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The Transcriptome Of The Bermuda Fireworm Odontosyllis Enopla (Annelida: Syllidae): A Unique Luciferase Gene Family And Putative Epitoky-Related Genes, Mercer R. Brugler, M. Teresa Aguado, Michael Tessler, Mark Siddall 2018 NYC College of Technology (CUNY)

The Transcriptome Of The Bermuda Fireworm Odontosyllis Enopla (Annelida: Syllidae): A Unique Luciferase Gene Family And Putative Epitoky-Related Genes, Mercer R. Brugler, M. Teresa Aguado, Michael Tessler, Mark Siddall

Publications and Research

The Bermuda fireworm Odontosyllis enopla exhibits an extremely tight circalunar circadian behavior that results in an impressive bioluminescent mating swarm, thought to be due to a conventional luciferase-mediated oxidation of a light-emitting luciferin. In addition, the four eyes become hypertrophied and heavily pigmented, and the nephridial system is modified to store and release gametes and associated secretions. In an effort to elucidate transcripts related to bioluminescence, circadian or circalunar periodicity, as well as epitoky-related changes of the eyes and nephridial system, we examined the transcriptomic profile of three female O. enopladuring a bioluminescent swarm in Ferry Reach, Bermuda. Using ...


Production Of A Candidate Recombinant Protein Vaccine For Mannheimia Haemolytica In Lettuce And Tobacco Chloroplasts, Coby K. Martin 2018 The University of Western Ontario

Production Of A Candidate Recombinant Protein Vaccine For Mannheimia Haemolytica In Lettuce And Tobacco Chloroplasts, Coby K. Martin

Electronic Thesis and Dissertation Repository

The cattle industry worldwide is ravaged by bovine respiratory disease (BRD), a bacterial disease caused by Mannheimia haemolytica. Recent efforts to design vaccines against M. haemolytica focus on a virulence factor, leukotoxin, in addition to surface lipoproteins. Plant-based protein production is a safe and inexpensive alternative to traditional methods. Edible vaccines deliver antigens to pharyngeal tissues, which can provide local immunization against M. haemolytica prior to its progression into the lungs. In this project, a chimeric protein containing M. haemolytica antigens was produced in tobacco chloroplasts as a candidate edible vaccine for BRD. Attempts were made to transform lettuce chloroplasts ...


Drosophila Species Learn Dialects Through Communal Living, Balint Z. Kacsoh, Julianna Bozler, Giovanni Bosco 2018 Dartmouth College

Drosophila Species Learn Dialects Through Communal Living, Balint Z. Kacsoh, Julianna Bozler, Giovanni Bosco

Open Dartmouth: Faculty Open Access Articles

Many species are able to share information about their environment by communicating through auditory, visual, and olfactory cues. In Drosophila melanogaster, exposure to para- sitoid wasps leads to a decline in egg laying, and exposed females communicate this threat to naïve flies, which also depress egg laying. We find that species across the genus Drosophila respond to wasps by egg laying reduction, activate cleaved caspase in oocytes, and communicate the presence of wasps to naïve individuals. Communication within a species and between closely related species is efficient, while more distantly related species exhibit partial communication. Remarkably, partial communication between some ...


Insects With Similar Social Complexity Show Convergent Patterns Of Adaptive Molecular Evolution, Kathleen A. Dogantzis, Brock A. Harpur, André Rodrigues, Laura Beani, Amy L. Toth, Amro Zayed 2018 York University

Insects With Similar Social Complexity Show Convergent Patterns Of Adaptive Molecular Evolution, Kathleen A. Dogantzis, Brock A. Harpur, André Rodrigues, Laura Beani, Amy L. Toth, Amro Zayed

Ecology, Evolution and Organismal Biology Publications

Eusociality has independently evolved multiple times in the hymenoptera, but the patterns of adaptive molecular evolution underlying the evolution and elaboration of eusociality remain uncertain. Here, we performed a population genomics study of primitively eusocial Polistes (paper wasps), and compared their patterns of molecular evolution to two social bees; Bombus (bumblebees), and Apis (honey bees). This species triad allowed us to study molecular evolution across a gradient of social complexity (Polistes < Bombus < Apis) and compare species pairs that have similar (i.e. Polistes and Bombus) or different (i.e. Polistes and Apis) life histories, while controlling for phylogenetic distance. We ...


A Humanized Hypertrophic Cardiomyopathy Model To Elucidate Molecular Mechanism In Disease Pathology, Ragavi Vijayakumar, Maxine Hong 2018 NUS High School of Mathematics and Science

A Humanized Hypertrophic Cardiomyopathy Model To Elucidate Molecular Mechanism In Disease Pathology, Ragavi Vijayakumar, Maxine Hong

The International Student Science Fair 2018

Hypertrophic cardiomyopathy (HCM), that clinically manifests as an enlarged heart is a highly prevalent cardiac disorder with propensity towards arrhythmia-induced sudden cardiac death. The mechanism of HCM remains poorly defined, necessitating further understanding of the disease for improved therapeutic strategies. As it is challenging to obtain cardiac biopsies from human subjects, using induced pluripotent stem cells technology, we generated cardiomyocytes (CMs) in a dish from HCM patients. These HCM-CMs presented the clinical manifestation in that they were significantly larger in size in comparison to control (healthy)-CMs. Furthermore, gene expression profiling of cardiac ion channels revealed increased transcripts encoding for ...


A Humanized Hypertrophic Cardiomyopathy Model To Elucidate Molecular Mechanism In Disease Pathology, Ragavi Vijayakumar, Maxine Hong 2018 NUS High School of Mathematics and Science

A Humanized Hypertrophic Cardiomyopathy Model To Elucidate Molecular Mechanism In Disease Pathology, Ragavi Vijayakumar, Maxine Hong

The International Student Science Fair 2018

Hypertrophic cardiomyopathy (HCM), that clinically manifests as an enlarged heart is a highly prevalent cardiac disorder with propensity towards arrhythmia-induced sudden cardiac death. The mechanism of HCM remains poorly defined, necessitating further understanding of the disease for improved therapeutic strategies. As it is challenging to obtain cardiac biopsies from human subjects, using induced pluripotent stem cells technology, we generated cardiomyocytes (CMs) in a dish from HCM patients. These HCM-CMs presented the clinical manifestation in that they were significantly larger in size in comparison to control (healthy)-CMs. Furthermore, gene expression profiling of cardiac ion channels revealed increased transcripts encoding for ...


Systematic Pan-Cancer Analysis Of Somatic Allele Frequency, Liam Spurr, Muzi Li, Nawaf Alomran, Qianqian Zhang, Paula Restrepo, Mercedeh Movassagh, Chris Trenkov, Nerissa Tunnessen, Tatiyana Apanasovich, Keith A. Crandall, Nathan Edwards, Anelia Horvath 2018 George Washington University

Systematic Pan-Cancer Analysis Of Somatic Allele Frequency, Liam Spurr, Muzi Li, Nawaf Alomran, Qianqian Zhang, Paula Restrepo, Mercedeh Movassagh, Chris Trenkov, Nerissa Tunnessen, Tatiyana Apanasovich, Keith A. Crandall, Nathan Edwards, Anelia Horvath

Open Access Articles

Imbalanced expression of somatic alleles in cancer can suggest functional and selective features, and can therefore indicate possible driving potential of the underlying genetic variants. To explore the correlation between allele frequency of somatic variants and total gene expression of their harboring gene, we used the unique data set of matched tumor and normal RNA and DNA sequencing data of 5523 distinct single nucleotide variants in 381 individuals across 10 cancer types obtained from The Cancer Genome Atlas (TCGA). We analyzed the allele frequency in the context of the variant and gene functional features and linked it with changes in ...


Tarbp2 -Mediated Post-Transcriptional Regulation Of Gene Expression During Murine Embryonic Development And Spermatogenesis, Sri Ramulu N. Pullagura 2018 University of Maine

Tarbp2 -Mediated Post-Transcriptional Regulation Of Gene Expression During Murine Embryonic Development And Spermatogenesis, Sri Ramulu N. Pullagura

Electronic Theses and Dissertations

Micro RNAs (miRNAs), which are ~22 nucleotide (nt) long RNA molecules and several RNA binding proteins (RBPs) engage in an RNA dependent post-transcriptional gene silencing process known as RNA interference (RNAi). In the canonical miRNA biogenesis pathway, an enzyme known as DICER cleaves the ~70nt pre-miRNA to a ~22nt long miRNA that is loaded into the RNAi effector mechanism, the RNA induced silencing complex (RISC).

Several in vitro studies provide suggestive evidence that mammalian double stranded RNA binding proteins (dsRBPs), such as TARBP2, act as DICER cofactors in miRNA processing and RISC loading to promote RNAi activity. A screen attempting ...


Involvement Of The Ino80 Complex In Chromosome Segregation, Jesus Moreno 2018 University of Arkansas, Fayetteville

Involvement Of The Ino80 Complex In Chromosome Segregation, Jesus Moreno

Theses and Dissertations

Chromatin remodeling complexes are multi-protein complexes that regulate the dynamics of the nucleosomes in the genome. The INO80 chromatin remodeling complex participates in varied biological processes such as: transcription, DNA repair, DNA replication and chromosome integrity. It catalyzes the eviction of the H2A.Z variant histone as well as whole nucleosome eviction. This complex is comprised of 15 subunits and the contribution of each to chromosome segregations remains unknown. To evaluate the contribution of each subunit to chromosome segregation, we tested deletion mutants of the non-essential subunits for DNA content and benomyl sensitivity. Also, we assessed members of the SWR1 ...


Functional Studies Of The E. Coli Proc And A Putative Ortholog Mrub_1345, Mourin Azar, Dr. Lori Scott 2018 Augustana College, Rock Island Illinois

Functional Studies Of The E. Coli Proc And A Putative Ortholog Mrub_1345, Mourin Azar, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of Escherichia coli and Meiothermus ruber proC genes using the complementation assay. In this research project, mutants of varying severity to the functional state of the protein were developed. The results showed that two or more amino acid deletions reduced or eliminated ProC function. Amino acid substitutions, on the other hand, were not severe enough to impact ProC function. Double and triple mutants ...


The Role Of Ferric Reduction Oxidases In Plant Anti-Herbivore Defense., Virginia C. Nunamaker 2018 University of Louisville

The Role Of Ferric Reduction Oxidases In Plant Anti-Herbivore Defense., Virginia C. Nunamaker

College of Arts & Sciences Senior Honors Theses

Iron is an essential element required for plants to carry out metabolic functions such as photosynthesis, heme biosynthesis, and chlorophyll biosynthesis. Within Arabidopsis thaliana, eight ferric reduction oxidase (FRO) genes function in iron uptake and homeostasis with tissue specific expression. However, little else is known regarding the biological role of FROs. Recent studies identify the FRO gene family as particularly responsive to the green leaf plant derived volatile (GLV) cis-3-hexenyl acetate (z3HAC). Since z3HAC acts as a wound signal and cues unaffected parts of the plant to prime defenses prior to herbivory, an increase in FRO activity in response to ...


Phylogeny Of The Orangethroat Darter (Etheostoma Spectabile) Species Complex In The Ozark Highlands Of Arkansas, McKenna George 2018 University of Arkansas, Fayetteville

Phylogeny Of The Orangethroat Darter (Etheostoma Spectabile) Species Complex In The Ozark Highlands Of Arkansas, Mckenna George

Animal Science Undergraduate Honors Theses

Darters are small, benthic fishes that live in freshwater rivers and streams and belong to the family Percidae. Pleistocene glaciations fragmented many darter species, resulting in speciation, but new species are often hard to detect if they are morphologically identical to pre-existing species. Intraspecific hybridization and resulting introgression, which occur frequently in glaciated areas, further complicate identification by introducing heterospecific genomes into mitochondrial DNA, making it difficult to accurately resolve phylogenetic relationships. The results of Bossu and Near’s 2009 study highlight this issue, showing a large degree of incongruence between mitochondrial and nuclear gene trees.

This study analyzed samples ...


Multivalency Regulates Activity In An Intrinsically Disordered Transcription Factor, Sarah Clark, Janette B. Myers, Ashleigh King, Radovan Fiala, Jiri Novacek, Grant Pearce, Steve L. Reichow, Elisar J. Barbar 2018 Department of Biochemistry and Biophysics, Oregon State University

Multivalency Regulates Activity In An Intrinsically Disordered Transcription Factor, Sarah Clark, Janette B. Myers, Ashleigh King, Radovan Fiala, Jiri Novacek, Grant Pearce, Steve L. Reichow, Elisar J. Barbar

Chemistry Faculty Publications and Presentations

The transcription factor ASCIZ (ATMIN, ZNF822) has an unusually high number of recognition motifs for the product of its main target gene, the hub protein LC8 (DYNLL1). Using a combination of biophysical methods, structural analysis by NMR and electron microscopy, and cellular transcription assays, we developed a model that proposes a concerted role of intrinsic disorder and multiple LC8 binding events in regulating LC8 transcription. We demonstrate that the long intrinsically disordered C-terminal domain of ASCIZ binds LC8 to form a dynamic ensemble of complexes with a gradient of transcriptional activity that is inversely proportional to LC8 occupancy. The preference ...


Functional And Structural Impact Of The Loss Of The Leucine-Rich Repeat Protein Lrit1 In The Mouse Retina., Catherine Ann Cobb 2018 University of Louisville

Functional And Structural Impact Of The Loss Of The Leucine-Rich Repeat Protein Lrit1 In The Mouse Retina., Catherine Ann Cobb

Electronic Theses and Dissertations

Mutations in genes encoding the leucine-rich repeat (LRR) proteins nyctalopin and LRIT3 lead to complete congenital stationary night blindness because they are critical to depolarizing bipolar cell function in the retina. LRIT3 has two closely related family members, LRIT1 and LRIT2. In silico analyses of publicly available RNA-Seq data showed that Lrit1 was highly expressed in the retina. Here I describe the expression pattern and impact of loss of LRIT1 on retinal function. To enable these studies, we used CRISPR/Cas9 technology to create an Lrit1-/- mouse line. Retinal morphology and morphometry analyses showed no gross changes in retinal structure ...


Investigation For Novel Anti-Apoptotic Factors In The Neurons Of Drosophila Melanogaster, Haylie Rachel Lam 2018 University of Tennessee, Knoxville

Investigation For Novel Anti-Apoptotic Factors In The Neurons Of Drosophila Melanogaster, Haylie Rachel Lam

University of Tennessee Honors Thesis Projects

No abstract provided.


Genotype-Specific Insertion Of Cytotoxic Genetic Elements Into Cancer Cells, Ryan Englander 2018 University of Connecticut

Genotype-Specific Insertion Of Cytotoxic Genetic Elements Into Cancer Cells, Ryan Englander

University Scholar Projects

The new gene editing system CRISPR/Cas9, composed of a complex composed of a guide RNA and the Cas9 endonuclease, promises to revolutionize biological research and potentially allow clinicians to directly modify patient DNA in vivo. While its applications in the treatment of genetic diseases and in modifying immune cells for immunotherapy are currently being explored, CRISPR/Cas9’s potential utility as a modular system for targeting tumor-specific mutated sequences has not as of yet been explored. While CRISPR/Cas9 is specific enough to target small insertions and deletions or gross chromosomal rearrangements, it is not specific enough to reliably ...


The Characterization Of The Transcription Factor Msab And Its Role In Staphylococcal Virulence, Justin Batte 2018 The University of Southern Mississippi

The Characterization Of The Transcription Factor Msab And Its Role In Staphylococcal Virulence, Justin Batte

Dissertations

Staphylococcus aureus is a common human pathogen that is responsible for a wide range of infections, ranging from relative minor skin infections to life-threatening disease such as bacteremia, septicemia, and endocarditis. S. aureus possesses many different virulent factors that aid in its ability to cause this wide array of infections. One major virulence factor includes the production of capsular polysaccharide (CP). The production of CP plays a major role in the virulence response during infection specifically by providing S. aureus an antiphagocytic mechanism that allows the pathogen to evade phagocytosis during an infection. S. aureus has developed complex genetic regulatory ...


Investigating The Role Of Dnc-2 And Dli-1 On Ampa Receptor Mediated Behaviors In Caenorhabditis Elegans, Natalie Oberding 2018 Carroll College, Helena, MT

Investigating The Role Of Dnc-2 And Dli-1 On Ampa Receptor Mediated Behaviors In Caenorhabditis Elegans, Natalie Oberding

Life and Environmental Sciences Undergraduate Theses

Γ-amino-3-hydroxy-5methylisoxazole-4-proprionic acid (AMPA) receptors (AMPARs) are protein complexes involved in excitatory neurotransmission. AMPARs are tetrameric structures consisting of the pairings of GluA1, GluA2, GluA3, and GluA4 subunits. Dctn2 and Dync1li1 were found to interact with GluA2 in an immunoprecipitation screen that was performed on postnatal day 14 rat brains. DNC-2 and DLI-1 were identified as the C. elegans homologs of Dctn2 and Dync1li1, respectively, and are components of motor proteins that transport cargo throughout the cell. The goal of this project was to determine whether knocking down DNC-2 and DLI-1 by RNAi affects AMPA Receptor-mediated behaviors, including mechanosensation and chemosensation ...


A Genetic Screen To Identify Fission Yeast Genes With Roles In Protecting Against Perturbation Of The Actin Cytoskeleton, Dorota Michalski 2018 The University of Western Ontario

A Genetic Screen To Identify Fission Yeast Genes With Roles In Protecting Against Perturbation Of The Actin Cytoskeleton, Dorota Michalski

Electronic Thesis and Dissertation Repository

In the fission yeast, Schizosaccharomyces pombe, stress upon the cell division machinery leads to the activation of a cytokinesis checkpoint. This checkpoint results in a delay in cell cycle progression and the prolonged maintenance of a cytokinesis competent cellular state. In this state the cell is able to continuously reform/repair the actomyosin ring until cell division is achieved. To uncover genes that play a role in enforcing this checkpoint, the actin depolymerizing drug Latrunculin A (LatA) was used to perturb the cytokinetic machinery in a set of 3400 viable haploid S. pombe gene deletion mutants. Thirty-eight gene deletion mutants ...


Oligonucleotides Targeting Tcf4 Triplet Repeat Expansion Inhibit Rna Foci And Mis-Splicing In Fuchs' Dystrophy, Jiaxin Hu, Ziye Rong, Xin Gong, Zhengyang Zhou, Vivek K. Sharma, Chao Xing, Jonathan K. Watts, David R. Corey, V. Vinod Mootha 2018 UT Southwestern Medical Center

Oligonucleotides Targeting Tcf4 Triplet Repeat Expansion Inhibit Rna Foci And Mis-Splicing In Fuchs' Dystrophy, Jiaxin Hu, Ziye Rong, Xin Gong, Zhengyang Zhou, Vivek K. Sharma, Chao Xing, Jonathan K. Watts, David R. Corey, V. Vinod Mootha

RNA Therapeutics Institute Publications

Fuchs' endothelial corneal dystrophy (FECD) is the most common repeat expansion disorder. FECD impacts 4% of U.S. population and is the leading indication for corneal transplantation. Most cases are caused by an expanded intronic CUG tract in the TCF4 gene that forms nuclear foci, sequesters splicing factors and impairs splicing. We investigated the sense and antisense RNA landscape at the FECD gene and find that the sense-expanded repeat transcript is the predominant species in patient corneas. In patient tissue, sense foci number were negatively correlated with age and showed no correlation with sex. Each endothelial cell has approximately 2 ...


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