, Daniele Silvestro, S. Kathleen Lyons, Pere Bover, Josep A. Alcover, Ana Benítez-López, Cheng-Hsiu Tsai, Masaki Fujita, Mugino O. Kubo, Janinie Ochoa, Matthew E, Scarborough, Samuel T. Turvey, Alexander Zizka, Jonathan M. Chase

School of Biological Sciences: Faculty Publications

Islands have long been recognized as distinctive evolutionary arenas leading to morphologically divergent species, such as dwarfs and giants. We assessed how body size evolution in island mammals may have exacerbated their vulnerability, as well as how human arrival has contributed to their past and ongoing extinctions, by integrating data on 1231 extant and 350 extinct species from islands and paleo islands worldwide spanning the past 23 million years. We found that the likelihood of extinction and of endangerment are highest in the most extreme island dwarfs and giants. Extinction risk of insular mammals was compounded by the arrival of …

Diatom Diversity And Functional Groups In 72 Florida Lakes: Assessing Ecological Changes For Improved Protection And Management, Francesca M. Lauterman

USF Tampa Graduate Theses and Dissertations

Florida lakes are diverse ecosystems and are an important part of the state's biodiversity and ecosystem services. As human population and development increase across the state, many lakes have been documented as nutrient impaired and are unable to maintain essential ecological functions. In this study, diatom diversity and functional groups in 72 Florida lakes were assessed for their relationships with associated water-quality data. Common alpha diversity indices, including Shannon-Weiner Index, the Gini-Simpson Index, and Hill’s numbers were utilized to measure trends in diatom communities, while the relationships between diatom lifeform characteristics and environmental data were explored using multivariate methods and …

Increasing Capture Rates Of Grassland Birds Over Thirteen Years Indicates Successful Restoration, Katie Stumpf, Charles Muise

Georgia Journal of Science

Grassland bird populations are being lost at an alarming rate due to human modifications to grassland ecosystems. Grassland restoration has been shown to mitigate population declines for many species that use these habitats at some point in their annual cycles. We examined capture rates of adult, breeding, and hatch-year birds at a restored grassland site in the piedmont of central Georgia to determine whether colonization, breeding success, hatching success, and recruitment processes were impacting populations of grassland birds. We banded birds approximately twice per month from January 2009 through December 2021 at Panola Mountain State Park. Restoration efforts started in …

Length Of Course-Based Undergraduate Research Experiences (Cure) Impacts Student Learning And Attitudinal Outcomes: A Study Of The Malate Dehydrogenase Cures Community (Mcc), Sue Ellen Dechenne-Peters, John Rakus, Amy D. Parente, Tamara L. Mans, Rebecca Eddy, Nicole Galport, Courtney Koletar, Joseph J. Provost, J. Ellis Bell, Jessica K. Bell

Biology: Faculty Publications

Course-based undergraduate research experiences (CUREs) are laboratory courses that integrate broadly relevant problems, discovery, use of the scientific process, collaboration, and iteration to provide more students with research experiences than is possible in individually mentored faculty laboratories. Members of the national Malate dehydrogenase CUREs Community (MCC) investigated the differences in student impacts between traditional laboratory courses (control), a short module CURE within traditional laboratory courses (mCURE), and CUREs lasting the entire course (cCURE). The sample included approximately 1,500 students taught by 22 faculty at 19 institutions. We investigated course structures for elements of a CURE and student outcomes including student …

Black Crowned Night Heron, Kevin Rafferty, Briana K. Zaffiro, David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

No abstract provided.

Ycnh 3d Skull, Kevin Rafferty, Briana K. Zaffiro, David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

No abstract provided.

Mafr 3d Skull, Kevin Rafferty, Briana K. Zaffiro, David W. Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

3D Scan of a Magnificent Frigatebird

Rosp 3d Skull (Roseate Spoonbill), Kevin Rafferty, Briana K. Zaffiro, David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

3D skull of a roseate spoonbill

Assessment Of Largemouth Bass (Micropterus Salmoides) Condition Using Liver Histopathology, Health Parameters And Water Quality Of The Central Chattahoochee River Watershed, Kari Carmack Goodwin

Theses and Dissertations

The health of Largemouth bass from west-central Georgia was assessed using liver histopathology and the degree of tissue change index (DTC), hepatosomatic indices (HSI), relative weight, condition factors, and intersex. These health parameters as well as water chemistry data were compared across four bodies of water, three within the Chattahoochee watershed, and one pseudo-control located in the Flint watershed. Fish from Lake Oliver, Lake Harding, and West Point Lake had severely impacted liver health compared to Warm Springs National Fish Hatchery, with DTC rankings over 100 for the three lakes within the Chattahoochee watershed, demonstrating severely damaged livers. There was …

Changes In Metal-Chelating Metabolites Induced By Drought And A Root Microbiome In Wheat, Anne J. Anderson, Joshua M. Hortin, Astrid R. Jacobson, David W. Britt, Joan E. Mclean

Biological Engineering Faculty Publications

The essential metals Cu, Zn, and Fe are involved in many activities required for normal and stress responses in plants and their microbiomes. This paper focuses on how drought and microbial root colonization influence shoot and rhizosphere metabolites with metal-chelation properties. Wheat seedlings, with and without a pseudomonad microbiome, were grown with normal watering or under water-deficit conditions. At harvest, metal-chelating metabolites (amino acids, low molecular weight organic acids (LMWOAs), phenolic acids, and the wheat siderophore) were assessed in shoots and rhizosphere solutions. Shoots accumulated amino acids with drought, but metabolites changed little due to microbial colonization, whereas the active …

A Global Phylogenomic Analysis Of The Shiitake Genus Lentinula, Sean Sierra-Patev, Byoungnam Min, Miguel Naranjo-Ortiz, Brian Looney, Zachary Konkel, Jason C. Slot, Yuichi Sakamoto, Jacob L. Steenwyk, Antonis Rokas, Juan Carro, Susana Camarero, Patricia Ferreira, Gonzalo Molpeceres, Francisco J. Ruiz-Dueñas, Ana Serrano, Bernard Henrissat, Elodie Drula, Karen W. Hughes, Juan L. Mata, Noemia Kazue Ishikawa, Ruby Vargas-Isla, Shuji Ushijima, Chris A. Smith, John Donoghue, Steven Ahrendt, William Andreopoulos, Guifen He, Kurt Labutti, Anna Lipzen, Vivian Ng, Robert Riley, Laura Sandor, David Hibbett

Biology

Lentinula is a broadly distributed group of fungi that contains the cultivated shiitake mushroom, L. edodes. We sequenced 24 genomes representing eight described species and several unnamed lineages of Lentinula from 15 countries on four continents. Lentinula comprises four major clades that arose in the Oligocene, three in the Americas and one in Asia–Australasia. To expand sampling of shiitake mushrooms, we assembled 60 genomes of L. edodes from China that were previously published as raw Illumina reads and added them to our dataset. Lentinula edodes sensu lato (s. lat.) contains three lineages that may warrant recognition as species, one including …