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Reading And Understanding The Scientific Literature: Ace 10 Course: Biochemistry 435 Advanced Topics, Ed Harris

Accreditation Quality Initiative

ACE 10 Question

Learning Objectives

Writing: Students will generally be writing in a scientific format for the first time. This may be very different from prior writing in the university. This will come from discussions in the classroom sessions and from feedback on the course paper chapters that are submitted during the progress of the course.

Oral Communication: This is reinforced by the presentation of relevant papers from the scientific literature during most of the class periods. Students need to learn to master the content of such papers, prioritize the important elements, and present them in a coherent …

Evidence For Hysteretic Substrate Channeling In The Proline Dehydrogenaseand ∆1-Pyrroline-5-Carboxylate Dehydrogenase Coupled Reaction Of Proline Utilizationa(Puta), Michael A Moxley, Nikhilesh Sanyal, Navasona Krishnan, John J. Tanner, Donald F. Becker

Department of Biochemistry: Faculty Publications

Background: PutA from Escherichia coli is a bifunctional enzyme and transcriptional repressor in proline catabolism.

Results: Steady-state and transient kinetic data revealed a mechanism in which the two enzymatic reactions are coupled by an activation step.

Conclusion: Substrate channeling in PutA exhibits hysteretic behavior.

Significance: This is the first kinetic model of bi-enzyme activity in PutA and reveals a novel mechanism of channeling activation.

A Proposed Emendation Of The Gray Flycatchers Type Locality And Formal Designation Of Its Lectotype', John P. Hubbard, Carla J. Dove

Occasional Papers

The Gray Flycatcher (Empidonax wrightii) now bears the specific epithet that Spencer Fullerton Baird provisionally designated' for a potential new species of this genus—which he described from two seemingly undated Smithsonian Institution museum skins (i.e., USNM 7234 and 7237), and which the United States and Mexican Boundary Survey botanist Charles Wright had purportedly collected at El Paso, El Paso County, Texas presumably in the early 1850s. However, our research indicates that: (a) the latter locality did not exist as such when Wright collected these specimens, which respective dates we have determined were almost certainly 4 May and 3 April 1852; …

Microscale And Fluorescence-Based Techniques/ Systems To Monitor Biological Changes In Real-Time, Manasa Paidipalli

Doctoral Dissertations

The long-term objective of this work is to develop an integrated continuous-flow microfluidic device for the analysis of genetic changes in DNA. Initially, this required the development of new techniques to simulate and then quantify DNA damage using existing laboratory instrumentation. Many analytical protocols exist for the quantification of varied types of DNA damage, which span a range of complexity and sensitivity. As an efficient alternative to the existing procedures, this work demonstrates the application of quantitative polymerase chain reaction (qPCR) and high-resolution DNA melting analysis (HRMA) to the detection and quantification of intramolecular DNA damage and/or strand breaks. These …

An Examination Of The Effectiveness Of The Louisiana Gear Up Program In Promoting Self-Efficacy, Improving Academic Achievement And Increasing Teachers' Aspirations For Their Students, Candi Hill

Doctoral Dissertations

Students are likely to avoid academic pursuits if they lack academic self-efficacy (Bandura, 2000). Furthermore, past poor academic performance contributes to the development of low academic self-efficacy. Students who participate in extracurricular activities, like LA GEAR UP, demonstrate better academic achievement and less risk-taking behaviors than non-participating students (Barber, Stone, & Hunt, 2003). Research supports the notion that LA GEAR UP is an effective way to improve students' academic performance and to reduce the number of disciplinary referrals students receive (Beer, 2009). Additionally, within the academic literature research has demonstrated that teachers' attributions about students are based upon their perceptions …

Primary Microrna Processing Assay Reconstituted Using Recombinant Drosha And Dgcr8., Ian Barr, Feng Guo

Natural Sciences and Mathematics | Faculty Scholarship

In animals, the Microprocessor complex cleaves primary transcripts of microRNAs (pri-miRNAs) to produce precursor microRNAs in the nucleus. The core components of Microprocessor include the Drosha ribonuclease and its RNA-binding partner protein DiGeorge critical region 8 (DGCR8). DGCR8 has been shown to tightly bind an Fe(III) heme cofactor, which activates its pri-miRNA processing activity. Here we describe how to reconstitute pri-miRNA processing using recombinant human Drosha and DGCR8 proteins. In particular, we present the procedures for expressing and purifying DGCR8 as an Fe(III) heme-bound dimer, the most active form of this protein, and for estimating its heme content.

Materializing The Anorectic Body: A Discourse Analytic, Phenomenological Investigation, Melayna Schiff

Theses & ETDs

This thesis is concerned with the materialization of the anorectic body. In the first chapter, I examine philosophical interventions into discourses on anorexia and assert what is attractive about these accounts, what is unattractive, and where an analysis of anorexia needs to go. I argue that what is missing from these accounts is an appreciation of the productive power of those acts, centralized in the psychiatric institution, in and through which a body is recognized as anorectic. The productive power of these practices I refer to as ‘pathologization.’ In the second chapter, I articulate a dialectical account of pathologization which …

Loud: Critical Practice Of Film, Sounds, And Environmental Conservation, Liat Krongrad

Theses & ETDs

This paper places my short, fictional, character-driven, thesis film Loud in environmental and cultural context. Loud observes the ways in which information and industry technologies such as cars, trains, refrigerators, radios, televisions, computers, and cell phones transform subjectivity. The nonlinear meta-narrative, the images, the sounds, and the editing techniques are all infused with metaphor and symbolism. Loud communicates environmental issues in a visceral, profoundly emotional manner. This paper discusses the environmental issues at hand -- whale strikes and noise pollution. Then, it goes on to discuss several filmmakers and musicians who have inspired the content and techniques used for the …

The Brazilian Invasion Of Florida: Review Of The Brazilian Peppertree (Schinus Terebinthifolius Raddi) Based Allelopathy In Florida Ecosystems With Suggested Experiments To Determine Presence And Soil Activity, Thomas Luehl

Theses & ETDs

Brazilian pepper is an invader of Central and South Florida that is displacing native animal and plant species. Theories of how Brazilian pepper has adapted to the Florida ecosystem and dominates the new environment vary between those based on environmental factors or plant factors. This research reviews the theory that allelopathic chemicals produced by Brazilian pepper are introduced into the soil to inhibit native and other invasive species. It was determined that this could be proven via observations gained through laboratory and field experimentation, based on EPA guidelines. This review concludes that there is adequate evidence to support claims that …

Challenging Motherhood Ideals: Impression Management In Rett Mom Blogs, Corey Rodda

Theses & ETDs

In this thesis, I explore how mothers of girls with Rett syndrome use blogs to portray their identity. I perform a content analysis of eight blogs written by mothers of “Rett girls” and code the data to determine how the bloggers reveal themselves through impression management. From this content analysis, I determine that mothers often shared their negative emotional experiences and the conflicting sources of knowledge that they had to sift through while caring for their daughters. Intensive mothering ideologies and the unique experience of caring for a daughter with Rett syndrome impact bloggers’ maternal identities. They must balance fitting …

Enzymatic Catalysis In B-Lactamases: Protonation States Of The Catalytic Triad, Kenneth Wang

Theses & ETDs

Molecular dynamics have been carried out on b-lactamase CTX-M structures resolved by the Chen group at USF. Several protonation states of CTX-M were set up using the CHARMM simulation package in order to mimic the hydrolysis mechanism upon ligand binding. 11 ns simulations show a short intermolecular hydrogen bond between the catalytic triad Serine and Lysine in probable states. Aspartate residues outside of the active site also show evidence of an intermolecular short hydrogen bond, which may play a role in overall protein stability. These results support the proposed mechanism of ligand induced low barrier hydrogen bond formation by Cleland …

Make It Or Break It: A Foray Into The Eating Habits Of Autotomized Stone Crabs Menippe Mercenaria (Say 1818), Hannah Schotman

Theses & ETDs

Numerous fisheries around the world suffer from overfishing, and finding more sustainable fishing techniques has become a major focus of marine researchers. In the United States, most fisheries require that the entire organism be harvested, however, the stone crab fishery takes advantage of the natural ability of the crabs to autotomize and regenerate their limbs by only removing the claws (chelipeds) of the crab, thus returning the live crab back into the fishery. The bulk of the fishery is located in Florida, where two species and their hybrids are harvested and marketed as stone crabs, Menippe mercenaria and M. adina. …

Probing Proteomes With Alternative Proteases: Lys-N & Arg-C, Thomas Earle Platé Iv

Theses & ETDs

Proteomics, the study of the protein functional complement of the genome, deals with similar issues of amino-acid sequence coverage and depth. Trypsin has been the most common protease used to cleave peptides into manageable units due the many optimum traits of tryptic digestions for mass spectrometry (MS) analyses for the entire history of “shotgun” proteomics. Instrumental and computational methods for proteomic analyses have been tailored for tryptic peptides as a result. This project explored the feasibility of an alternative approach that utilizes a sequential digestion by lesser-used proteases, a C-terminal arginine peptidase (Arg-C or Clostripain) and a specific N-terminal lysine …

Exploring Associations Between Assertiveness, Health, And Gender In Children Ages 6-11, Kelsey Jae Smith

Theses & ETDs

There is considerable evidence of a gender difference in health among adolescents and adults, however there is a lack of data surrounding the development of these disparities in children. In addition to gender, research in assertiveness shows clear associations with health, but the literature is unclear how gender and assertiveness interact with one another (Sarkova et.al., 2013). The current study sought to fill the gap through exploratory research into children’s assertiveness skills and self-reported health outcomes and by examining sex differences in assertiveness skills when gender socialization, measured by child’s perceptions of parent and peer pressure to conform to a …

The Development Of General Anesthesia, Andrew Williams

Theses & ETDs

This thesis was structured into two distinct parts. The first part is a brief history of the development of both the field of anesthesia and anesthetic agents, while the second part is focused on the last 100 years and is less about the history of anesthesia and more about the pharmacological properties of the anesthetics and their effects on human physiology. Regarding the history section, I chose to highlight those people and events that I felt most important to the development of the field of anesthesia. The latter section is meant to delve more into the chemistry and biology associated …

A Mathematical Model Relating Soil Organic Matter Decomposition To Microbial Community Dynamics, Vanessa Chastain

Theses & ETDs

Soil organic matter (SOM) decomposition releases the nutrients and minerals stored long-term in soil, so they can be consumed by a variety of soil biota via direct assimilation or trophic interactions. It is involved in both carbon and nitrogen cycling and also has relevance to climate change research due to its effect on net CO2 respired and N2O emitted via denitrication. K strategist microbes only con- sume SOM-derived substrate and are primarily responsible for SOM decomposition, so their population dynamics influence and are affected by SOM decomposition rates. On the other hand, r strategist microbes take advantage of soluble substrate …

Genetic Determinants For The Epigenetic Silencing Of Tumor Suppressor Genes In Lung Cancer, Phillip Edward Pope

Theses & ETDs

In this thesis we investigate the role of genetic variants in epigenetic phenomena. Specifically, we study the correlation between single nucleotide polymorphisms (SNPs), a type of genetic variant, and the epigenetic event DNA methylation. This work is in the context of lung cancer: the genes selected are tumor suppressors related to lung carcinogenesis. In general, disruption of DNA methylation patterns is associated with cancer, and genetic variants are associated with epigenomic variation. Beta regression was used to model the proportion of DNA methylation explained by categorical SNP variables. We provide evidence for SNPs as in-cis genetic determinants for the epigenetic …

“So Long And Thanks For All The Fish”: Human Interactions With A Begging Bottlenose Dolphin (Tursiops Truncatus) And Effects Of Educational Efforts, Madelaine Verbeek

Theses & ETDs

Human-animal interaction (HI) is defined as any interaction humans and animals have with each other, ranging from cooperation to direct conflict. Although HI is a frequent occurrence, the categories these interactions are divided into range within the scientific community, making comparisons between studies difficult due to inconsistent definitions and approaches among researchers. The “interactor” category, the individual who engages in the interaction, is readily missed during the evaluation process, however knowing the perspective from which the interaction took place is critical to understanding the interaction as a whole. For potentially harmful HI situations, understanding the interactor’s perspective along with the …

Troubled Grounds: Florida’S Stand Your Ground Law And The Threat Of Covert Racism Against Blacks In The United States, Alexander Nicoleau

Theses & ETDs

The United States has always had to grapple with its deep-seeded history of racial discrimination against Blacks since the start of the Antebellum era. While the U.S has progressively become more inclusive of Blacks thanks to periods of great reform like Reconstruction, and the Civil Rights Movement, laws that discriminate on the basis of race have transitioned from overt to covert. The Florida Stand Your Ground law has come under fire for being covertly racist against Blacks. The objective of this thesis is it to analyze the history of covert and overt racism in the U.S. and reveal whether or …

Performance Dialogues: Conversations In Poetry And Dance, Rebekah Moriah Bray

Theses & ETDs

This thesis was concerned with the problem of identifying a relationship between poetry and dance as performance arts. The first chapter explored historical developments among the arts of poetry, music, and dance to suggest that these areas, though distinct, are also harmonious. The second chapter of this thesis was an exercise in interdisciplinary experimentation through the conception and production of a poetry and dance performance. The final chapter of this thesis argues for the recognition of poetry and dance as languages in dialogue with their audiences. Through the process of researching and writing this thesis I discovered evidence to support …

Effects Of Frequency And Distance Of Intruders On Aggression Of Threespot Damselfish (Stegastes Planifrons), Grace Otto

Theses & ETDs

Many members of the Pomacentridae family, commonly referred to as damselfish, are herbivorous, consuming algae regularly as part of their diet, and territorial, aggressively defending where they feed and reproduce. These characteristics affect coexisting species and the physical reef, making damselfish behavior an important component of coral reef ecosystems. The purpose of this study is to analyze how the familiarity of other fish that enter damselfish territories, called intruders, may affect the variation of aggressive behaviors of threespot damselfish (Stegastes planifrons). In an observational study (Study 1), threespot damselfish on the reef were observed and intruding species and aggressive behaviors …

Fluctuations Of The Beta Rhythm: Mathematical Modeling And Periodic Forcing Of A Cortical Microcircuit, Michael Leone

Theses & ETDs

A network of neurons is, in many aspects, a coupled system of nonlinear oscillators. We adopt this interpretation for the purpose of mathematically modeling a beta-rhythmic, Layer 5 cortical microcircuit which supports selective attention through interlaminar interaction (28). We assume that the foundation of the beta rhythm is the interaction between the intrinsic bursting pyramidal neuron and the low-threshold spike interneuron, where the period of the rhythm is determined by the period of the M-current inherent to both neuron types. We test the robustness of oscillations and circuit response to periodic forcing in the (5-20 Hz) range. Differences between synaptic …

The Monster Within And Without: Identity Assignment And Construction In Slave Narratives And Horror Fiction, Chelsey Lucas

Theses & ETDs

This thesis presents an analysis of the relation between the human and the monster as it is used in nineteenth-century American slave narratives (Frederick Douglass, Harriet Jacobs) and British and American horror fiction (Mary Shelley’s Frankenstein and Glen Duncan’s Last Werewolf trilogy). I begin with Mary Shelley’s Frankenstein (1818), asserting that Victor Frankenstein attempts to abject his own monstrousness through the creation of his monster. The creature tries to discover his nature in relation to human persons, and acquires language and literacy. Through this, he becomes a recognizable person despite his physical deformity, at least for the reader. He remains …

The Effects Of Fish Waste Nutrient Enrichment On Thalassia Testudinum Banks Ex König In Sarasota Bay, Florida, Kyle Mccormick

Theses & ETDs

Seagrass has numerous vital functions in marine ecosystems worldwide that range from binding substrate to providing food and shelter for fauna. However, seagrass loss is at a dangerously high rate across the globe. Anthropogenic factors such as dredging and pollution have caused seagrass beds to decline in recent years. The lack of methodical restoration efforts as well as the general variability of open ocean restorations has made restoration efforts difficult, but new emerging techniques and advances in technology give hope for improvement. In this experiment the use of nutrient enrichment to affect Thalassia testudinum colonization was studied in the New …

Common Ground And Discursive Justification: Approaching The Traditional Epistemological Questions From An Untraditional Angle, Ryan Simonelli

Theses & ETDs

One of the classic issues in the field of epistemology is the question of how we are justified in holding the beliefs that we do in fact hold. Traditionally, epistemologists, drawing from the tradition of Descartes and Locke, have thought that this question is to be answered purely by internal reflection. In this thesis, I argue for a conception of justification that takes its explanatory starting point on the social practices surrounding the act of discursive justification, turning the traditional individualist conception of justification on its head. This often been seen as a mere changing of the subject from the …

Initiating Synthesis Of Multidentate Ligands With Sulfur And Nitrogen Donors For Study Of Their Copper Complexes, Melissa Campbell

Theses & ETDs

Blue copper proteins are important metalloproteins that are found in plants and bacteria and are involved in photosynthesis, respiration, oxidative deamination of primary amines and reduction of nitrite reductase. They more specifically are involved in reduction and oxidation reactions, mostly as transporters for electrons. They contain at least one type 1 copper center and are characterized by a sulfur to copper charge transfer giving the proteins a blue color. Blue copper proteins generally have a reduction potential between +150 and 800 mV (vs NHE) depending on the coordination sphere. The immediate environment of the copper influences the redox potential of …

“Why Are There No Black Kids At Southside And No White Kids At Booker?”: Teachers’ Opinions On The Educational Achievement Gap In The City Of Sarasota, Grace Fisher

Theses & ETDs

In our current society, the work of teachers has often been criticized and devalued. So much so that much of the existing literature on the educational achievement gap fails to include their opinions on the matter. Therefore, my work examined Sarasota teachers’ opinions on the educational achievement gap. I used semi-structured interviews of eight elementary school teachers to show the teachers’ understanding of the cause of the gap and to explain these voices in relation to the existing literature. I find that teachers believe the achievement gap is influenced more by social class than preconceived beliefs of race. Social class, …

Big Building: The Political Economy Of Place And Displacement In Coconut Grove Florida, Daniel Ducassi

Theses & ETDs

The physical construction of urban space has a concrete impact on the lives of those who inhabit it. However, the development and redevelopment of some neighborhoods has differed from that of others, and the disparity in the qualities and environment of constructed urban space is closely intertwined with the social relations of a particular community. This thesis explores the processes of redevelopment in the historically segregated neighborhood of Coconut Grove in Miami, Florida. It reviews the development history of the neighborhood, as well as recent development issues that serve as focal points of interaction between residents, developers and municipal government. …

Allelopathic Effects Of Crude And Purified Common Ragweed (Ambrosia Artemisiifolia L.) Root Extracts On The Invasive Brazilian Pepper (Schinus Terebinthifolia Raddi) And Several Florida Native Plant Species, Sean Binninger

Theses & ETDs

Ambrosia artemisiifolia (common ragweed) is a widespread native throughout North America and is invasive in Europe and Asia. Therefore, it has the potential to affect many habitats and plant communities. Its allelopathic effects were studied to help determine its environmental impacts. Previous experimental protocol showed thiarubrine A from root extracts negatively affects plant growth. Therefore, a crude root extract was applied to Schinus terebinthifolia (Brazilian pepper), Aeschynomene americana (shyleaf), Solidago stricta (wand goldenrod), Callicarpa americana (American beautyberry), and Symphyotrichum dumosum (rice button aster) seeds. A purified root extract, obtained by liquid-liquid extraction and column chromatography, was applied to Brazilian pepper …

The Competition Between Microrna 495 And Hud And Its Effects On The Regulation Of Mrna Targets Involved In Cocaine Addiction, Alexandra Quezada

Theses & ETDs

RNA-binding protein, HuD, is necessary for proper neuronal development in mammals and is also involved in neuronal growth during synaptic plasticity. HuD also acts as a trans-acting factor by stabilizing mRNA transcripts in the cytoplasm and promoting translation. MicroRNA-495 (miR-495) acts as a destabilizing trans-acting factor by promoting deadenylation or repression mechanisms. HuD and miR-495 share homologous sequences in the RNA binding domains of mRNA targets, making them competitors. Many of the mRNA targets of HuD and miR-495 are addiction-related genes involved in cocaine addiction. To see the effect of HuD and miR-495 competition on addiction related-genes, we used a …