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2017

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Transcriptome-Wide Identification Of The Rna-Binding Landscape Of The Chromatin-Associated Protein Parp1 Reveals Functions In Rna Biogenesis, Manana Melikishvili, Julia H. Chariker, Eric C. Rouchka, Yvonne N. Fondufe-Mittendorf Nov 2017

Transcriptome-Wide Identification Of The Rna-Binding Landscape Of The Chromatin-Associated Protein Parp1 Reveals Functions In Rna Biogenesis, Manana Melikishvili, Julia H. Chariker, Eric C. Rouchka, Yvonne N. Fondufe-Mittendorf

Molecular and Cellular Biochemistry Faculty Publications

Recent studies implicate Poly (ADP-ribose) polymerase 1 (PARP1) in alternative splicing regulation, and PARP1 may be an RNA-binding protein. However, detailed knowledge of RNA targets and the RNA-binding region for PARP1 are unknown. Here we report the first global study of PARP1–RNA interactions using PAR–CLIP in HeLa cells. We identified a largely overlapping set of 22 142 PARP1–RNA-binding peaks mapping to mRNAs, with 20 484 sites located in intronic regions. PARP1 preferentially bound RNA containing GC-rich sequences. Using a Bayesian model, we determined positional effects of PARP1 on regulated exon-skipping events: PARP1 binding upstream and downstream of the skipped exons …


Mechanism Of Transcription Anti-Termination In Human Mitochondria., Hauke S Hillen, Andrey V Parshin, Karen Agaronyan, Yaroslav I Morozov, James J Graber, Aleksandar Chernev, Kathrin Schwinghammer, Henning Urlaub, Michael Anikin, Patrick Cramer, Dmitry Temiakov Nov 2017

Mechanism Of Transcription Anti-Termination In Human Mitochondria., Hauke S Hillen, Andrey V Parshin, Karen Agaronyan, Yaroslav I Morozov, James J Graber, Aleksandar Chernev, Kathrin Schwinghammer, Henning Urlaub, Michael Anikin, Patrick Cramer, Dmitry Temiakov

Rowan-Virtua School of Osteopathic Medicine Faculty Scholarship

In human mitochondria, transcription termination events at a G-quadruplex region near the replication origin are thought to drive replication of mtDNA by generation of an RNA primer. This process is suppressed by a key regulator of mtDNA-the transcription factor TEFM. We determined the structure of an anti-termination complex in which TEFM is bound to transcribing mtRNAP. The structure reveals interactions of the dimeric pseudonuclease core of TEFM with mobile structural elements in mtRNAP and the nucleic acid components of the elongation complex (EC). Binding of TEFM to the DNA forms a downstream "sliding clamp," providing high processivity to the EC. …


“I’M Not Talking To You” “You Don’T Have To!” Trans/Scripting The Bland-Encinia Case, Melisa Cahnmann-Taylor Sep 2017

“I’M Not Talking To You” “You Don’T Have To!” Trans/Scripting The Bland-Encinia Case, Melisa Cahnmann-Taylor

Pedagogy and Theatre of the Oppressed Journal

This manifesto and trans/scription is a response to the specific violence that occurred between a Black female driver (Sandra Bland) and a white police officer (Brian Encinia) in Texas in July 2015 which resulted in Bland’s death. As an urgent #BlackLivesMatter concern, the author considers post-structuralist theories of identity and trans/scription as resources to inform identity performance and trans/imagination with more opportunities for life-giving rather than life-taking results. The author provides a series of questions and challenges to Theatre of the Oppressed practitioners for trans/scripting and trans/imaging moments of racial discrimination and terrorism for long-term rehearsal into, through, and beyond …


Transcription Of The Virus-Like Agent Responsible For Carcinogenesis In Bicolor Damselfish, Jazmine S. Pritchett Aug 2017

Transcription Of The Virus-Like Agent Responsible For Carcinogenesis In Bicolor Damselfish, Jazmine S. Pritchett

Open Access Theses

Damselfish Neurofibromatosis (DNF) is a naturally occurring cancer that affects Bicolor Damselfish (Stegastes partitus) located on South Florida reefs. Damselfish Neurofibromatosis is characterized by tumor development within the pigmented cells of the skin (chromatophoromas) as well as Schwann cells (neurofibromas and malignant peripheral nerve sheath tumors). Damselfish Neurofibromatosis has been shown to be caused by a virus-like agent with a 2.4 kb DNA genome named the Damselfish Virus-like Agent (DVLA). Studies of DVLA have shown that this DNA is located and replicates within the mitochondria of infected cells. Five RNAs are transcribed from the DVLA genome but the …


Disruption Of Cdk-Resistant Chromatin Association By Prb Causes Dna Damage, Mitotic Errors, And Reduces Condensin Ii Recruitment, Charles A. Ishak, Courtney H. Coschi, Michael V. Roes, Frederick A. Dick Aug 2017

Disruption Of Cdk-Resistant Chromatin Association By Prb Causes Dna Damage, Mitotic Errors, And Reduces Condensin Ii Recruitment, Charles A. Ishak, Courtney H. Coschi, Michael V. Roes, Frederick A. Dick

Paediatrics Publications

Organization of chromatin structure is indispensible to the maintenance of genome integrity. The retinoblastoma tumor suppressor protein (pRB) mediates both transcriptional repression and chromatin organization, but the independent contributions of these functions have been difficult to study. Here, we utilize a synthetic Rb1 mutant allele (F832A) that maintains pRB association at cell cycle gene promoters, but disrupts a cyclin-dependent kinase (CDK)-resistant interaction with E2F1 to reduce occupancy of pRB on intergenic chromatin. Reduced pRB chromatin association increases spontaneous γH2AX deposition and aneuploidy. Our data indicates that the CDK-resistant pRB-E2F1 scaffold recruits Condensin II to major satellite repeats to stabilize chromatin …


Characterizing The Interaction Between Human Adenovirus E1a And The Transcriptional Repressor Bs69, Ali Zhang May 2017

Characterizing The Interaction Between Human Adenovirus E1a And The Transcriptional Repressor Bs69, Ali Zhang

Electronic Thesis and Dissertation Repository

Protein products of the Early Region 1A (E1A) gene in human adenovirus 5 (HAdV-5) are the first viral proteins expressed upon adenovirus infection. E1A disrupts many cellular physiological events by binding to and regulating an impressive number of host factors. Of particular interest is BS69, a repressor of E1A transactivation. Due to the strong interaction observed between E1A and BS69, I hypothesize that these two proteins function together to disrupt gene expression within an infected cell.

Using in silico modelling and a series of yeast two-hybrid assays, I determined that residues 112-119 of HAdV-5 E1A is the minimal interacting region …


N-Blr, A Primate-Specific Non-Coding Transcript Leads To Colorectal Cancer Invasion And Migration., Isidore Rigoutsos, Sang Kil Lee, Su Youn Nam, Simone Anfossi, Barbara Pasculli, Martin Pichler, Yi Jing, Cristian Rodriguez-Aguayo, Aristeidis G. Telonis, Simona Rossi, Cristina Ivan, Tina Catela Ivkovic, Linda Fabris, Peter M. Clark, Hui Ling, Masayoshi Shimizu, Roxana S. Redis, Maitri Y Shah, Xinna Zhang, Yoshinaga Okugawa, Eun Jung Jung, Aristotelis Tsirigos, Li Huang, Jana Ferdin, Roberta Gafà, Riccardo Spizzo, Milena S. Nicoloso, Anurag N. Paranjape, Maryam Shariati, Aida Tiron, Jen Jen Yeh, Raul Teruel-Montoya, Lianchun Xiao, Sonia A. Melo, David Menter, Zhi-Qin Jiang, Elsa R. Flores, Massimo Negrini, Ajay Goel, Menashe Bar-Eli, Sendurai A. Mani, Chang Gong Liu, Gabriel Lopez-Berestein, Ioana Berindan-Neagoe, Manel Esteller, Scott Kopetz, Giovanni Lanza, George A. Calin May 2017

N-Blr, A Primate-Specific Non-Coding Transcript Leads To Colorectal Cancer Invasion And Migration., Isidore Rigoutsos, Sang Kil Lee, Su Youn Nam, Simone Anfossi, Barbara Pasculli, Martin Pichler, Yi Jing, Cristian Rodriguez-Aguayo, Aristeidis G. Telonis, Simona Rossi, Cristina Ivan, Tina Catela Ivkovic, Linda Fabris, Peter M. Clark, Hui Ling, Masayoshi Shimizu, Roxana S. Redis, Maitri Y Shah, Xinna Zhang, Yoshinaga Okugawa, Eun Jung Jung, Aristotelis Tsirigos, Li Huang, Jana Ferdin, Roberta Gafà, Riccardo Spizzo, Milena S. Nicoloso, Anurag N. Paranjape, Maryam Shariati, Aida Tiron, Jen Jen Yeh, Raul Teruel-Montoya, Lianchun Xiao, Sonia A. Melo, David Menter, Zhi-Qin Jiang, Elsa R. Flores, Massimo Negrini, Ajay Goel, Menashe Bar-Eli, Sendurai A. Mani, Chang Gong Liu, Gabriel Lopez-Berestein, Ioana Berindan-Neagoe, Manel Esteller, Scott Kopetz, Giovanni Lanza, George A. Calin

Computational Medicine Center Faculty Papers

BACKGROUND: Non-coding RNAs have been drawing increasing attention in recent years as functional data suggest that they play important roles in key cellular processes. N-BLR is a primate-specific long non-coding RNA that modulates the epithelial-to-mesenchymal transition, facilitates cell migration, and increases colorectal cancer invasion.

RESULTS: We performed multivariate analyses of data from two independent cohorts of colorectal cancer patients and show that the abundance of N-BLR is associated with tumor stage, invasion potential, and overall patient survival. Through in vitro and in vivo experiments we found that N-BLR facilitates migration primarily via crosstalk with E-cadherin and ZEB1. We showed that …


Modulation Of Estrogen Related Receptor Alpha Activity By The Kinesin Kif17, Am Pramodh Bandara Seneviratne, Zeynep Turan, Aurelie Hermant, Patrick Lecine, William O. Smith, Jean-Paul Borg, Fanny Jaulin, Geri Kreitzer May 2017

Modulation Of Estrogen Related Receptor Alpha Activity By The Kinesin Kif17, Am Pramodh Bandara Seneviratne, Zeynep Turan, Aurelie Hermant, Patrick Lecine, William O. Smith, Jean-Paul Borg, Fanny Jaulin, Geri Kreitzer

Publications and Research

Estrogen-related receptor alpha (ERR1) is an orphan nuclear receptor that can bind transcriptional co-activators constitutively. ERR1 expression correlates with poor patient outcomes in breast cancer, heightening interest in this nuclear receptor as a therapeutic target. Because ERR1 has no known regulatory ligand, a major challenge in targeting its activity is to find cellular or synthetic modulators of its function. We identified an interaction between ERR1 and KIF17, a kinesin-2 family microtubule motor, in a yeast-2-hybrid screen. We confirmed the interaction using in vitro biochemical assays and determined that binding is mediated by the ERR1 ligand-binding/AF2 domain and the KIF17 C-terminal …


Investigating Adenovirus E1a As An Rna Polymerase Ii C-Terminal Domain Mimic And Its Role In Transcription Activation, Kristianne Jc Galpin May 2017

Investigating Adenovirus E1a As An Rna Polymerase Ii C-Terminal Domain Mimic And Its Role In Transcription Activation, Kristianne Jc Galpin

Electronic Thesis and Dissertation Repository

Viruses rely on host cell machinery, often mimicking cellular components, in order to circumvent host cell defenses and hijack cellular processes. DNA viruses, such as human Adenovirus (hAdV), rely on RNA Polymerase II (RNAPII) to transcribe viral genes. RNAPII has a C-terminal domain (CTD), made up of highly conserved heptad repeats of tyrosine-serine-proline-threonine-serine-proline-serine (YSPTSPS). Post-translational modifications of residues within the CTD, including phosphorylation, coordinates the transcription cycle. Several viruses, including Human Immunodeficiency Virus (HIV), Human Cytomegalovirus (hCMV), Epstein-Bar Virus (EBV) and Herpes Simplex Virus (HSV), modify the phosphorylation state of the RNAPII CTD by hijacking cellular cyclin dependent kinases (CDKs) …


Improving Speech And Speaker Recognition For Multi-Speaker Conversations, Eric R. Youngberg May 2017

Improving Speech And Speaker Recognition For Multi-Speaker Conversations, Eric R. Youngberg

Honors Capstones

This paper outlines an effective process for transcribing conversations from an audio file. The process involves combining speech recognition and speaker recognition to prepare the audio signals for transcription without relying on a database of preexisting vocal models. This process is intended for multi-speaker conversations where vocal models are not available or otherwise impossible to create from the amount of data provided. We find in conclusion that we can improve the performance of speech recognition on multi-speaker conversations by leveraging the classifying properties of speaker recognition to reduce variance in the dataset thus producing a result that is just as …


The Transcriptional Regulation Of The Human Angiotensinogen Gene After High-Fat Diet Is Haplotype-Dependent: Novel Insights Into The Gene-Regulatory Networks And Implications For Human Hypertension, A Rana, S Jain, N Puri, M Kaw, N Sirianni, D Eren, Brahma Mopidevi, Anand Kumar May 2017

The Transcriptional Regulation Of The Human Angiotensinogen Gene After High-Fat Diet Is Haplotype-Dependent: Novel Insights Into The Gene-Regulatory Networks And Implications For Human Hypertension, A Rana, S Jain, N Puri, M Kaw, N Sirianni, D Eren, Brahma Mopidevi, Anand Kumar

NYMC Faculty Publications

Single nucleotide polymorphisms (SNPs) in the human angiotensinogen (hAGT) gene may modulate its transcription and affect the regulation of blood pressure via activation of the renin-angiotensin aldosterone system (RAAS). In this regard, we have identified polymorphisms in the 2.5 Kb promoter of the hAGT gene that form two haplotype (Hap) blocks: -6A/G (-1670A/G, -1562C/T, -1561T/C) and -217A/G (-532T/C, -793A/G, -1074T/C & -1178G/A). hAGT gene with Hap -6A/-217A (Hap I) is associated with increased blood pressure whereas, Hap -6G/-217G (Hap II) is associated with normal blood pressure in human subjects. Since RAAS over activity contributes to hypertension in obesity, we have …


John Philip Sousa And The Wagner Overture: A New Transcription Of The Overture To Der Fliegende Holländer For Wind Orchestra, Stephen H. Goldeck May 2017

John Philip Sousa And The Wagner Overture: A New Transcription Of The Overture To Der Fliegende Holländer For Wind Orchestra, Stephen H. Goldeck

UNLV Theses, Dissertations, Professional Papers, and Capstones

This research examines John Philip Sousa’s 1893 wind band transcription of Richard Wagner’s overture to Der fliegende Holländer, and focuses specifically on how Sousa reconceived orchestral sonorities and solved particular problems posed by Wagner’s complex orchestrational textures. Findings include that, while appropriate for the era and instrumentation of Sousa’s band, his transcription contains certain limitations for the twenty-first-century wind orchestra. Due to the fact that Sousa’s compositions, arrangements, and transcriptions were written to accommodate frequent outdoor performances, Sousa’s transcription uses more doubled voicings than would be necessary in an indoor concert hall setting. Further, while Sousa’s instrumentation approximates that of …


Tres Danzas Cubanas By Alejandro García Caturla: A Transcription For Wind Orchestra With Accompanying Biographical Sketch And Transcription Method, Darrell Brown May 2017

Tres Danzas Cubanas By Alejandro García Caturla: A Transcription For Wind Orchestra With Accompanying Biographical Sketch And Transcription Method, Darrell Brown

UNLV Theses, Dissertations, Professional Papers, and Capstones

Alejandro García Caturla was a Modernist Cuban composer of the early 20th Century. In his compositions and orchestrations, Caturla predominantly featured woodwind, brass, and percussion instruments (and incorporated Afro-Cuban percussion instruments). Caturla’s musical vernacular is a hybridization of styles, not just of the colloquial idioms of Cuba and the music of the European avant-garde, but of the unification of the island’s musical cultures. One of Caturla’s earliest, international successes was his orchestral work Tres danzas cubanas written in 1929. This document includes the creation of a new transcription for wind orchestra of the three-movement work. A biographical sketch of Caturla’s …


Effects Of Nicotine On The Cyp6a8 Gene Promoter Of Drosophila Melanogaster, Leslie M. Stroud May 2017

Effects Of Nicotine On The Cyp6a8 Gene Promoter Of Drosophila Melanogaster, Leslie M. Stroud

Chancellor’s Honors Program Projects

No abstract provided.


Functional Studies Of Ccaat/Enhancer Binding Protein Site Located Downstream Of The Transcriptional Start Site., Yujie Liu, Michael R. Nonnemacher, Aikaterini Alexaki, Vanessa Pirrone, Anupam Banerjee, Luna Li, Evelyn Kilareski, Brian Wigdahl Mar 2017

Functional Studies Of Ccaat/Enhancer Binding Protein Site Located Downstream Of The Transcriptional Start Site., Yujie Liu, Michael R. Nonnemacher, Aikaterini Alexaki, Vanessa Pirrone, Anupam Banerjee, Luna Li, Evelyn Kilareski, Brian Wigdahl

Kimmel Cancer Center Papers, Presentations, and Grand Rounds

Previous studies have identified a CCAAT/enhancer binding protein (C/EBP) site located downstream of the transcriptional start site (DS3). The role of the DS3 element with respect to HIV-1 transactivation by Tat and viral replication has not been characterized. We have demonstrated that DS3 was a functional C/EBPβ binding site and mutation of this site to the C/EBP knockout DS3-9C variant showed lower HIV-1 long terminal repeat (LTR) transactivation by C/EBPβ. However, it was able to exhibit similar or even higher transcription levels by Tat compared to the parental LTR. C/EBPβ and Tat together further enhanced the transcription level of the …


Calmodulin Lobes Facilitate Dimerization And Activation Of Estrogen Receptor-Alpha, Zhigang Li, Yonghong Zhang, Andrew C. Hedman, James B. Ames, David B. Sacks Mar 2017

Calmodulin Lobes Facilitate Dimerization And Activation Of Estrogen Receptor-Alpha, Zhigang Li, Yonghong Zhang, Andrew C. Hedman, James B. Ames, David B. Sacks

Chemistry Faculty Publications and Presentations

Estrogen receptor α (ER-α) is a nuclear hormone receptor that controls selected genes, thereby regulating proliferation and differentiation of target tissues, such as breast. Gene expression controlled by ER-α is modulated by Ca2+ via calmodulin (CaM). Here we present the NMR structure of Ca2+-CaM bound to two molecules of ER-α (residues 287–305). The two lobes of CaM bind to the same site on two separate ER-α molecules (residues 292, 296, 299, 302, and 303), which explains why CaM binds two molecules of ER-α in a 1:2 complex and stabilizes ER-α dimerization. Exposed glutamate residues in CaM (Glu-11, …


Zhx2 (Zinc Fingers And Homeoboxes 2) Regulates Major Urinary Protein Gene Expression In The Mouse Liver, Jieyun Jiang, Kate Townsend Creasy, Justin Purnell, Martha L. Peterson, Brett T. Spear Mar 2017

Zhx2 (Zinc Fingers And Homeoboxes 2) Regulates Major Urinary Protein Gene Expression In The Mouse Liver, Jieyun Jiang, Kate Townsend Creasy, Justin Purnell, Martha L. Peterson, Brett T. Spear

Microbiology, Immunology, and Molecular Genetics Faculty Publications

The mouse major urinary proteins (Mups) are encoded by a large family of highly related genes clustered on chromosome 4. Mups, synthesized primarily and abundantly in the liver and secreted through the kidneys, exhibit male-biased expression. Mups bind a variety of volatile ligands; these ligands, and Mup proteins themselves, influence numerous behavioral traits. Although urinary Mup protein levels vary between inbred mouse strains, this difference is most pronounced in BALB/cJ mice, which have dramatically low urinary Mup levels; this BALB/cJ trait had been mapped to a locus on chromosome 15. We previously identified Zhx2 (zinc fingers and homeoboxes 2) as …


Transcription Tools And Software, Rebecca Bakker Mar 2017

Transcription Tools And Software, Rebecca Bakker

Works of the FIU Libraries

This presentation was given as part of the digital humanities workshop series at the Digital Scholar Studio. It includes a brief overview of transcribing for oral histories, as well as techniques and tools that can be used. Various speech recognition software are analyzed, and information given on the hardware available at the Digital Scholar Studio at Florida International University.


Inhibition Of Cdk8 Mediator Kinase Suppresses Estrogen Dependent Transcription And The Growth Of Estrogen Receptor Positive Breast Cancer, Martina S. Mcdermott, Alexander A. Chumanevich, Chang-Uk Lim, Jiaxin Liang, Mengqian Chen, Serena Altilia, David Oliver, James M. Rae, Michael Shtutman, Hippokratis Kiaris, Balázs Győrffy, Igor Roninson, Eugenia Broude Feb 2017

Inhibition Of Cdk8 Mediator Kinase Suppresses Estrogen Dependent Transcription And The Growth Of Estrogen Receptor Positive Breast Cancer, Martina S. Mcdermott, Alexander A. Chumanevich, Chang-Uk Lim, Jiaxin Liang, Mengqian Chen, Serena Altilia, David Oliver, James M. Rae, Michael Shtutman, Hippokratis Kiaris, Balázs Győrffy, Igor Roninson, Eugenia Broude

Faculty Publications

Hormone therapy targeting estrogen receptor (ER) is the principal treatment for ER-positive breast cancers. However, many cancers develop resistance to hormone therapy while retaining ER expression. Identifying new druggable mediators of ER function can help to increase the efficacy of ER-targeting drugs. Cyclin-dependent kinase 8 (CDK8) is a Mediator complex-associated transcriptional regulator with oncogenic activities. Expression of CDK8, its paralog CDK19 and their binding partner Cyclin C are negative prognostic markers in breast cancer. Meta-analysis of transcriptome databases revealed an inverse correlation between CDK8 and ERα expression, suggesting that CDK8 could be functionally associated with ER. We have found that …


Development Of A Novel Method To Express And Purify Vaccinia Virus Early Transcription Factors A7 And D6 Using Bacteria, Omkar M. Gandbhir Jan 2017

Development Of A Novel Method To Express And Purify Vaccinia Virus Early Transcription Factors A7 And D6 Using Bacteria, Omkar M. Gandbhir

Seton Hall University Dissertations and Theses (ETDs)

The eradication of Smallpox is one of the greatest human achievements. However other poxviruses still exist infecting humans (Molluscum Contagiosum, monkeypox, and Vaccinia) or livestock (cowpox, sheeppox). Though vaccines and anti-virals exist, the side effects are serious, and viral resistance has been detected. The genome amongst poxviruses is highly conserved, early gene promoters maintain a specific critical consensus region that can be targeted for development of novel broad spectrum therapeutics. Using Vaccinia early transcription factors (VETFs) a novel method of expressing and purifying VETF A7 and D6 was developed. A7 and D6 are required for transcription of early genes recruiting …


Inferring Condition-Specific Targets Of Human Tf-Tf Complexes Using Chip-Seq Data, Chia-Chun Yang, Min-Hsuan Chen, Sheng-Yi Lin, Erik H. Andrews, Chao Cheng, Jeremy J.W Chen Jan 2017

Inferring Condition-Specific Targets Of Human Tf-Tf Complexes Using Chip-Seq Data, Chia-Chun Yang, Min-Hsuan Chen, Sheng-Yi Lin, Erik H. Andrews, Chao Cheng, Jeremy J.W Chen

Dartmouth Scholarship

Background:

Transcription factors (TFs) often interact with one another to form TF complexes that bind DNA and regulate gene expression. Many databases are created to describe known TF complexes identified by either mammalian two-hybrid experiments or data mining. Lately, a wealth of ChIP-seq data on human TFs under different experiment conditions are available, making it possible to investigate condition-specific (cell type and/or physiologic state) TF complexes and their target genes.

Results:

Here, we developed a systematic pipeline to infer Condition-Specific Targets of human TF-TF complexes (called the CST pipeline) by integrating ChIP-seq data and TF motifs. In total, we predicted …


Mutual Regulation Of Crp And N(Epsilon)-Lysine Acetylation In Escherichia Coli, Robert James Davis Jan 2017

Mutual Regulation Of Crp And N(Epsilon)-Lysine Acetylation In Escherichia Coli, Robert James Davis

Dissertations

Post-translational modifications, such as N(epsilon)-lysine acetylation, are known to alter the behavior of transcriptional regulators in eukaryotes, but very little is known about the consequences of acetylation on transcriptional regulation in bacteria. Here, I provide evidence that a global transcriptional regulator of carbon metabolism, cAMP Receptor Protein (CRP), promotes both enzymatic and non-enzymatic lysine acetylation in E. coli. Non-enzymatic lysine acetylation occurs when cells ferment acetate, such as during growth on high concentrations of glucose. Intriguingly, CRP can be non-enzymatically acetylated on several lysines, including lysine 100 (K100). I provide evidence that neutralization of the K100 positive charge, as would …


Trans-Ancestry Fine Mapping And Molecular Assays Identify Regulatory Variants At The Angptl8 Hdl-C Gwas Locus, Maren E. Cannon, Qing Duan, Ying Wu, Monica Zeynalzadeh, Zheng Xu, Antti J. Kangas, Pasi Soininen, Mika Ala-Korpela, Mete Civelek, Aldons J. Lusis, Johanna Kuusisto, Francis S. Collins, Michael Boehnke, Hua Tang, Markku Laakso, Yun Li, Karen L. Mohlke Jan 2017

Trans-Ancestry Fine Mapping And Molecular Assays Identify Regulatory Variants At The Angptl8 Hdl-C Gwas Locus, Maren E. Cannon, Qing Duan, Ying Wu, Monica Zeynalzadeh, Zheng Xu, Antti J. Kangas, Pasi Soininen, Mika Ala-Korpela, Mete Civelek, Aldons J. Lusis, Johanna Kuusisto, Francis S. Collins, Michael Boehnke, Hua Tang, Markku Laakso, Yun Li, Karen L. Mohlke

Department of Statistics: Faculty Publications

Recent genome-wide association studies (GWAS) have identified variants associated with highdensity lipoprotein cholesterol (HDL-C) located in or near the ANGPTL8 gene. Given the extensive sharing of GWAS loci across populations, we hypothesized that at least one shared variant at this locus affects HDL-C. The HDL-C–associated variants are coincident with expression quantitative trait loci for ANGPTL8 and DOCK6 in subcutaneous adipose tissue; however, only ANGPTL8 expression levels are associated with HDL-C levels. We identified a 400-bp promoter region of ANGPTL8 and enhancer regions within 5 kb that contribute to regulating expression in liver and adipose. To identify variants functionally responsible for …


Toxoplasma Gondii Ap2ix-4 Regulates Gene Expression During Bradyzoite Development, Sherri Huang, Michael J. Holmes, Joshua B. Radke, Dong-Pyo Hong, Ting-Kai Liu, Michael W. White, William J. Sullivan Jr. Jan 2017

Toxoplasma Gondii Ap2ix-4 Regulates Gene Expression During Bradyzoite Development, Sherri Huang, Michael J. Holmes, Joshua B. Radke, Dong-Pyo Hong, Ting-Kai Liu, Michael W. White, William J. Sullivan Jr.

Molecular Medicine Faculty Publications

Toxoplasma gondii is a protozoan parasite of great importance to human and animal health. In the host, this obligate intracellular parasite persists as a tissue cyst that is imperceptible to the immune response and unaffected by current therapies. The tissue cysts facilitate transmission through predation and give rise to chronic cycles of toxoplasmosis in immunocompromised patients. Transcriptional changes accompany conversion of the rapidly replicating tachyzoites into the encysted bradyzoites, and yet the mechanisms underlying these alterations in gene expression are not well defined. Here we show that AP2IX-4 is a nuclear protein exclusively expressed in tachyzoites and bradyzoites undergoing division. …


Mass Spectrometric Analysis And Machine Learning Enable Microorganism Classification Based On Rna Posttranscriptional Modifications, Colin Christopher Aldrich Jan 2017

Mass Spectrometric Analysis And Machine Learning Enable Microorganism Classification Based On Rna Posttranscriptional Modifications, Colin Christopher Aldrich

Legacy Theses & Dissertations (2009 - 2024)

RNA post-transcriptional modifications (PTMs) are dynamic features that can be up- or down-regulated by the health and metabolic state of a cell. These covalent modifications are installed and removed on RNA nucleosides by enzymes controlled by the activation and deactivation of specific genes. The goal of this research was to demonstrate that RNA PTMs can serve as a unique feature for the classification/identification of microorganisms. We utilized a scheme based on electrospray ionization mass spectrometry (ESI-MS) to obtain global PTM profiles from total RNA extracted from various microorganisms in optimal growth conditions as well as Salmonella typhimurium (S. typhimurium) spiked …


A Tale Of Two Regulators : Characterization Of The Novel Transcription Factor Abmr And The Small Non-Coding Rna Mcr11 In Mycobacterium Tuberculosis, Roxanne Candice Girardin Jan 2017

A Tale Of Two Regulators : Characterization Of The Novel Transcription Factor Abmr And The Small Non-Coding Rna Mcr11 In Mycobacterium Tuberculosis, Roxanne Candice Girardin

Legacy Theses & Dissertations (2009 - 2024)

Genes of unknown function make up nearly one third of Mtb’s genome (Cole,


Influence Of The Pre-Initiation Complex On Mediator Recruitment In Saccharomyces Cerevisiae, Elisabeth Rose Knoll Jan 2017

Influence Of The Pre-Initiation Complex On Mediator Recruitment In Saccharomyces Cerevisiae, Elisabeth Rose Knoll

Legacy Theses & Dissertations (2009 - 2024)

The Mediator complex plays a central, highly conserved role in eukaryotic transcription by RNA Polymerase II (Pol II) by stimulating the cooperative assembly of a pre-initiation complex (PIC) and recruitment of Pol II for gene activation. Mediator recruitment has generally been ascribed to sequence-specific activators engaging subunits from the tail module which in turn function to recruit the middle and head for complete assembly at the UAS. Mediator subunits of the middle and head then bridge the enhancer to connect with the PIC at the core promoter. It is reported that Mediator recruitment at the UAS preferentially occurs at SAGA-dependent, …


The Role Of The Mediator Transcriptional Co-Activator Complex And Promoter Dependence In Ty1 Retrotransposition In Saccharomyces Cerevisiae, Alicia Salinero Jan 2017

The Role Of The Mediator Transcriptional Co-Activator Complex And Promoter Dependence In Ty1 Retrotransposition In Saccharomyces Cerevisiae, Alicia Salinero

Legacy Theses & Dissertations (2009 - 2024)

Retrotransposons are mobile genetic elements that replicate via an RNA intermediary and constitute a significant portion of most eukaryotic genomes. Saccharomyces cerevisiae has been invaluable to retrotransposon research due to the presence of an active retroelement known as Ty1. The mobility of Ty1 is regulated both positively and negatively by numerous host factors, including several subunits of the Mediator transcriptional co-activator complex. The Mediator core complex is organized into genetically and structurally defined head, middle, and tail modules, along with a transiently associated kinase module. We show that with the exception of the kinase module, deletion of non-essential subunits from …


Using Conversation Analysis In Data-Driven Aviation Training With Large-Scale Qualitative Datasets, William A. Tuccio Ph.D., Maurice Nevile Ph.D. Jan 2017

Using Conversation Analysis In Data-Driven Aviation Training With Large-Scale Qualitative Datasets, William A. Tuccio Ph.D., Maurice Nevile Ph.D.

Journal of Aviation/Aerospace Education & Research

This paper contributes to a growing body of work related to the Conversation Analytic Role-play Method (CARM) by studying the primary flight instruction environment to create training interventions related to radio communications and flight instruction practices. Framed in the context of conversation analysis, an approach to the detailed analysis of naturally occurring interaction, the large-scale, long-duration qualitative audio/video data collection and coding methodology is discussed, followed by trends identified in the ongoing study. The concept of CARM “trainables” are discussed with examples. The study shows that large-scale qualitative datasets may be leveraged to produce valuable data-driven training interventions.


Eduardo Gamboa's Life, Music, And Inspiration. Understanding The Influence Of Folk Music On His Work "Transparencias:" An Analysis, Performance Guide, And Violin Transcription, Perla Del Rocio Fernandez Lopez Jan 2017

Eduardo Gamboa's Life, Music, And Inspiration. Understanding The Influence Of Folk Music On His Work "Transparencias:" An Analysis, Performance Guide, And Violin Transcription, Perla Del Rocio Fernandez Lopez

LSU Doctoral Dissertations

The purpose of this dissertation is to explore the life and music of Mexican living composer Eduardo Gamboa. This study intends to fill a void on the research of Gamboa. This document provides detailed biographical information, information about the influences on his music, and an edition of Transparencias for violin. The first chapter provides a broad biography of the composer including his musical formation, folk experience, and a complete catalog of his works. The second chapter is an introduction about Transparencias and contains the point of view of the composer and of the flutist Tadeu Coelho, to whom Gamboa dedicated …