Digital Commons Network^™

Nonlinear Dynamics And Stochasticity Of Core Genetic Regulation, Hongguang Xi

Mathematics Theses - Archive

Bacillus subtilis is one of the very well-studied organisms in biology. Recent results show that an alternative competence regulation circuit for this bacterium, differing only in the order of the composite negative feedback loop onto the master competence regulator gene comK, despite presenting equivalent functionality, exhibits physiologically important differences.It is not clear why Nature only selects a specific gene regulation circuit other than a plethora of equivalent others. Here, we hope, from the point of view of reverse engineering, to discover the fundamental reasons for natural selection of a particular circuit structure over another. Based on the wild-type Bacillus subtilis …

Similarity Measures And Indexing Methods For Time Series And Multiclass Recognition, Alexandra Stefan

Computer Science and Engineering Dissertations - Archive

This thesis investigates the problem of similarity search in multimedia databases. A key application domain of the proposed work is pattern classification, with emphasis on classification of gestures, handshapes, faces, and time series. A secondary application of the proposed work is efficient similarity search in large biological databases of protein sequences.More specifically, the thesis makes contributions both by defining novel similarity measures, that are used to identify the best database matches, and by proposing methods to improve efficiency. On the topic of similarity measures, the thesis contributes a method for measuring similarity in a database of videos from American Sign …

Characterization Of Mocr, A Gntr Transcriptional Regulator In Bradyrhizobium Japonicum, May Nyan Taw

Biology Theses - Archive

The GntR family is one of the most widely distributed and prolific groups of the helix-turn-helix (HTH) transcription factors. In particular, microorganisms that live in complex, fast-changing environments such as soil tend to have a larger aggregate of the gntR regulatory genes. Bradyrhizobium japonicum is a Gram-negative soil bacterium capable of forming nodules and fixing nitrogen when in a symbiosis with the leguminous soybean plant (Glycine max). Although these metabolite-responsive gntR genes have been found to be involved in many cellular processes, little is known about their role in the B. japonicum-soybean symbiosis. The blr6977 gene (mocR), one of 35 …

Molecular Engineered Myoglobin With Unnatural Amino Acids As A Peroxidase, Kananke Sriyani Liyanage

Chemistry & Biochemistry Theses - Archive

Myoglobin (Mb) has been used as a model system to mimic other biologically important heme proteins like cytochrome P450 due to its ability to prepare mixed ligand complexes with different valencies, such as ferric, ferrous and ferryl species. It has been engineered to perform peroxidase, peroxygenase, monooxygenase and catalase activities. However, previous work on this area has shown that the distal histidine (H64) in the active of wild-type Mb is a critical residue, which destabilizes compound I, the reactive intermediate of the catalytic cycle (a ferryl ð-porphyrin radical cation). Therefore in this study we replaced H64 with a smaller residue, …

Arctic Arthropod Communities In Habitats Of Differing Shrub Abundance, Matthew E. Rich

Biology Theses - Archive

Recent global warming, which has been severe in the Arctic, has caused advancement in the timing of snowmelt and expansion of shrubs into open tundra. Such an altered climate may directly and indirectly (via effects on vegetation) affect arctic arthropod populations. I conducted research at four sites in the vicinity of the Arctic Long Term Ecological Research (LTER) site at Toolik Field Station in northern Alaska in the summers of 2010 and 2011 to determine how vegetation and environmental variables affect arthropod abundance, diversity, and phenology (the timing of life history events) in habitats of differing shrub abundance. Shrub-dominated habitats …

The Role Of Life History In The Toxicity Of The Toxic Golden Haptophyte Prymnesium Parvum, Betty Zitoon

Biology Dissertations - Archive

Prymnesium parvum is a harmful algal species that causes widespread fish kills. It is usually motile, but non-motile stages have been observed that may represent an encysted stage. The relationship of these life history changes to the abundance and acute toxicity to fish of P. parvum was studied. As part of research into factors regulating abundance and toxicity of this species, a series of experiments was conducted. The first was a semi-continuous culture experiment examining limiting nutrient (N vs. P), temperature (14 or 20 °C), and dilution rate (at four levels). Samples from the lower temperature generally exhibited greater acute …

Phylogenetic Relationships And Feeding Behavior Of Neotropical Snail-Eating Snakes (Dipsadinae, Dipsadini), Coleman Matthew Sheehy

Biology Dissertations - Archive

The snake subfamily Dipsadinae contains more than 350 ecologically diverse species in about 32 genera. Members of the tribe Dipsadini are gastropod specialists, and many possess a suite of adaptations for eating snails. I tested chemosensory prey preference in Dipsas, Sibon and Tropidodipsas species. Additionally, I described the feeding behavior of Tropidodipsas annuliferus, T. philippii and Sibon nebulatus. All snakes preferred gastropod prey. Tropidodipsas philippii also showed strong interest in the earthworm scent and subsequently consumed earthworms. Snakes snagged or wedged snail shells on surface irregularities and extracted snails using muscular contractions of the body, representing an undescribed feeding behavior …

The Long Road To Integrating Public Health Into Sustainable Development Of Shared Freshwaters In International Environmental Law: Lessons From Lake Victoria In East Africa, William Onzivu

The International Lawyer

No abstract provided.

Progressive Ip Reform In The Middle Kingdom: An Overview Of The Past, Present, And Future Of Chinese Intellectual Property Law, Jennifer Wai-Shing Maguire

The International Lawyer

No abstract provided.

Phylogenetic Systematics, Population Genetics, And The Evolution Of Color Pattern Polymorphism And Coralsnake Mimicry In The Snake Genus Sonora, Christian L. Cox

Biology Dissertations - Archive

Mimicry is a widespread biological phenomenon and is simply defined as the resemblance of one organism to another for some sort of protective purpose. Specifically, Batesian mimicry occurs when a harmless species imitates a noxious or harmful species. Neotropical coralsnakes and their colubrid snake mimics are a very diverse example of Batesian mimicry and coralsnake mimicry has been posited as a major factor underlying the diversity of Neotropical colubrids. One type of phenotypic diversity that is widespread among Neotropical coralsnake mimics is geographic variation in color and color pattern polymorphism. Color pattern polymorphism is the presence of multiple color pattern …

The Cchc Motif In Non-Ltr Retrotransposons Modulates Rna Associated Protein Conformational Changes, Athena Jagdish

Biology Theses - Archive

Non-LTR retrotransposons encode a conserved cysteine histidine motif of undetermined function. The spacing of the cysteines and histidine residues in the motif is CX₃CX₇HX4C. The site specific non-LTR retrotransposon R2Bm inserts into a specific site within the 28S ribosomal gene. Two subunits of the R2 protein, bound to distinct segments of the element RNA, are involved in the integration reaction. The subunit bound to the 5′ protein binding motif of the element RNA binds to target DNA downstream of the insertion site. The subunit bound to the 3′ protein binding motif of the element RNA binds to target DNA upstream …

A New Integrative Data Mining Framework For Analyzing The Cancer Genome Atlas Data, Dijun Luo

Computer Science and Engineering Dissertations - Archive

Besides accuracy and efficiency, understandability is another key issue of predictive modeling in real-world applications, especially in biomedical and healthcare data analysis. We develop a new integrative framework to enhance the interpretability of data by sparsity-based learning. We proposed several novel sparsity-based learning models, emphasizing different understandable properties of data, such as explicit sparsity, low redundancy, and low rank, and apply to The Cancer Genome Atlas (TCGA) data analysis. Results indicate that the proposed methods provide more insights from TCGA data while maintaining stable and competitive performances in predictive modeling. To further enhance the interpretability of biological processes and disease …

Phisigns: An Online Tool To Identify Signaturegenes In Phages And Design Pcr Primers Forexamining Phage Diversity, Bhakti Dwivedi, Robert Schmieder, Dawn Goldsmith, Robert Edwards, Mya Breitbart

Marine Science Faculty Publications

Background

Phages (viruses that infect bacteria) have gained significant attention because of their abundance, diversity and important ecological roles. However, the lack of a universal gene shared by all phages presents a challenge for phage identification and characterization, especially in environmental samples where it is difficult to culture phage-host systems. Homologous conserved genes (or "signature genes") present in groups of closely-related phages can be used to explore phage diversity and define evolutionary relationships amongst these phages. Bioinformatic approaches are needed to identify candidate signature genes and design PCR primers to amplify those genes from environmental samples; however, there is currently …

Apolipoprotein E: Essential Catalyst Of The Alzheimer Amyloid Cascade, Huntington Potter, Thomas Wisniewski

Molecular Medicine Faculty Publications

The amyloid cascade hypothesis remains a robust model of AD neurodegeneration. However, amyloid deposits contain proteins besides Aβ, such as apolipoprotein E (apoE). Inheritance of the apoE4 allele is the strongest genetic risk factor for late-onset AD. However, there is no consensus on how different apoE isotypes contribute to AD pathogenesis. It has been hypothesized that apoE and apoE4 in particular is an amyloid catalyst or “pathological chaperone”. Alternatively it has been posited that apoE regulates Aβ clearance, with apoE4 been worse at this function compared to apoE3. These views seem fundamentally opposed. The former would indicate …

Free Cysteine Modulates The Conformation Of Human C/Ebp Homologous Protein, Vinay K. Singh, Mona M. Rahman, Kim Munro, Vladimir N. Uversky, Steven P. Smith, Zongchao Jia

Molecular Medicine Faculty Publications

The C/EBP Homologous Protein (CHOP) is a nuclear protein that is integral to the unfolded protein response culminating from endoplasmic reticulum stress. Previously, CHOP was shown to comprise extensive disordered regions and to self-associate in solution. In the current study, the intrinsically disordered nature of this protein was characterized further by comprehensive in silico analyses. Using circular dichroism, differential scanning calorimetry and nuclear magnetic resonance, we investigated the global conformation and secondary structure of CHOP and demonstrated, for the first time, that conformational changes in this protein can be induced by the free amino acid l-cysteine. Addition of l-cysteine caused …

Analyzing Thioflavin T Binding To Amyloid Fibrils By An Equilibrium Microdialysis-Based Technique, Irina M. Kuznetsova, Anna I. Sulatskaya, Vladimir N. Uversky, Konstantin K. Turoverov

Molecular Medicine Faculty Publications

A new approach for the determination of the amyloid fibril - thioflavin T (ThT) binding parameters (the number of binding modes, stoichiometry, and binding constants of each mode) is proposed. This approach is based on the absorption spectroscopy determination of the concentration of free and bound to fibril dye in solutions, which are prepared by equilibrium microdialysis. Furthermore, the proposed approach allowed us, for the first time, to determine the absorption spectrum, molar extinction coefficient, and fluorescence quantum yield of the ThT bound to fibril by each binding modes. This approach is universal and can be used for determining the …

Disordered Competitive Recruiter: Fast And Foldable, Vladimir N. Uversky

Molecular Medicine Faculty Publications

We report the crystal structure of the Escherichia coli TolB-Pal complex, a protein−protein complex involved in maintaining the integrity of the outer membrane (OM) in all Gram-negative bacteria that is parasitized by colicins (protein antibiotics) to expedite their entry into cells. Nuclease colicins competitively recruit TolB using their natively disordered regions (NDRs) to disrupt its complex with Pal, which is thought to trigger translocation of the toxin across a locally destabilized OM. The structure shows induced-fit binding of peptidoglycan-associated lipoprotein (Pal) to the β-propeller domain of TolB causing the N-terminus of one of its α-helices to unwind and several residues …

An Intrinsically Disordered Region Of The Acetyltransferase P300 With Similarity To Prion-Like Domains Plays A Role In Aggregation, Alexander Kirilyuk, Mika Shimoji, Jason Catania, Geetaram Sahu, Nagarajan Pattabiraman, Antonio Giordano, Christopher Albanese, Italo Mocchetti, Jeffrey A. Toretsky, Vladimir N. Uversky, Maria Laura Avantaggiati

Molecular Medicine Faculty Publications

Several human diseases including neurodegenerative disorders and cancer are associated with abnormal accumulation and aggregation of misfolded proteins. Proteins with high tendency to aggregate include the p53 gene product, TAU and alpha synuclein. The potential toxicity of aberrantly folded proteins is limited via their transport into intracellular sub-compartments, the aggresomes, where misfolded proteins are stored or cleared via autophagy. We have identified a region of the acetyltransferase p300 that is highly disordered and displays similarities with prion-like domains. We show that this region is encoded as an alternative spliced variant independently of the acetyltransferase domain, and provides an interaction interface …

Disease-Associated Mutations Disrupt Functionally Important Regions Of Intrinsic Protein Disorder, Vladimir Vacic, Phineus R. L. Markwick, Christopher J. Oldfield, Xiaoyue Zhao, Chad Haynes, Vladimir N. Uversky, Lilia M. Iakoucheva

Molecular Medicine Faculty Publications

The effects of disease mutations on protein structure and function have been extensively investigated, and many predictors of the functional impact of single amino acid substitutions are publicly available. The majority of these predictors are based on protein structure and evolutionary conservation, following the assumption that disease mutations predominantly affect folded and conserved protein regions. However, the prevalence of the intrinsically disordered proteins (IDPs) and regions (IDRs) in the human proteome together with their lack of fixed structure and low sequence conservation raise a question about the impact of disease mutations in IDRs. Here, we investigate annotated missense disease mutations …

Understanding Viral Transmission Behavior Via Protein Intrinsic Disorder Prediction: Coronaviruses, Gerard Kian-Meng Goh, A. Keith Dunker, Vladimir N. Uversky

Molecular Medicine Faculty Publications

Besides being a common threat to farm animals and poultry, coronavirus (CoV) was responsible for the human severe acute respiratory syndrome (SARS) epidemic in 2002–4. However, many aspects of CoV behavior, including modes of its transmission, are yet to be fully understood. We show that the amount and the peculiarities of distribution of the protein intrinsic disorder in the viral shell can be used for the efficient analysis of the behavior and transmission modes of CoV. The proposed model allows categorization of the various CoVs by the peculiarities of disorder distribution in their membrane (M) and nucleocapsid (N). This categorization …

Cover, Ornitología Neotropical

Ornitología Neotropical

No abstract provided.

Cover, Ornitología Neotropical

Ornitología Neotropical

No abstract provided.

Cover, Ornitología Neotropical

Ornitología Neotropical

No abstract provided.

Cover, Ornitología Neotropical

Ornitología Neotropical

No abstract provided.

2012 Annual Report Usf System, Usf

USF Accountability Reports

No abstract provided.

2012 Annual Report Usf Tampa, Usf

USF Accountability Reports

No abstract provided.

2012 Work Plan Usf Tampa, Usf

USF Accountability Reports

No abstract provided.

Speleothem Laminae Counting And Growth Rate, Corey Wilson

Undergraduate Journal of Mathematical Modeling: One + Two

The goal of this project is to determine if there is a correlation between annual laminae in speleothems and Uranium dating. To do this, we counted laminae using high-resolution images and calculated a line of the best fit for the resulting data. We found that our data could supplement Uranium dating, but unless more data is obtained, laminae counting gives relatively imprecise age and growth rate estimates.

Where Is The Rain-On-Snow Zone In The West-Central Washington Cascades?: Monte Carlo Simulation Of Large Storms In The Northwest, Matthew John Brunengo

Dissertations and Theses

Rain-on-snow (ROS) occurs when warm, wet air moves into latitudes and/or elevations having vulnerable snowpacks, where it can alter water inputs to infiltration, runoff and erosion. The Pacific Northwest is particularly susceptible: winter storms off the Pacific cause locally heavy rain plus snowmelt almost annually, and disastrous flooding and landsliding intermittently. In maritime mountainous terrain, the effects seem more likely and hydrologically important where warm rains and seasonal snowpacks are liable to coincide, in middle elevations. Several questions arise: (1) In the PNW, does ROS affect the long-term frequency and magnitude of water delivery to the ground, versus total precipitation …

Pegylated Silicon Nanowire Coated Silica Microparticles For Drug Delivery Across Intestinal Epithelium, Vuk Uskoković, Phin-Peng Lee, Laura Walsh, Kathleen Fischer, Tejal Dasai

Pharmacy Faculty Articles and Research

Composite particles made by growing nanoscopic silicon wires from the surface of monodispersed, microsized silica beads were tested in this study for their ability to affect the integrity and permeability of an epithelial cell layer. Polyethylene glycol (PEG) is known to sterically stabilize particles and prevent protein binding; as such, it is a routine way to impart in vivo longevity to drug carriers. The effect of the silica beads, both with and without silicon nanowires and PEG, on the disruption of the tight junctions in Caco-2 cells was evaluated by means of: (a) analysis of the localization of zonula occludens-1 …