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Investigating The Role Of Wolbachia Endosymbionts In The Expansion Of The F Element In Drosophila Ananassae, Elizabeth J. Chen 2015 Washington University in St Louis

Investigating The Role Of Wolbachia Endosymbionts In The Expansion Of The F Element In Drosophila Ananassae, Elizabeth J. Chen

Undergraduate Theses—Unrestricted

At 4.2 Mb overall, the Drosophila melanogaster Muller F element (dot chromosome) is an unusual autosome; it is broadly heterochromatic, but the distal 1.3 Mb has a gene density and expression pattern similar to other autosomes. More intriguing is the large expansion of the D. ananassae F element (~20 Mb). Elucidating the factors that contribute to this expansion could improve our understanding of how heterochromatic domains are maintained and amplified.

Previous analyses show that the lateral gene transfer (LGT) of Wolbachia (the most widespread intracellular bacteria in the Rickettsiales order) into the D. ananassae genome is an important ...


Environmental Stimuli And Intragenerational Epigenetics, Nicholas J. Napier 2015 Wofford College

Environmental Stimuli And Intragenerational Epigenetics, Nicholas J. Napier

Student Scholarship

Epigenetics is the study of any change in gene expression that is not mediated by DNA sequence. The effects of environmental stimuli on epigenetic changes have been studied extensively in recent years. Multiple reviews have provided comprehensive summations of the effects of environmental stimuli on transgenerational epigenetic changes, but few reviews have focused upon environment-induced intragenerational epigenetic changes. This review will summarize current knowledge of the intragenerational epigenetic changes that are induced by two groups of well-studied environmental stimuli: nutritional deficiencies and carcinogens. This survey of intragenerational epigenetic changes will focus upon the mechanisms behind them, the disorders associated with ...


Deciphering The Functional Collaboration Of Mid And Bric-A-Brac 2 As Potential Regulators Of Cellular Proliferation Within Adult Drosophila Ovaries, Petra Visic 2015 University of Southern Mississippi

Deciphering The Functional Collaboration Of Mid And Bric-A-Brac 2 As Potential Regulators Of Cellular Proliferation Within Adult Drosophila Ovaries, Petra Visic

Master's Theses

Stem cell niches are highly organized and specialized microenvironments located within specific tissues of both vertebrate and invertebrate organisms [1]. In Drosophila melanogaster, three distinct stem cell niches have been identified within the ovary including the germline stem cell (GSC), follicle stem cell (FSC), and escort stem cell (ESC) niche. Recently, Fregoso-Lomas et al. [2] reported that Gurken/Epidermal Growth Factor Receptor (EGFR) signaling is modulated within posterior ovarian follicle cells by Midline (Mid). The mid gene encodes a T-box transcription factor protein that specifies cell fates in the developing heart [3][4], central nervous system [5][6], epidermis [7 ...


Short Germ Insects Utilize Both The Ancestral And Derived Mode Of Polycomb Group-Mediated Epigenetic Silencing Of Hox Genes, Yuji Matsuoka, Tetsuya Bando, Takahito Watanabe, Yoshiyasu Ishimaru, Sumihare Noji, Aleksander Popadic, Taro Mito 2015 University of Tokushima

Short Germ Insects Utilize Both The Ancestral And Derived Mode Of Polycomb Group-Mediated Epigenetic Silencing Of Hox Genes, Yuji Matsuoka, Tetsuya Bando, Takahito Watanabe, Yoshiyasu Ishimaru, Sumihare Noji, Aleksander Popadic, Taro Mito

Biological Sciences Faculty Research Publications

In insect species that undergo long germ segmentation, such as Drosophila, all segments are specified simultaneously at the early blastoderm stage. As embryogenesis progresses, the expression boundaries of Hox genes are established by repression of gap genes, which is subsequently replaced by Polycomb group (PcG) silencing. At present, however, it is not known whether patterning occurs this way in a more ancestral (short germ) mode of embryogenesis, where segments are added gradually during posterior elongation. In this study, two members of the PcG family, Enhancer of zeste (E(z)) and Suppressor of zeste 12 (Su(z)12), were analyzed in ...


Characterization Of A Novel Clade Of Transporters In Phytophthora, Stephanie Padula, Paul F. Morris Dr, Howard Casey Cromwell Dr., Menaka Ariyaratne, Andrew Wagner 2015 Bowling Green State University - Main Campus

Characterization Of A Novel Clade Of Transporters In Phytophthora, Stephanie Padula, Paul F. Morris Dr, Howard Casey Cromwell Dr., Menaka Ariyaratne, Andrew Wagner

Honors Projects

The oomycete Phytophthora parasitica has a worldwide distribution and is an economically important pathogen of more than 100 species4. RNA-seq analysis showed that one gene, PPTG_16698 has the 5th highest level of expression of all transport proteins in the zoospore stage, and is highly conserved throughout Phytophthora species. This project attempts to characterize the important biological role that PPTG_16698 plays in P. parasitica and other oomycetes. Three strategies have been implemented to accomplish this goal: growth analysis by heterologous expression in yeast, metabolite analysis in yeast, and construction of a GFP fusion protein to enable localization of the ...


Examination Of Polymorphism In The Serine Proteinase Inhibitor Gene In The Eastern Oyster, Crassostrea Virginica., Aine Lehane 2015 University of Rhode Island

Examination Of Polymorphism In The Serine Proteinase Inhibitor Gene In The Eastern Oyster, Crassostrea Virginica., Aine Lehane

Senior Honors Projects

Oysters are a keystone species; they are filter-feeders and reef-builders. Additionally, oysters are extremely important within the shellfish aquaculture industry; they are the second most widely produced species in world aquaculture production. Eastern oysters, Crassostrea virginica, are produced in aquaculture and are unfortunately susceptible to Dermo disease. Dermo is caused by a protozoan parasite, Perkinsus marinus, and infection is often fatal in oysters due to widespread tissue damage and blockage of blood vessels. Research in oyster disease is particularly needed because disease is one of the largest impediments faced by the aquaculture industry as entire oyster populations can be decimated ...


The Cancer Genome Atlas (Tcga): Breast And Ovarian Cancers, Laura Ann Riccio 2015 University of Rhode Island

The Cancer Genome Atlas (Tcga): Breast And Ovarian Cancers, Laura Ann Riccio

Senior Honors Projects

The field of genomics originated in the 1970’s starting with the sequencing of small organisms’ genomes such as the bacterium, Haemophilus influenzae, and the yeast, Saccharomyces cerevisiae. A genome is the complete ordered sequence of DNA bases (A, C, G, and T) comprising all of the protein- and RNA-coding genes, as well as all of the regulatory sequences necessary for the construction of an organism. Over time, scientists sequenced the genomes of larger and more complex organisms, eventually leading to the sequencing of the human genome. The Human Genome Project (HGP) was initiated in 1990 and took over ten ...


Bioinformatic Game Theory And Its Application To Cluster Multi-Domain Proteins, Brittney Keel 2015 University of Nebraska-Lincoln

Bioinformatic Game Theory And Its Application To Cluster Multi-Domain Proteins, Brittney Keel

Dissertations, Theses, and Student Research Papers in Mathematics

The exact evolutionary history of any set of biological sequences is unknown, and all phylogenetic reconstructions are approximations. The problem becomes harder when one must consider a mix of vertical and lateral phylogenetic signals. In this dissertation we propose a game-theoretic approach to clustering biological sequences and analyzing their evolutionary histories. In this context we use the term evolution as a broad descriptor for the entire set of mechanisms driving the inherited characteristics of a population. The key assumption in our development is that evolution tries to accommodate the competing forces of selection, of which the conservation force seeks to ...


Dominance Of Old End Growth Is Inherited In Fission Yeast, Julie Tia Rich 2015 University of Tennessee, Knoxville

Dominance Of Old End Growth Is Inherited In Fission Yeast, Julie Tia Rich

University of Tennessee Honors Thesis Projects

No abstract provided.


A Two-Component Regulatory System Associated With Scytonemin Biosynthesis In Nostoc Punctiforme Atcc 29133, Jacob P. Janssen 2015 Indiana University - Purdue University Fort Wayne

A Two-Component Regulatory System Associated With Scytonemin Biosynthesis In Nostoc Punctiforme Atcc 29133, Jacob P. Janssen

Masters' Theses

As phototrophic bacteria, cyanobacteria are continually exposed to ultraviolet radiation as they harvest solar energy. In particular, long-wavelength ultraviolet radiation (UVA) damages living cells by releasing reactive oxygen species. To mitigate damage to the cell, some cyanobacteria produce a UVA-absorbing pigment in the extracellular sheath, known as scytonemin. Scytonemin is a heterocyclic, dimeric molecule that is only produced upon induction by UVA. In Nostoc punctiforme ATCC 29133, it is hypothesized that scytonemin is regulated by the two component regulatory system (TCRS) of NpF1277 (sensor kinase) and NpF1278 (response regulator). Gene expression of the TCRS was studied after exposure to UVA ...


Integrating Motif, Dna Accessibility And Gene Expression Data To Build Regulatory Maps In An Organism, Charles Blatti, Majid Kazemian, Scot A. Wolfe, Michael H. Brodsky, Saurabh Sinha 2015 University of Illinois at Urbana-Champaign

Integrating Motif, Dna Accessibility And Gene Expression Data To Build Regulatory Maps In An Organism, Charles Blatti, Majid Kazemian, Scot A. Wolfe, Michael H. Brodsky, Saurabh Sinha

Molecular, Cell and Cancer Biology Publications

Characterization of cell type specific regulatory networks and elements is a major challenge in genomics, and emerging strategies frequently employ high-throughput genome-wide assays of transcription factor (TF) to DNA binding, histone modifications or chromatin state. However, these experiments remain too difficult/expensive for many laboratories to apply comprehensively to their system of interest. Here, we explore the potential of elucidating regulatory systems in varied cell types using computational techniques that rely on only data of gene expression, low-resolution chromatin accessibility, and TF-DNA binding specificities ('motifs'). We show that static computational motif scans overlaid with chromatin accessibility data reasonably approximate experimentally ...


Repsa-Directed Identification Of Dna-Binding Specificity For Orphan Transcription Factors, Kamir Hiam 2015 Kennesaw State University

Repsa-Directed Identification Of Dna-Binding Specificity For Orphan Transcription Factors, Kamir Hiam

Symposium of Student Scholars

The function of many genes and the biological roles of their encoded products are still not well characterized. Given the sequence-specific DNA-binding properties of transcription factor proteins, it is possible to purify them, identify the responsible polypeptide(s), determine their consensus binding sequences, and identify their genomic binding sites. Thus, one can go from cellular extract to proposed biological regulatory roles in relatively short order. Our goal is to identify and characterize orphan DNA-binding proteins in the model organism E. coli K12 using the novel combinatorial technique, REPSA (Restriction Endonuclease Protection Selection Amplification), as well as further develop the REPSA ...


Mapping And Analysis Of Caenorhabditis Elegans Transcription Factor Sequence Specificities, Kamesh Narasimhan, Samuel A. Lambert, Ally Yang, Jeremy Riddell, Sanie Mnaimneh, Hong Zheng, Mihai Albu, Hamed S. Najafabadi, John S. Reece-Hoyes, Juan Fuxman Bass, Albertha J. M. Walhout, Matthew T. Weirauch, Timothy R. Hughes 2015 University of Toronto

Mapping And Analysis Of Caenorhabditis Elegans Transcription Factor Sequence Specificities, Kamesh Narasimhan, Samuel A. Lambert, Ally Yang, Jeremy Riddell, Sanie Mnaimneh, Hong Zheng, Mihai Albu, Hamed S. Najafabadi, John S. Reece-Hoyes, Juan Fuxman Bass, Albertha J. M. Walhout, Matthew T. Weirauch, Timothy R. Hughes

Program in Systems Biology Publications and Presentations

Caenorhabditis elegans is a powerful model for studying gene regulation, as it has a compact genome and a wealth of genomic tools. However, identification of regulatory elements has been limited, as DNA-binding motifs are known for only 71 of the estimated 763 sequence-specific transcription factors (TFs). To address this problem, we performed protein binding microarray experiments on representatives of canonical TF families in C. elegans, obtaining motifs for 129 TFs. Additionally, we predict motifs for many TFs that have DNA-binding domains similar to those already characterized, increasing coverage of binding specificities to 292 C. elegans TFs (~40%). These data highlight ...


Resolution Of Telomere Fragility In Mammalian Celss, Mai R. Nguyen 2015 Washington University in St Louis

Resolution Of Telomere Fragility In Mammalian Celss, Mai R. Nguyen

Undergraduate Research Symposium Posters & Abstracts

Genomic stability is vital for the survival of cells and organisms. Telomeres, the nucleoprotein complexes capping the ends of linear chromosomes, prevent loss of genetic information and play an important role in the regulation of cell division. Due to their repetitive sequence and ability to form secondary structures, telomeres are especially sensitive to mutations or deletions of DNA replication and repair proteins. Telomere fragility, a phenotype in which multiple telomere signals or aberrant signals are observed on metaphase chromosomes stained by fluorescent in situ hybridization, is induced when cells experience replication stress. Although telomere fragility has been observed in many ...


Isolation And Comparative Genomic Analysis Of Mycobacteriophage Enkatz, Thomas Van Horn, Micah Rickles-Young, Shaarada Srivasta, Tina Zudock 2015 Washington University in St Louis

Isolation And Comparative Genomic Analysis Of Mycobacteriophage Enkatz, Thomas Van Horn, Micah Rickles-Young, Shaarada Srivasta, Tina Zudock

Thomas Van Horn

Phage Enkatz is a temperate mycobacteriophage isolated from an un-enriched soil sample collected from the South Forty housing area of the Washington University in St. Louis campus. Enkatz displays unequally sized plaques with a clear center that become cloudier with radial distance from the center. Genome analysis indicates that Enkatz is a cluster A1 mycobacteriophage with a genome size of 49,738 bases and 82 identified genes, 33 of which have been assigned functions. This analysis reveals that the majority of the genes in the positive strand code for structural proteins, while the majority of the genes in the negative ...


Complex Eukaryotic Protein Expression Using A Prokaryotic Chassis (Escherichia Coli), Derrica Burke, Julia Dave, Jasmine Padalla, Tre Landry 2015 Georgia State University

Complex Eukaryotic Protein Expression Using A Prokaryotic Chassis (Escherichia Coli), Derrica Burke, Julia Dave, Jasmine Padalla, Tre Landry

Georgia State Undergraduate Research Conference

No abstract provided.


Preliminary Report On The Production Of A Shiga-Like Toxoid Fusion Protein As Associated With Novel Flic Vaccine, Michael Maulin 2015 Georgia State University

Preliminary Report On The Production Of A Shiga-Like Toxoid Fusion Protein As Associated With Novel Flic Vaccine, Michael Maulin

Georgia State Undergraduate Research Conference

No abstract provided.


The Role Of Calcium Signaling Genes In Schizophrenia Development, Nisha Bhatia 2015 Georgia State University

The Role Of Calcium Signaling Genes In Schizophrenia Development, Nisha Bhatia

Georgia State Undergraduate Research Conference

No abstract provided.


From Shelf To Shelf: Assessing Historical And Contemporary Genetic Differentiation And Connectivity Across The Gulf Of Mexico In Gag, Mycteroperca Microlepis, Nathaniel Kenneth Jue, Thierry Brule, Felicia C. Coleman, Christopher C. Koenig 2015 Florida State University

From Shelf To Shelf: Assessing Historical And Contemporary Genetic Differentiation And Connectivity Across The Gulf Of Mexico In Gag, Mycteroperca Microlepis, Nathaniel Kenneth Jue, Thierry Brule, Felicia C. Coleman, Christopher C. Koenig

FSU Coastal and Marine Laboratory Publications

Describing patterns of connectivity among populations of species with widespread distributions is particularly important in understanding the ecology and evolution of marine species. In this study, we examined patterns of population differentiation, migration, and historical population dynamics using microsatellite and mitochondrial loci to test whether populations of the epinephelid fish, Gag, Mycteroperca microlepis, an important fishery species, are genetically connected across the Gulf of Mexico and if so, whether that connectivity is attributable to either contemporary or historical processes. Populations of Gag on the Campeche Bank and the West Florida Shelf show significant, but low magnitude, differentiation. Time since divergence ...


The Effect Of Serrate Transmembrane Domain Substitution On Notch Signaling, James Z. Curlin 2015 Trinity College

The Effect Of Serrate Transmembrane Domain Substitution On Notch Signaling, James Z. Curlin

Senior Theses and Projects

The Notch signaling pathway is a crucial means by which organisms differentiate cells during development. Notch is regulated primarily through the interaction of a Notch receptor protein and a ligand protein, in two specific ways. Cis-inhibition occurs when both a ligand and receptor are present on the same cellular membrane. This results in the cis-ligand binding to the receptor and preventing the ligand on an adjacent cell from binding and activating the receptor. Alternatively, trans-activation occurs when the ligand and receptor are on adjacent cells, and results in the activation of the Notch pathway. Both the receptor ...


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