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Insights Into The Transmission Of Helitrons And Their Impact On The Genome Architecture Of Myotis Lucifugus, The Little Brown Bat, Jainy Thomas

Biology Dissertations - Archive

Probably the most dynamic proportion of multicellular eukaryotic genomes is composed of teeming populations of parasitic mobile DNA, called transposable elements (TEs). Helitrons are rolling circle TEs that have a limited distribution among mammals, having been identified only in the genome of the little brown bat, Myotis lucifugus, and a few closely related species. One family of Helitrons, called Helibat, was estimated to make up as much as 3% of the M. lucifugus genome. In addition, Helibat was shown to have captured and amplified the promoter and 5' UTR of a highly conserved single copy gene to >1000 copies. Together …

Reproductive Isolation In Drosophila: From Behavior To Genome, Daina Ma

Biology Dissertations - Archive

In this study, I investigate factors underlying reproductive isolation in Drosophila. I begin (Part I) by measuring behavioral isolation between Zimbabwe and cosmopolitan D. melanogaster, and asking the following questions: What is the pattern? What are the sensory cues leading to isolation? In Part II, I present results of a genomic screen for candidate genes underlying behavioral isolation between Zimbabwe and cosmopolitan D. melanogaster. Then I turn to the genomic causes of postzygotic reproductive isolation (Parts III and IV): What are the possible genes associated with hybrid sterility? What are the relationships between fertility/sterility and genotypes and allelic expression? What …

Comparison Of The Dna Methylation Patterns Between Interspecific Xenopus F1 Hybrids And Their Parental Species, Alie Patrick Koroma

Biology Dissertations - Archive

In this study the main focus is to compare the methylation patterns of interspecific Xenopus F1 hybrids to the parental species using Methyl-Sensitive Amplification Polymorphisms (MSAPs). Genomic DNA was extracted from the liver and muscle tissues from a representative sample of F1 hybrids and the parental species (Xenopus laevis and X. muelleri). First, the MSAP markers were very effective in comparing the methylation patterns of hybrids and the parental species. Genetic analysis of 504 liver and 364 muscle MSAP markers revealed that these markers were highly polymorphic. Principal coordinate analysis showed four distinct clusters with the two parental species separate …

Effects Of The Exotic Invader, Tamarix Spp., On Aspects Of The Aquatic Ecosystem At Mccomb Creek, Presidio County, Texas, Jane Blaisdell Nellan Moore

Biology Dissertations - Archive

The effects of saltcedar, Tamarix spp., invasion in riparian zones of the western United States have been well documented. These include, but are not limited to soil salinization, and shifts in hydrology and water use. Comparatively unknown are the effects on the associated aquatic systems and if a significant increase in water salinity accompanies these invasions. Shifts in stream metabolism have been reported, but the impacts of saltcedar invasion on the algal species, which are the dominant primary producers in desert aquatic ecosystems, are unknown. A two year study was conducted in an oligotrophic desert stream, currently experiencing an invasion, …

Role Of Repetitive Dna In Apicomplexan Genome Evolution, Assiatu B. Barrie

Biology Theses - Archive

The Apicomplexa represent a phylum of obligate intracellular parasites that impart significant medical, veterinary, and socioeconomic burdens worldwide. The opportunistic, AIDS-associated, pathogen Toxoplasma gondii for instance, infects about one-third of the human population causing serious, life-threatening illness and birth defects in some. The genomes of fifteen apicomplexan species ranging in size from 8.3Mb to 64.0Mb have been sequenced and reveal a significant amount of plasticity in terms of size, AT-richness, introns and gene density. In many instances, genome size variation can be explained by differential expansion of repetitive DNA acquired through varying processes: intracellular organellar DNA transfer events, and proliferation …

West Florida Shelf: A Natural Laboratory For The Study Of Ocean Acidification, Pamela Hallock, Lisa L. Robbins, Rebekka Larson, Tanya Beck, Patrick Schwing, Michael Martínez-Colón, Brad Gooch

Marine Science Faculty Publications

Declining oceanic pH and carbonate-ion concentrations are well-known consequences of increased atmospheric and surface-ocean partial pressure of carbon dioxide (pCO₂). The possible subject of shifts in seawater carbonate chemistry on biocalcification and survival rates of marine organisms provides questions amenable to both experimental and field study (Kleypas and Langdon, 2006). To date, limited quantitative data exist with which to formalize and test hypotheses regarding such impacts, particularly in continental-shelf settings. The continental shelves of Florida provide an ideal natural laboratory in which to test latitudinal (and temperature and depth) shifts in habitat ranges of calcifying organisms. Both the …

Transposases Are The Most Abundant, Most Ubiquitous Genes In Nature, Ramy Aziz, Mya Breitbart, Robert Edwards

Marine Science Faculty Publications

Genes, like organisms, struggle for existence, and the most successful genes persist and widely disseminate in nature. The unbiased determination of the most successful genes requires access to sequence data from a wide range of phylogenetic taxa and ecosystems, which has finally become achievable thanks to the deluge of genomic and metagenomic sequences. Here, we analyzed 10 million protein-encoding genes and gene tags in sequenced bacterial, archaeal, eukaryotic and viral genomes and metagenomes, and our analysis demonstrates that genes encoding transposases are the most prevalent genes in nature. The finding that these genes, classically considered as selfish genes, outnumber essential …

Archaic Chaos: Intrinsically Disordered Proteins In Archaea, Bin Xue, Robert W. Williams, Christopher J. Oldfield, A. Keith Dunker, Vladimir N. Uversky

Molecular Medicine Faculty Publications

Background: Many proteins or their regions known as intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) lack unique 3D structure in their native states under physiological conditions yet fulfill key biological functions. Earlier bioinformatics studies showed that IDPs and IDRs are highly abundant in different proteomes and carry out mostly regulatory functions related to molecular recognition and signal transduction. Archaea belong to an intriguing domain of life whose members, being microbes, are characterized by a unique mosaic-like combination of bacterial and eukaryotic properties and include inhabitants of some of the most extreme environments on the planet. With the expansion …

Fluorescence Quantum Yield Of Thioflavin T In Rigid Isotropic Solution And Incorporated Into The Amyloid Fibrils, Anna I. Sulatskaya, Alexander A. Maskevich, Irina M. Kuznetsova, Vladimir N. Uversky, Konstantin K. Turoverov

Molecular Medicine Faculty Publications

In this work, the fluorescence of thioflavin T (ThT) was studied in a wide range of viscosity and temperature. It was shown that ThT fluorescence quantum yield varies from 0.0001 in water at room temperature to 0.28 in rigid isotropic solution (T/η→0). The deviation of the fluorescence quantum yield from unity in rigid isotropic solution suggests that fluorescence quantum yield depends not only on the ultra-fast oscillation of ThT fragments relative to each other in an excited state as was suggested earlier, but also depends on the molecular configuration in the ground state. This means that the fluorescence …

Retro-Morfs: Identifying Protein Binding Sites By Normal And Reverse Alignment And Intrinsic Disorder Prediction, Bin Xue, A. Keith Dunker, Vladimir N. Uversky

Molecular Medicine Faculty Publications

Many cell functions in all living organisms rely on protein-based molecular recognition involving disorder-to-order transitions upon binding by molecular recognition features (MoRFs). A well accepted computational tool for identifying likely protein-protein interactions is sequence alignment. In this paper, we propose the combination of sequence alignment and disorder prediction as a tool to improve the confidence of identifying MoRF-based protein-protein interactions. The method of reverse sequence alignment is also rationalized here as a novel approach for finding additional interaction regions, leading to the concept of a retro-MoRF, which has the reversed sequence of an identified MoRF. The set of retro-MoRF binding …

Calbindin-D28k Acts As A Calcium-Dependent Chaperone Suppressing Α-Synuclein Fibrillation In Vitro, Wenbo Zhou, Chunmei Long, Anthony L. Fink, Vladimir N. Uversky

Molecular Medicine Faculty Publications

α-Synuclein, a natively unfolded protein aggregation which is implicated in the pathogenesis of Parkinson’s disease and several other neurodegenerative diseases, is known to interact with a great number of unrelated proteins. Some of these proteins, such as ß-synuclein and DJ-1, were shown to inhibit α-synuclein aggregation in vitro and in vivo therefore acting as chaperones. Since calbindin-D28K is co-localized with Ca2+ neuronal membrane pumps, and since α-synuclein is also found in the membrane proximity, these two proteins can potentially interact in vivo. Here we show that calbindin-D28K interacts with α-synuclein and inhibits its fibrillation in a calcium-dependent manner, therefore potentially …

N-Terminal Domains Of Della Proteins Are Intrinsically Unstructured In The Absence Of Interaction With Gid1/Gibberellic Acid Receptors, Xiaolin Sun, William T. Jones, Dawn Harvey, Patrick J. B. Edwards, Steven M. Pascale, Christopher Kirk, Thérèse Considine, David J. Sheerin, Jasna Rakonjac, Christopher J. Oldfield, Bin Xue, A. Keith Dunker, Vladimir N. Uversky

Molecular Medicine Faculty Publications

The plant growth-repressing DELLA proteins (DELLAs) are known to represent a convergence point in integration of multiple developmental and environmental signals in planta, one of which is hormone gibberellic acid (GA). Binding of the liganded GA receptor (GID1/GA) to the N-terminal domain of DELLAs is required for GA-induced degradation of DELLAs via the ubiquitin-proteasome pathway, thus derepressing plant growth. However, the conformational changes of DELLAs upon binding to GID1/GA, which are the key to understanding the precise mechanism of GID1/GA-mediated degradation of DELLAs, remain unclear. Using biophysical, biochemical, and bioinformatics approaches, we demonstrated for the first time that the …

Patterns Of Subnet Usage Reveal Distinct Scales Of Regulation In The Transcriptional Regulatory Network Of Escherichia Coli, Carsten Marr, Fabian J. Theis, Larry S. Liebovitch, Marc-Thorsten Hutt

Publications and Research

The set of regulatory interactions between genes, mediated by transcription factors, forms a species’ transcriptional regulatory network (TRN). By comparing this network with measured gene expression data, one can identify functional properties of the TRN and gain general insight into transcriptional control. We define the subnet of a node as the subgraph consisting of all nodes topologically downstream of the node, including itself. Using a large set of microarray expression data of the bacterium Escherichia coli, we find that the gene expression in different subnets exhibits a structured pattern in response to environmental changes and genotypic mutation. Subnets with fewer …

Cover, Ornitología Neotropical

Ornitología Neotropical

No abstract provided.

Cover, Ornitología Neotropical

Ornitología Neotropical

No abstract provided.

2010 Work Plan Usf Polytechnic, Usf

USF Accountability Reports

No abstract provided.

2010 Work Plan Usf Tampa, Usf

USF Accountability Reports

No abstract provided.

The Sir Epidemiology Model In Predicting Herd Immunity, Joanna Nicho

Undergraduate Journal of Mathematical Modeling: One + Two

The Simple Epidemic Model uses three states to describe the spread of an infection: the susceptible (S), the infected (I), and the recovered (R). This model follows the trend of an infection over time and can predict whether an infection will spread. Using this model, epidemiologists may calculate the percentage of the population that needs to be vaccinated in order to provide a population immunity from a disease. This study will compare the vaccination percentage required for herd immunity to measles, mumps, and rubella against the current percentage of vaccinated individuals.

Locomotion Of A Running Quadruped Robotic System, Bradley Savon

Undergraduate Journal of Mathematical Modeling: One + Two

Very little is known about the locomotion of quadruped robotic systems. In Latin, the term quadruped means 'having four feet'. The robotic system analyzed in this project was a software simulation program modeled after a horse. Simulation data was recorded to resolve the relationship between foot position and impulses required to accelerate or to decelerate the system while trotting. These sets of data were then analyzed in MATLAB to produce graphical representations which allowed for a better understanding of the robot's motion in the simulation environment. A function was fit to the graph of discrete data values measured in the …

2010 Intersession Catalog, Illinois Mathematics And Science Academy

Intersession Catalogs

No abstract provided.

Phma, A Ph-Sensitive Gfp Reporter For Cell Engulfment In Drosophila Embryos, Tissues And Cells, Elane Fishilevich, James A. J. Fitzpatrick, Jonathan S. Minden

Department of Entomology: Faculty Publications

Engulfment of apoptotic cells by phagocytosis ensures the removal of unwanted and defective cells. We developed a genetically encoded marker for cell engulfment, pHMA, which consists of the pH-sensitive derivative of GFP, pHluorin, fused to the actin-binding domain of Moesin. In healthy cells of Drosophila embryos and cultured cells, pHMA resides at the cell cortex. In dying cells, pHMA loses its cortical localization and reports a modest decrease in pH. In embryos, the dying cells lose their apical contacts, then move basally and are ultimately engulfed by neighboring cells or macrophages. The cell corpse material is strongly acidified soon after …

Computational Micromodel For Epigenetic Mechanisms, Karthika Raghavan, Heather J. Ruskin, Dimitri Perrin, Francois Goasmat, John Burns

Articles

Characterization of the epigenetic profile of humans since the initial breakthrough on the human genome project has strongly established the key role of histone modifications and DNA methylation. These dynamic elements interact to determine the normal level of expression or methylation status of the constituent genes in the genome. Recently, considerable evidence has been put forward to demonstrate that environmental stress implicitly alters epigenetic patterns causing imbalance that can lead to cancer initiation. This chain of consequences has motivated attempts to computationally model the influence of histone modification and DNA methylation in gene expression and investigate their intrinsic interdependency. In …

An Integrative Approach To Genomic Introgression Mapping, Andrew J. Severin, Gregory A. Peiffer, Wayne W. Xu, D. L. Hyten, Bruna Bucciarelli, Jamie A. O'Rourke, Yung-Tsi Bolon, David Grant, Andrew Farmer, Gregory D. May, Carroll P. Vance, Randy C. Shoemaker, Robert M. Stupar

Department of Agronomy and Horticulture: Faculty Publications

Near-isogenic lines (NILs) are valuable genetic resources for many crop species, including soybean (Glycine max). The development of new molecular platforms promises to accelerate the mapping of genetic introgressions in these materials. Here, we compare some existing and emerging methodologies for genetic introgression mapping: single-feature polymorphism analysis, Illumina GoldenGate single nucleotide polymorphism (SNP) genotyping, and de novo SNP discovery via RNA-Seq analysis of next-generation sequence data. We used these methods to map the introgressed regions in an iron-inefficient soybean NIL and found that the three mapping approaches are complementary when utilized in combination. The comparative RNA-Seq approach offers …

Soydb: A Knowledge Database Of Soybean Transcription Factors, Zheng Wang, Marc Libault, Trupti Joshi, Babu Valliyodan, Henry T. Nguyen, Dong Xu, Gary Stacey, Jianlin Cheng

Department of Agronomy and Horticulture: Faculty Publications

Background: Transcription factors play the crucial rule of regulating gene expression and influence almost all biological processes. Systematically identifying and annotating transcription factors can greatly aid further understanding their functions and mechanisms. In this article, we present SoyDB, a user friendly database containing comprehensive knowledge of soybean transcription factors.

Description: The soybean genome was recently sequenced by the Department of Energy-Joint Genome Institute (DOE-JGI) and is publicly available. Mining of this sequence identified 5,671 soybean genes as putative transcription factors. These genes were comprehensively annotated as an aid to the soybean research community. We developed SoyDB - a knowledge database …

Transgenic Maize Lines With Cell-Type Specific Expression Of Fluorescent Proteins In Plastids, Amir Sattarzadeh, Jonathan Fuller, Salvador Moguel, Katia Wostrikoff, Shirley Sato, Sarah Covshoff, Tom Clemente, Maureen Hanson, David Stern

Department of Agronomy and Horticulture: Faculty Publications

Plastid number and morphology vary dramatically between cell types and at different developmental stages. Furthermore, in C4 plants such as maize, chloroplast ultrastructure and biochemical functions are specialized in mesophyll and bundle sheath cells, which differentiate acropetally from the proplastid form in the leaf base. To develop visible markers for maize plastids, we have created a series of stable transgenics expressing fluorescent proteins fused to either the maize ubiquitin promoter, the mesophyll-specific phosphoenolpyruvate carboxylase (PepC) promoter, or the bundle sheath-specific Rubisco small subunit 1 (RbcS) promoter. Multiple independent events were examined and revealed that maize codon-optimized versions of YFP and …

Subtype-Associated Differences In Hiv-1 Reverse Transcription Affect The Viral Replication, Sergey Iordanskiy, Mackenzie Waltke, Yanjun Feng, Charles Wood

Nebraska Center for Virology: Faculty Publications

Background: The impact of the products of the pol gene, specifically, reverse transcriptase (RT) on HIV-1 replication, evolution, and acquisition of drug resistance has been thoroughly characterized for subtype B. For subtype C, which accounts of almost 60% of HIV cases worldwide, much less is known. It has been reported that subtype C HIV-1 isolates have a lower replication capacity than B; however, the basis of these differences remains unclear.

Results: We analyzed the impact of the pol gene products from HIV-1 B and C subtypes on the maturation of HIV virions, accumulation of reverse transcription products, integration of …

Great Lakes Emerging Legal Issues Regarding The International Boundary Waters Treaty And The Great Lakes Water Quality Agreement, Noah Hall, Murray Clamen, Lorne Thomas, David Naftzger

Canada-United States Law Journal

No abstract provided.

Commemoration Of The 100 Year Anniversary Of The International Boundary Waters Treaty, Peter V. Neffenger

Canada-United States Law Journal

No abstract provided.

The Care, Custody, And Control Of Incarcerated Women In Ecuador, Jill Harrison, Maureen Norton-Hawk

Societies Without Borders

This paper presents findings on the custody, care and control of incarcerated women in Ecuador. Although the interrelationship of abuse, poverty, drugs and incarceration is often perceived as a U.S. phenomenon, this paper presents data on a group of structurally and institutionally vulnerable women who are serving mandatory sentences of 6 to 8 years for drug possession and trafficking. Our mixed methodology of survey data, personal interviews, and secondary source materials uncovers some disturbing human rights violations and documents the challenges these incarcerated women face as mothers and inmates.

Juggling Toddlers, Teens, And Tenure: The Personal And Professional Realities Of Women On The Tenure Track With Children, Jennifer Lynn Sipes

All-Inclusive List of Electronic Theses and Dissertations

The purpose of this study was to understand the personal and professional experiences of women faculty on the tenure track with children. Despite more than 30 years of conversation about gender equity since the passage of Title IX as part of the Education Amendments of 1972, an inverse relationship persists between the prestige of an academic rank and the percentage of women in that rank. Recent research has drawn attention to differences in marital and family status between men and women faculty in higher education, suggesting that childrearing may serve as an impediment to the career advancement of women faculty …