Biology Commons^™

Nanozymes—Hitting The Biosensing “Target”, Yingfen Wu, Diane Darland, Julia Zhao

Biology Faculty Publications

Nanozymes are a class of artificial enzymes that have dimensions in the nanometer range and can be composed of simple metal and metal oxide nanoparticles, metal nanoclusters, dots (both quantum and carbon), nanotubes, nanowires, or multiple metal-organic frameworks (MOFs). They exhibit excellent catalytic activities with low cost, high operational robustness, and a stable shelf-life. More importantly, they are amenable to modifications that can change their surface structures and increase the range of their applications. There are three main classes of nanozymes including the peroxidase-like, the oxidase-like, and the antioxidant nanozymes. Each of these classes catalyzes a specific group of reactions. …

Androgen Receptor Modulates Multimodal Displays In The Bornean Rock Frog (Staurois Parvus), Sarah M. Smith, Amelia R. Eigerman, Kerry M. Lecure, Eseza Kironde, Auxenia Grace Privett-Mendoza, Matthew J. Fuxjager, Doris Preininger, Lisa A. Mangiamele

Biological Sciences: Faculty Publications

Multimodal communication is common in the animal kingdom. It occurs when animals display by stimulating two or more receiver sensory systems, and often arises when selection favors multiple ways to send messages to conspecifics. Mechanisms of multimodal display behavior are poorly understood, particularly with respect to how animals coordinate the production of different signals. One important question is whether all components in a multimodal display share an underlying physiological basis, or whether different components are regulated independently. We investigated the influence of androgen receptors (ARs) on the production of both visual and vocal signal components in the multimodal display repertoire …

Evidence That Toxin Resistance In Poison Birds And Frogs Is Not Rooted In Sodium Channel Mutations And May Rely On “Toxin Sponge” Proteins, Fayal Abderemane-Ali, Nathan D. Rossen, Megan E. Kobiela, Robert A. Craig Ii, Catherine E. Garrison, Zhou Chen, Claire M. Colleran, Lauren A. O'Connell, J Du Bois, John P. Dumbacher, Daniel L. Minor Jr

School of Biological Sciences: Faculty Publications

Many poisonous organisms carry small-molecule toxins that alter voltage-gated sodium channel (Na_V) function. Among these, batrachotoxin (BTX) from Pitohui poison birds and Phyllobates poison frogs stands out because of its lethality and unusual effects on Na_V function. How these toxin-bearing organisms avoid autointoxication remains poorly understood. In poison frogs, a NaV DIVS6 pore-forming helix N-to-T mutation has been proposed as the BTX resistance mechanism. Here, we show that this variant is absent from Pitohui and poison frog NaVs, incurs a strong cost compromising channel function, and fails to produce BTX-resistant channels in poison frog NaVs. We also …

Characterizing The Temporal And Spatial Distribution Of The Cannonball Jellyfish (Stomolophus Meleagris) In The South Atlantic Bight, Lauren G. Faulk

Theses and Dissertations

The cannonball jellyfish, Stomolophus meleagris, is commercially harvested throughout its range in the tropical and sub-tropical Americas, including in the South Atlantic Bight, where an estimated 4,000 tons (less than 2.4% of the estimated stock in South Carolina during the spring) are harvested annually. Like many Scyphozoan jellyfish, cannonball jellies have high interannual variability and little is known about the environmental drivers of their distribution and phenology. To better understand the ecology of this targeted species, we used fisheries-independent abundance data of cannonball jellyfish from 2001 to 2019 collected by the Southeast Area Monitoring and Assessment Program (SEAMAP) throughout the …

Human Cst (Ctc1-Stn1-Ten1) Promotes Topbp1 Stability And Chk1 Phosphorylation In Response To Telomere Dysfunction And Global Replication Stress, Stephanie Michelle Ackerson

Theses and Dissertations

Genomic DNA is constantly damaged by both internal and external genotoxins and cellular processes. A consequence of unrepaired or misrepaired DNA damage is genome instability, a hallmark of cancer and numerous other diseases. Eukaryotic cells have developed complex mechanisms to repair DNA damage, which is collectively referred to as a DNA damage response (DDR). CST (CTC1-STN1-TEN1) is a heterotrimeric, RPA-like protein complex that binds to single stranded (ss)DNA. In humans, CST functions in the replication and maintenance of telomeres, structures found at the ends of linear chromosomes, as well as non-telomeric DNA. Previous studies showed that deletion of the largest …

Genetic And Epigenetic Regulations Of Eds1-Mediated Plant Immunity And Identification Of Bacterial Type Iii Effectors Targeting De Novo Dna Methyltransferase Drm2 In Arabidopsis, Ming Zhao

Theses and Dissertations

In Arabidopsis thaliana, Enhanced Disease Susceptibility1 (EDS1) acts as an indispensable hub in plant immunity and is mainly responsible for plant basal defense, systemic acquired resistance (SAR), increase of endogenous content of salicylic acid (SA) and effector-triggered immunity (ETI). Epigenetic regulators play crucial roles in multiple important cellular processes. As one catalytic core of Polycomb Repressive Complex (PRC2), CURLY LEAF (CLF/SDG1) protein promotes H3K27me3 deposition at specific loci for genes repression. In this work, I found that EDS1 interacted with epigenetic regulators SDG1, SDG9, SDG15, SDG22 and SDG35 in yeast two-hybrid assays. The growth of the bacterial pathogen Pseudomonas …

Trans-Axonal Signaling And Activity-Dependent Mechanisms Of Topographic Mapping And Refinement In Vivo, Olivia Marie Spead

Theses and Dissertations

Brain connectivity and function depend on the precise formation of neuronal connections during development. In the central nervous system, most axonal projections are organized into topographic maps according to the spatial organization of the neurons they originate from or the type of stimulus they respond to. Topographic mapping is in large part established by interactions between axons and their target as well as by activity-dependent pruning of mistargeted or excessive arbors. Another important mechanism contributing to topographic map formation is pre-target axon sorting, where axons become pre-ordered en route to their destination. Both topographic mapping and pre-target sorting involve the …

The Development Of A Tractable System To Assess Caulobacter-Plant Interactions, Louis Berrios

Theses and Dissertations

Bacteria play an integral role in regulating plant growth and development. However, many of the mechanisms encompassing bacteria-plant interactions are poorly understood and thus require detailed assessments (see CHAPTER 1). To this end, I coupled bacterial (Caulobacter sp.) and plant model organisms (Arabidopsis) to determine 1) the degree to which select bacteria can enhance the growth and development of plants, and 2) what functions these bacteria possess that enable them to aid plant development. Employing bacterial isolation techniques, monoculture inoculum-based plant growth assays, biochemical assays, comparative genomics, functional genetics, and real-time quantitative PCR (RT-qPCR), I determined that …

Genetically Encoded Multivalent Liquid Glycan Array Displayed On M13 Bacteriophage, Amira Khalil, Mirat Sojitra, Jasmine Maghera, Emily Rodrigues, Eric J. Carpenter, Shaurya Seth, Daniel Ferrer Vinals, Todd L. Lowary

Pharmacy

The central dogma of biology does not allow for the study of glycans using DNA sequencing. We report a liquid glycan array (LiGA) platform comprising a library of DNA ‘barcoded’ M13 virions that display 30–1,500 copies of glycans per phage. A LiGA is synthesized by acylation of the phage pVIII protein with a dibenzocyclooctyne, followed by ligation of azido-modified glycans. Pulldown of the LiGA with lectins followed by deep sequencing of the barcodes in the bound phage decodes the optimal structure and density of the recognized glycans. The LiGA is target agnostic and can measure the glycan-binding profile of lectins, …

Mitochondrial Genome Structure And Double Strand Break Repair In Arabidopsis Thaliana, Sterling Ericsson

School of Biological Sciences: Dissertations, Theses, and Student Research

The mitochondrial genomes of plants are known for their variability in size and arrangement, yet low mutation rates in coding sequences. These opposing characteristics have been suggested to be due to the stability of their DNA maintenance processes and the usage of a double strand break repair (DSBR) system. The components of this repair complex remain poorly understood and only a few of the involved enzymes have been identified, making direct analysis difficult. The flowering plant species Arabidopsis thaliana has been used as a model organism for genome modification and subsequent phenotypic and genotypic impacts. The aims of this research …

The Conservation Status Of The World’S Freshwater Molluscs, M. Böhm, N. I. Dewhurst-Richman, M. Seddon, C. Albrecht, D. Allen, A. E. Bogan, K. Cummings, G. Darrigran, W. Darwall, Kathryn E. Perez

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

With the biodiversity crisis continuing unchecked, we need to establish levels and drivers of extinction risk, and reassessments over time, to effectively allocate conservation resources and track progress towards global conservation targets. Given that threat appears particularly high in freshwaters, we assessed the extinction risk of 1428 randomly selected freshwater molluscs using the IUCN Red List Categories and Criteria, as part of the Sampled Red List Index project. We show that close to one-third of species in our sample are estimated to be threatened with extinction, with highest levels of threat in the Nearctic, Palearctic and Australasia and among gastropods. …

Of Biodiversity, Boundaries, And Distribution: The Myxomycetes Of The Philippines And Beyond, Sittie Aisha Bustamante Macabago

Graduate Theses and Dissertations

This dissertation contains a compilation of independently performed studies primarily focusing on the myxomycetes (plasmodial slime molds) from the Philippines and integrating local and worldwide data to demonstrate regional and global trends. The major themes include the following: (I) a review of the diverse group of spore-producing amoeboid protists, including the myxomycetes; (II-IV) diversity assessments in three different groups of islands in the Philippine archipelago; (V) mapping the myxomycetes found in the Philippines for databasing and analyzing the geocoded data; (VI) a study on regional boundaries, including the Philippines, using myxomycete species composition; and, (VII) creating a global species distribution …

Examining Melt Pond Dynamics And Light Availability In The Arctic Ocean Via High Resolution Satellite Imagery, Austin Wesley Abbott

OES Theses and Dissertations

As the Arctic experiences consequences of climate change, a shift from thicker, multi-year ice to thinner, first-year ice has been observed. First-year ice is prone to extensive pools of meltwater (“melt ponds”) forming on its surface, which enhance light transmission to the ocean. Changes in the timing and distribution of melt pond formation and associated increases in under-ice light availability are the primary drivers for seasonal progression of water column primary production and warming. Observations of melt pond development and distribution require meter scale resolution and have traditionally been limited to airborne images. However, recent advances in high spatial resolution …

The Impact Of Nanopulse Treatment On The Tumor Microenvironment In Breast Cancer: Overturning The Treg Immunosuppressive Dominance, Anthony Nanajian

Biomedical Sciences Theses & Dissertations

Nanopulse treatment (NPT) is a high-power electric engineering modality that has been shown to be an effective local tumor treatment approach in multiple cancer models. Our previous studies on the orthotopic 4T1-luc breast cancer model demonstrated that NPT ablated local tumors. The treatment consequently conferred protection against a second live tumor challenge and minimized spontaneous metastasis. This study aims to understand how NPT mounts a potent immune response in a predominantly immunosuppressive tumor.

NPT changed the local and systemic dynamics of immunosuppressive cells by significantly reducing the numbers of regulatory T cells (Tregs), myeloid-derived suppressor cells (MDSCs), and tumor-associated macrophages …

Transcriptomic And Proteomic Identification Of Signaling Molecules Involved In Egg Activation In The Sea Star, Patiria Miniata, Lauren Shea Bates

Theses and Dissertations

During egg activation in all species, the critical mechanism to restart the zygote metabolism and prevent polyspermy is an intracellular Ca2+ increase. The signaling molecules, including the receptors on the sperm and egg, leading to the Ca2+ rise are not fully known. In the sea star, Patiria miniata, SFK1, SFK3, and PLCγ are known signaling molecules who are responsible for causing the internal Ca2+ rise from the endoplasmic reticulum. These three proteins share common features including signaling through SH2 domains and their activity is controlled by tyrosine phosphorylation. Using transcriptomics and phospho-proteomics to search for more molecules with these same …

Spatial Ecology And Stable Isotope Composition Of Cetaceans In The Bohol Sea, Edna Sabater

Theses and Dissertations

Studies on Philippine cetaceans (i.e., whales and dolphins) began in the early 1980s, and have resulted in the location and identification of species in Philippine waters. However, the population estimates of most of the cetacean species are uncertain, which is important in evaluating whether the populations are stable, decreasing, or increasing in relation to potential threats and conservation measures. I conducted line-transect surveys between 2010 and 2019 in the Bohol Sea, Philippines. A total of 2009.5 km survey efforts were made, which covered an area of 8041 km2 throughout the 5-year survey period. Distance sampling methods estimated the total abundance …

Late Quaternary Vegetation And Climate History From The Lake Junín Plateau, Jacob Daniel Schiferl

Theses and Dissertations

Whether the Andean ecosystem is resilient against future climate change remains unclear. A 2018 IPCC special report identified that warming more than 1.5ºC above pre-industrial temperatures by the year 2100 would be a major disrupter to natural systems, by causing more frequent extreme heatwaves, prolonged droughts, extreme precipitation events, and biome shifts. The tropical Andes will likely exceed this 1.5ºC threshold within the next century, threatening the diverse and endemic biota found in one of the world’s largest biodiversity hot spots. Yet few studies have examined the response of the Andean system through past interglacial periods when the temperatures were …

Lead And Cadmium Detoxification By Halophilic Bacteria Isolated From Solar Salterns In Lebanon, Nadine G. Zmorrod N. G. Zmorrod, Nawal Al Hakawati, Ranya A. Amer, Hoda H. Yusef

BAU Journal - Science and Technology

Water contamination by heavy metals has gained considerable attention globally. These inorganic pollutants can enter the aquatic environments via different routes thereby threatening biodiversity and human health. Lead and cadmium are hazardous pollutants where their removal by traditional techniques is identified to be costly and ineffective. However, bioremediation by extremophilic microorganisms is considered to be a promising technique as they have considerable potentials to grow in harsh environmental conditions. The present study deals with the isolation of halophilic bacterial isolates from solar salterns in North Lebanon. The isolate H1S9 was identified as Halomonas venusta H9 after showing tolerance to 500 …

Implications Of The Links Between Demography And Ecology For The Economy Of The Republic Of Karakalpakstan, Keunimjay Allanazarov, Gulya Khodjaeva, Katherine Shields

Karakalpak Scientific Journal

This article analyzes the impact of demographic factor on territorial organization of production in rural areas of the Republic of Karakalpakstan and reveals the main trends in production development. The analysis of statistical data of rural areas is given and proposals to improve the negative situation are given. More than 1306.8 thousand people live in rural areas of the Republic of Karakalpakstan, where they are concentrated in 1187 settlements, 26 urban settlements, and 11 towns of district subordination. All this testifies to the presence of large undeveloped production reserves and huge human potential. However, due to reduction of Amudarya water …

Investigation Of The Twist Of A Yarn With A Square Structure, Liza Toreniyazova, R. Orazbayeva, D. Kadirova, R. Rakhimkhodzhaev

Karakalpak Scientific Journal

The article presents the results of a study of the effect of yarn twist on the surface density of clothing fabrics with a square structure and the filling calculation of the fabric depending on the weave. The tension in the process of weaving square fabric on a loom with short overlaps is higher relative to weaving of fabric with long overlaps. With an increase in the twist of the yarn, the surface density of the fabric, the coefficient of filling (CST) and the coefficient of connectivity of the fabric (FTC) of the square structure increase.

Current Transportation Processes In P-N-N+ - Structures Under Saturation Of Recombination Rate, Abat K. Uteniyazov, A Leyderman, M Nsanbaev, Sh Annayeva

Karakalpak Scientific Journal

In the article, the model of the recombination of non - equilibrium carriers through a pair recombination complex of the donor-acceptor pair type is studied under conditions when the concentration of such paired complexes changes (decreases) during the excitation of the material. Also, the article describes that the injection into the p-n-n⁺ - structure can lead to fundamental changes in the distribution of the concentration of free carriers, especially, to the appearance of a periodic term depending on the concentration of the sample length (instead of the usual exponential dependence).

Yakety Sacs: Laryngeal Air Sac Usage In Great Apes, Chelsea Trenbeath

Master of Science in Integrative Biology Theses

Except for humans, extant great apes have evolutionarily conserved lateral ventricular air sacs extending from laryngeal saccules. Humans are the only species of Hominidae that lack this anatomical feature attached to the primary vocal apparatus. As we are the only species that produces spoken language, this association has led to the hypothesis that the loss of lateral ventricular air sacs was necessary for the evolution of spoken language. However, why these sacs are conserved in all other hominids remains unclear. Computer modeling has indicated that air sacs may increase resonance properties, but there are no data from great apes indicating …

Somatic Inhibition By Microscopic Magnetic Stimulation, Hui Ye

Biology: Faculty Publications and Other Works

Electric currents can produce quick, reversible control of neural activity. Externally applied electric currents have been used in inhibiting certain ganglion cells in clinical practices. Via electromagnetic induction, a miniature-sized magnetic coil could provide focal stimulation to the ganglion neurons. Here we report that high-frequency stimulation with the miniature coil could reversibly block ganglion cell activity in marine mollusk Aplysia californica, regardless the firing frequency of the neurons, or concentration of potassium ions around the ganglion neurons. Presence of the ganglion sheath has minimal impact on the inhibitory effects of the coil. The inhibitory effect was local to the …

Evolution Of Targeted Therapy Resistance In Eml4-Alk Positive Non-Small Cell Lung Cancer, Robert Vander Velde

USF Tampa Graduate Theses and Dissertations

Targeted therapies have emerged as potent treatments that lead to the remission of many tumors. However, they rarely cure cancers in advanced, metastatic settings. This is due to the evolution of resistance, which in turn can be ascribed to the survival of small subpopulations of tolerant and/or resistant cells. Here we investigated the evolution of resistance to EML4-ALK inhibitors in non-small cell lung cancer (NSCLC) and demonstrated that resistance evolves gradually, from unique pre-treatment sub-populations, as multiple resistance mechanisms accumulate in a Darwinian fashion. Despite accumulating multiple changes, cells evolved, in parallel, toward similar inhibitor specific phenotypes. Evolving cells have …

Elucidating The Evolution And Function Of Srnas That Facilitate Bacterial Stress Tolerance, Madeline Claire Krieger

Dissertations and Theses

Non-coding small RNAs (sRNAs) are ubiquitous post-transcriptional regulators found in both gram-negative and gram-positive bacteria. Despite their integral role in many regulatory pathways, including those that facilitate stress-tolerance, little is known about the evolutionary forces that drive the emergence of novel sRNAs, how prevalent sRNAs are within bacterial species, or the functions of a majority of these transcripts. In this work, I first describe the evolution of OxyS, a well-characterized sRNA in gram-negative Enterobacteriaceae that is involved in coordinating the bacterial response to oxidative stress. Next, I identify novel sRNAs differentially produced by the gram-positive oral pathogen Streptococcus mutans in …

Stable Isotopes And Community Surveys Reveal Differential Use Of Artificial And Natural Reefs By South Florida Fishes, Christopher Blanar, Joseph R. Hornbeck, David Kerstetter, Amy Hirons

Biology Faculty Articles

Artificial reefs may enhance the biological production of reef-associated flora and fauna, but their trophic structure relative to that of natural reefs remains understudied. We assessed trophic relationships by 1) comparing reef fish communities and 2) comparing δ13C and δ15N in 43 fish species from both artificial reef sites and adjacent natural reef tracts in Broward County, Florida. We tested the effect of sampling location (artificial, first, and second reef), general feeding strategy (herbivore, omnivore, invertivore, and carnivore), phylogeny, and standard length on δ13C and δ15N. The reef fish communities of the artificial and natural reef tracts were significantly different; …

The Neurological Asymmetry Of Self-Face Recognition, Aleksandra Janowska, Brianna Balugas, Matthew Pardillo, Victoria Mistretta, Katherine Chavarria, Janet Brenya, Taylor Shelansky, Vanessa Martinez, Kitty Pagano, Nathira Ahmad, Samantha Zorns, Abigail Straus, Sarah Sierra, Julian Keenan

Department of Biology Faculty Scholarship and Creative Works

While the desire to uncover the neural correlates of consciousness has taken numerous directions, self-face recognition has been a constant in attempts to isolate aspects of self-awareness. The neuroimaging revolution of the 1990s brought about systematic attempts to isolate the underlying neural basis of self-face recognition. These studies, including some of the first fMRI (functional magnetic resonance imaging) examinations, revealed a right-hemisphere bias for self-face recognition in a diverse set of regions including the insula, the dorsal frontal lobe, the temporal parietal junction, and the medial temporal cortex. In this systematic review, we provide confirmation of these data (which are …

Metabolic Rate, Critical Oxygen Partial Pressure, And Oxygen Supply Capacity Of Farfantepenaeus Duorarum At Their Lower Thermal Limit, Alexandra L. Burns

USF Tampa Graduate Theses and Dissertations

Temperature and environmental oxygen availability affect oxygen supply and demand in ectotherms, which are hypothesized to control the geographic limits of many marine species. The oxygen supply capacity (α) is calculated from commonly measured metabolic traits, including the standard metabolic rate (SMR) and critical oxygen partial pressure at SMR (Pcrit). It may be used to estimate the metabolic capacity and aerobic scope across changes in temperature and oxygen partial pressures as α reflects adaptations of the cardiorespiratory system to meet maximum energy demands at a given oxygen partial pressure (PO2). In this study, α was measured for the Tampa Bay …

Examining The Presence Of A Possible Species Complex Of Octopus Joubini (Cephalopoda: Octopodidae) In The Eastern Gulf Of Mexico, Haley Holloway

USF Tampa Graduate Theses and Dissertations

The Pygmy Octopus Octopus joubini (Robson, 1929) is a small, shallow water species found throughout the Gulf of Mexico (GoM), western Atlantic Ocean and the northeastern Caribbean Sea (Mather, 1982; Jereb & Roper, 2014; Judkins, 2009). This species is believed to belong to a complex based upon morphological features including arm length, web depth, sucker size, egg size, hatchling ecology, and chromatophore coloration. It has been proposed that Octopus mercatoris, another pygmy species found in the GoM, may belong in this complex; however, no analyses have been performed to verify this claim. The present study incorporated morphological comparisons with …

Phenotypic Diversity And Costs Of Early Hatching In Lizards, Zachary Winstead

USF Tampa Graduate Theses and Dissertations

Early hatching is a form of environmentally cued hatching in which embryos can emerge early to improve chances of survival and is considered a means of antipredator defense. Early hatching as a response to predation has been well documented in amphibians, but its prevalence among other animal groups is unknown. Moreover, any trade-offs between early hatching and other traits, and thus survival, are not well understood. There is anecdotal evidence that lizards exhibit early hatching behavior, but quantitative evidence is limited to one study. In the present study, I tested for the presence of early hatching in six species of …