Biochemistry, Biophysics, and Structural Biology Commons^™

Determining The Role Of Epigenetic Factors In Antifungal Drug Resistance, Abigail R. Gress, Scott D. Briggs, Nina Serratore

The Summer Undergraduate Research Fellowship (SURF) Symposium

Epigenetic factors are proteins that regulate gene expression by altering transcriptional machinery access to nucleosomes, DNA wrapped around histone proteins. Two classes of epigenetic factors are ATP-dependent chromatin remodelers and histone modifiers such as histone methyltransferases (HMTs), proteins that add methyl groups to histone tails. This study focuses on AIF4 (Antifungal-Induced Factor 4), a possible HMT induced upon neutral lipid depletion that we hypothesize is regulating antifungal drug resistance genes. Overexpression of AIF4 results in hypersensitivity to antifungal drugs. Studying epigenetic factors in the yeast Saccharomyces cerevisiae, including AIF4, can lead to better understanding of cell adaptation to their environments …

Microarray Analysis Of Aging-Associated Immune System Alterations In The Rostral Ventrolateral Medulla Of F344 Rats, Sivasai Balivada, Chanran Ganta, Yongqing Zhang, Hitesh Pawar, Richard Ortiz, Kevin Becker, Arshad Khan, Michael Kenney

Selected Works Temporary Series

The rostral ventrolateral medulla (RVLM) is an area of the brain stem that contains diverse neural substrates that are involved in systems critical for physiological function. There is evidence that aging affects some neural substrates within the RVLM, although age-related changes in RVLM molecular mechanisms are not well established. The goal of the present study was to characterize the transcriptomic profile of the aging RVLM and to test the hypothesis that aging is associated with altered gene expression in the RVLM, with an emphasis on immune system associated gene transcripts. RVLM tissue punches from young, middle-aged, and aged F344 rats …

Microarray Analysis Of Aging-Associated Immune System Alterations In The Rostral Ventrolateral Medulla Of F344 Rats, Balivada, Chanran Ganta, Yongqing Zhang, Hitesh Pawar, Richard Ortiz, Kevin Becker, Arshad Khan, Michael Kenney

Departmental Papers (Biology)

The rostral ventrolateral medulla (RVLM) is an area of the brain stem that contains diverse neural substrates that are involved in systems critical for physiological function. There is evidence that aging affects some neural substrates within the RVLM, although age-related changes in RVLM molecular mechanisms are not well established. The goal of the present study was to characterize the transcriptomic profile of the aging RVLM and to test the hypothesis that aging is associated with altered gene expression in the RVLM, with an emphasis on immune system associated gene transcripts. RVLM tissue punches from young, middle-aged, and aged F344 rats …

A Comparison Of Nucleosome Organization In Drosophila Cell Lines, Rebecca L. Martin, John Maiorano, Greg J. Beitel, John F. Marko, Graham Mcvicker, Yvonne N. Fondufe-Mittendorf

Molecular and Cellular Biochemistry Faculty Publications

Changes in the distribution of nucleosomes along the genome influence chromatin structure and impact gene expression by modulating the accessibility of DNA to transcriptional machinery. However, the role of genome-wide nucleosome positioning in gene expression and in maintaining differentiated cell states remains poorly understood. Drosophila melanogastercell lines represent distinct tissue types and exhibit cell-type specific gene expression profiles. They thus could provide a useful tool for investigating cell-type specific nucleosome organization of an organism’s genome. To evaluate this possibility, we compared genome-wide nucleosome positioning and occupancy in five different Drosophila tissue-specific cell lines, and in reconstituted chromatin, and then …

Elucidating The Interplay Between Sodium Selenite On The Tick Amblyomma Maculatum Selenoprotein Gene Expression, Afnan M. Beauti

Honors Theses

Selenium (Se) is an element recognized as an essential micronutrient in eukaryote organisms. Selenoproteins contain selenium as selenocysteine, the 21st amino acid. Selenium plays a role in cell growth and functioning. At low concentrations, it can induce growth and at high concentrations, it can cause a cell to stop growing and potentially have toxic effects on the cell and organism. When selenium levels are high, oxidative stress results by the production of reactive oxidative species. Selenoproteins, however, can aid the antioxidant response in the cell. Ticks are arthropods of interest, as they are one of few that contain many selenogenes, …

The Role Of N-Myc Downstream Regulated Gene 1 In Breast Cancer Lipid Metabolism, Christopher James Sevinsky

Legacy Theses & Dissertations (2009 - 2024)

Altered carbohydrate and lipid metabolism are increasingly well characterized hallmarks of aggressive breast cancers. While aerobic glycolysis, or “the Warburg effect”, is a well-established metabolic adaptation exploited by tumor cells, the understanding of unique aspects of cancer lipid metabolism lags behind. This is especially true regarding the coordination of complex lipid synthesis and trafficking pathways, which remains poorly understood. N-Myc Downstream Regulated Gene1 (NDRG1) is overexpressed in many solid tumors, but its function is unclear. The importance of NDRG1 is best exemplified by the effect of null mutations on human physiology: inactivating mutations give rise to the severe autosomal recessive …

Biochemical And Histological Differences Between Costal And Articular Cartilages, Michael W. Stacey

Bioelectrics Publications

Biologically, costal cartilage is an understudied tissue type and much is yet to be learned regarding underlying mechanisms related to form and function, and how these relate to disease states, specifically chest wall deformity. Chest wall deformities have a component of inheritance, implying underlying genetic causes; however the complexity of inheritance suggests multiple genetic components. At our Centre investigations were performed on gene expression of key select genes from costal cartilage removed at surgery of patients with chest wall deformity to show high expression of decorin, a key player in collagen fiber formation and growth. Also, the degree of tissue …

A Bioinformatics Methodology For The Annotation And Analysis Of Sperm Chromatin Remodeling Proteins In Sequenced Drosophila Species, Zain A. Alvi

Seton Hall University Dissertations and Theses (ETDs)

Spermatogenesis is the process by which mature functional spermatozoa are formed, and is initiated in the stem cell niche of the testes. During the post-meiotic stage of spermatogenesis, spermiogenesis, transition proteins facilitate the transformation of chromatin from a histone-based nucleosome structure to a protamine-based nucleosome structure. This study is aimed at analyzing genomic, transcript, and protein sequences of transition proteins in 13 sequenced Drosophila species. The Drosophila melanogaster spermatid specific transition protein-like protein (Tpl^94D) was used as the reference sequence in this study. An extensive bioinformatics approach was employed in establishing the Tpl^94D orthologs. We identified …

Role Of Hnrnp A1 In The Regulation Of Hdm2 Gene Expression, Heriberto Moran

Dissertations, Theses, and Capstone Projects

hnRNP A1 is one of the most abundant and ubiquitously expressed member of hnRNPs (Heterogenous Nuclear Ribonucleoproteins) family of proteins that play multiple roles in gene expression by participating in major steps in the processing of nascent RNA transcripts 1. It is involved in mRNA biogenesis mechanisms such as the transcription, splicing, stability, export and translation of cellular and viral transcripts. The functions of hnRNP A1 extend to the processing of microRNAs, telomere maintenance and DNA repair 1. Our previous studies have shown that hnRNPA1 had reduced protein level and increased cytoplasmic accumulation in senescent human diploid fibroblasts 2,10. Our …

Epigenetic Regulation Of Gene Expression During Spermatogenesis, Karishma Nayak

Senior Honors Projects

In the US livestock production industry, improving reproductive efficiency will improve animal welfare and maintain reasonable costs of meat and milk for consumers. In recent research, abnormalities in epigenetic markers in sperm during spermatogenesis, has been linked to male subfertility in many species. Epigenetics is the study of changes in organisms caused by modifications of gene expression, including DNA methylation, rather than alteration of the genetic code itself. When this process is disturbed, it can negatively impact semen therefore decreasing its fertility. Through further research on how DNA methylation influences gene expression during spermatogenesis and its impact on sperm quality, …

Gene Expression And Physiological Analysis To Study Differences Between Oryza Sativa Cultivars Susceptible And Resistant To Chalky Grain Formation Subjected To High Nighttime Temperatures., Nicholas Lawson

Graduate Theses and Dissertations

Starch composition and grain quality of rice is greatly influenced by genotype and environmental factors. The detrimental effects of high nighttime temperatures on rice yield and quality has recently become apparent, with some of the warmest average nighttime temperatures being recorded in the past few years. One of the most notable effects of this stress, an increase in grain chalk formation, correlates with a decrease in quality. This effect varies greatly between cultivars as some show less temperature-sensitive quality reduction than others. The goal of this research is to elucidate fundamental changes that occur in developing plants and grains as …

The Role Of Microrna In Cardioprotection: Ischemic Preconditioning And Mesenchymal Stem Cell Paracrine Effects, Kristin Luther

Dissertations

Changes in gene expression and protein levels are an important aspect of cardioprotection in which short non-coding RNA known as miRNA may play a key regulatory role. We investigated the functions of several miRNAs in the context of two cardioprotective stimuli, ischemic preconditioning (IPC) and mesenchymal stem cell (MSC) paracrine effects. We hypothesized that downregulation of a set of miRNAs (miR-148a/b, miR-30b, and let-7a*) augments expression of protective heat shock proteins during IPC, and that MSC exosomes transfer miR-21 to cardiomyocytes, resulting in downregulation of pro-apoptotic genes and reduction of infarct size.

IPC increased the level of Hsp70, Hsp90, and …

Characterizing The Role Of Aif4 In Saccharomyces Cerevisiae, Antonia L. Hur Ms., Nina Serratore Ms., Scott D. Briggs

The Summer Undergraduate Research Fellowship (SURF) Symposium

Chromatin remodelers are important regulatory mechanisms that eukaryotic cells use to modify the structure of chromatin, which is made up of DNA and proteins. DNA wraps around histone proteins to make up chromatin. When these proteins are modified, the shape of the chromatin is altered. “Loosening” the chromatin structure by chromatin modifications allows for active gene expression whereas “tightening” or compaction of chromatin results in gene repression. Therefore the modifications on chromatin modulate gene expression in all eukaryotes. It has been shown that mis-regulation of chromatin remodelers contribute to various cancers. Understanding the biochemistry behind how chromatin associating proteins modify …

Inorganic Arsenic-Induced Cellular Transformation Is Coupled With Genome Wide Changes In Chromatin Structure, Transcriptome And Splicing Patterns, Caitlyn Riedmann, Ye Ma, Manana Melikishvili, Steven Grason Godfrey, Zhuo Zhang, Kuey-Chu Chen, Eric C. Rouchka, Yvonne N. Fondufe-Mittendorf

Molecular and Cellular Biochemistry Faculty Publications

BACKGROUND: Arsenic (As) exposure is a significant worldwide environmental health concern. Low dose, chronic arsenic exposure has been associated with a higher than normal risk of skin, lung, and bladder cancer, as well as cardiovascular disease and diabetes. While arsenic-induced biological changes play a role in disease pathology, little is known about the dynamic cellular changes resulting from arsenic exposure and withdrawal.

RESULTS: In these studies, we sought to understand the molecular mechanisms behind the biological changes induced by arsenic exposure. A comprehensive global approach was employed to determine genome-wide changes to chromatin structure, transcriptome patterns and splicing patterns in …

Analyzing The Interactions Of Kdm5/Lid And Sin3 In Drosophila Melanogaster, Ambikai Gajan

Wayne State University Dissertations

SIN3, the scaffold protein of a histone modifying complex is conserved from yeast to mammals. Drosophila SIN3 associates with both a histone deactylase RPD3 and a histone demethylase dKDM5/LID. Immunopurification of dKDM5/LID verifies a previously observed interaction with SIN3 and RPD3. Furthermore, deficiency of dKDM5/LID phenocopies deficiency of SIN3 in many cellular and developmental processes. Knockdown of both Sin3A and lid hinder cell proliferation in Drosophila cultured cells and developing flies. Knockdown of these genes also results in a curved wing phenotype implicating a role in wing development. Analysis of underlying gene expression changes upon decreased expression of SIN3, dKDM5/LID …

The Effects Of Jasmonic Acid And Chemicals In The Ja Pathway On The Defense Systems And Gene Expression In Moss, Physcomitrella Patens And Amblystegium Serpens, Allison Shanks

Undergraduate Honors Thesis Collection

Systemic acquired resistance (SAR) is a defense system used by plants that results in increased resistance to future pathogen infection following an initial pathogen exposure. SAR in vascular plants has been well documented; however, a similar defense system has only recently been documented in non-vascular plants. It is believed that chemicals in the jasmonic acid (JA) pathway are able to activate the SAR response in vascular plants. The non-vascular plant, Amb/ystegium serpens, will be used as a model to test if SAR is triggered by JA and two other molecules in the JA pathway, 12-oxo-phytodieonic acid, and methyl jasmonate. To …

Transcriptional Control Of Toxoplasma Development, Joshua Byran Radke

USF Tampa Graduate Theses and Dissertations

Toxoplasma gondii is an obligate intracellular protozoan parasite of animals and man. The asexual life cycle of Toxoplasma involves three very distinct, but tightly coordinated developmental stages. In nature, the sporozoite (contained within an oocyst) and bradyzoite (contained within a tissue cyst) initiate infection of the intermediate host, followed by rapid differentiation into the actively replicating tachyzoite. When countered by an effective host response, the tachyzoite differentiates back into the latent bradyzoite and this unique ability of Toxoplasma to interconvert between the replicating tachyzoite and the latent bradyzoite within a single host is the cause of life long infection. The …

Lineage-Specific Transcriptional Profiles Of Symbiodinium Spp. Unaltered By Heat Stress In A Coral Host, Daniel J. Barshis, Jason T. Ladner, Thomas A. Oliver, Stephen R. Palumbi

Biological Sciences Faculty Publications

Dinoflagellates of the genus Symbiodinium form an endosymbiosis with reef building corals, in which photosynthetically derived nutrients comprise the majority of the coral energy budget. An extraordinary amount of functional and genetic diversity is contained within the coral-associated Symbiodinium, with some phylotypes (i.e., genotypic groupings), conferring enhanced stress tolerance to host corals. Recent advances in DNA sequencing technologies have enabled transcriptome-wide profiling of the stress response of the cnidarian coral host; however, a comprehensive understanding of the molecular response to stress of coral-associated Symbiodinium, as well as differences among physiologically susceptible and tolerant types, remains largely unexplored. Here, …

Using Expression Profiling To Understand The Effects Of Chronic Cadmium Exposure On Mcf-7 Breast Cancer Cells, Zelmina Lubovac-Pilav, Daniel M. Borras, Esmeralda Ponce, Maggie Louie

Collected Faculty Scholarship

Cadmium is a metalloestrogen known to activate the estrogen receptor and promote breast cancer cell growth. Previous studies have implicated cadmium in the development of more malignant tumors; however the molecular mechanisms behind this cadmium-induced malignancy remain elusive. Using clonal cell lines derived from exposing breast cancer cells to cadmium for over 6 months (MCF-7-Cd4, -Cd6, -Cd7, -Cd8 and -Cd12), this study aims to identify gene expression signatures associated with chronic cadmium exposure. Our results demonstrate that prolonged cadmium exposure does not merely result in the deregulation of genes but actually leads to a distinctive expression profile. The genes deregulated …

Gene Expression Studies For The Analysis Of Domoic Acid Production In The Marine Diatom Pseudo-Nitzschia Multiseries, Katie Boissonneault, Brooks M. Henningsen, Stephen S. Bates, Deborah L. Robertson, Sean Milton, Jerry Pelletier, Deborah A. Hogan, David E. Housman

Dartmouth Scholarship

Pseudo-nitzschia multiseries Hasle (Hasle) (Ps-n) is distinctive among the ecologically important marine diatoms because it produces the neurotoxin domoic acid. Although the biology of Ps-n has been investigated intensely, the characterization of the genes and biochemical pathways leading to domoic acid biosynthesis has been limited. To identify transcripts whose levels correlate with domoic acid production, we analyzed Ps-n under conditions of high and low domoic acid production by cDNA microarray technology and reverse-transcription quantitative PCR (RT-qPCR) methods. Our goals included identifying and validating robust reference genes for Ps-n RNA expression analysis under these conditions.

Chronic Cadmium Exposure Stimulates Sdf-1 Expression In An Erα Dependent Manner, Esmeralda Ponce, Natalie B. Aquino, Maggie Louie

Collected Faculty Scholarship

Cadmium is an omnipotent environmental contaminant associated with the development of breast cancer. Studies suggest that cadmium functions as an endocrine disruptor, mimicking the actions of estrogen in breast cancer cells and activating the receptor to promote cell growth. Although acute cadmium exposure is known to promote estrogen receptor-mediated gene expression associated with growth, the consequence of chronic cadmium exposure is unclear. Since heavy metals are known to bioaccumulate, it is necessary to understand the effects of prolonged cadmium exposure. This study aims to investigate the effects of chronic cadmium exposure on breast cancer progression. A MCF7 breast cancer cell …

Germline Transgenic Methods For Tracking Cells And Testing Gene Function During Regeneration In The Axolotl, Shahryar Khattak, Maritta Schuez, Tobias Richter, Dunja Knapp, Saori L. Haigo, Tatiana Sandoval-Guzmán, Kristyna Hradlikova, Annett Duemmler, Ryan R. Kerney, Elly M. Tanaka

Biology Faculty Publications

The salamander is the only tetrapod that regenerates complex body structures throughout life. Deciphering the underlying molecular processes of regeneration is fundamental for regenerative medicine and developmental biology, but the model organism had limited tools for molecular analysis. We describe a comprehensive set of germline transgenic strains in the laboratory-bred salamander Ambystoma mexicanum(axolotl) that open up the cellular and molecular genetic dissection of regeneration. We demonstrate tissue-dependent control of gene expression in nerve, Schwann cells, oligodendrocytes, muscle, epidermis, and cartilage. Furthermore, we demonstrate the use of tamoxifen-induced Cre/loxP-mediated recombination to indelibly mark different cell types. Finally, we inducibly …

Molecular Characterization Of A Patient Presumed To Have Prader-Willi Syndrome, Marina Falaleeva, Carlos R. Sulsona, Horst R. Zielke, Kathleen M. Currey, Pierre De La Grange, Vahid Aslanzadeh, Daniel J. Driscoll, Stefan Stamm

Molecular and Cellular Biochemistry Faculty Publications

Prader-Willi syndrome (PWS) is caused by the loss of RNA expression from an imprinted region on chromosome 15 that includes SNRPN, SNORD115, and SNORD116. Currently, there are no mouse models that faithfully reflect the human phenotype and investigations rely on human post-mortem material. During molecular characterization of tissue deposited in a public brain bank from a patient diagnosed with Prader-Willi syndrome, we found RNA expression from SNRPN, SNORD115, and SNORD116 which does not support a genetic diagnosis of Prader-Willi syndrome. The patient was a female, Caucasian nursing home resident with history of morbid obesity (BMI 56.3) and mental retardation. She …

Delineating Key Genetic Components On Linear Plasmid 36 That Contribute To Its Essential Role In Borrelia Burgdorferi Mammalian Infectivity., Tisha Choudhury

Electronic Theses and Dissertations

The spirochete Borrelia burgdorferi is the etiologic agent of Lyme disease. This pathogen has a complex enzootic life cycle that involves passage between the tick vector (Ixodes scapularis) and various vertebrate hosts with humans being inadvertent hosts. There is a pressing need to study the genetic aspects of the B. burgdorferi infectious cycle and particularly spirochete genes involved in mammalian infectivity so as to develop novel therapeutic and diagnostic strategies to combat Lyme disease. The B. burgdorferi genome is fragmented and comprised of a single 900 kb linear chromosome and multiple linear and circular plasmids. It has been observed that …

Live-Cell Monitoring Of Periodic Gene Expression In Synchronous Human Cells Identifies Forkhead Genes Involved In Cell Cycle Control, Gavin D. Grant, Joshua Gamsby, Viktor Martyanov, Lionel Brooks, Lacy K. George, J. Matthew Mahoney, Jennifer J. Loros, Jay C. Dunlap, Michael L. Whitfield

Dartmouth Scholarship

We developed a system to monitor periodic luciferase activity from cell cycle-regulated promoters in synchronous cells. Reporters were driven by a minimal human E2F1 promoter with peak expression in G1/S or a basal promoter with six Forkhead DNA-binding sites with peak expression at G2/M. After cell cycle synchronization, luciferase activity was measured in live cells at 10-min intervals across three to four synchronous cell cycles, allowing unprecedented resolution of cell cycle-regulated gene expression. We used this assay to screen Forkhead transcription factors for control of periodic gene expression. We confirmed a role for FOXM1 and identified two novel cell cycle …

Gld-1 Represses Its Puf Mrna Targets Prior To/At Initiation Of Translation In The C.Elegans Germline, Gautham Sarathy

Legacy Theses & Dissertations (2009 - 2024)

The C.elegans germline offers an ideal system to study posttranscriptional regulation of gene expression as it is a major mechanism through which the control over gene expression is achieved. GLD-1 (defective in GermLine Development) is a maxi-KH motif containing RNA binding protein that controls various aspects of germline development from decision over germcell proliferation vs. meiotic entry to the production of mature gametes suggesting that GLD-1 likely controls many mRNA targets.

Signals Delivered By Interleukin-7 Regulate The Activities Of Bim And Jund In T Lymphocytes, Shannon Moore Ruppert

Electronic Theses and Dissertations

Interleukin-7 (IL-7) is an essential cytokine for lymphocyte growth that has the potential for promoting proliferation and survival. While the survival and proliferative functions of IL-7 are well established, the identities of IL-7 signaling components in pathways other than JAK/STAT, that accomplish these tasks remain poorly defined. To this end, we used IL-7 dependent T-cells to examine those components necessary for cell growth and survival. Our studies revealed two novel signal transducers of the IL-7 growth signal: BimL and JunD. IL-7 promoted the activity of JNK (Jun N-terminal Kinase), and that JNK, in turn, drove the expression of JunD, a …

Host-Virus Interactions Of Infectious Laryngotracheitis Virus Infection In Cultured Cells, Jeong Yoon Lee

Graduate Theses and Dissertations

Infectious laryngotracheitis virus (ILTV; Gallid herpesvirus 1) causes upper respiratory diseases in mainly chickens and exhibits 90-100% of high morbidity and up to 70% of mortality, resulting in huge economic losses in the poultry industry worldwide.

To study host-ILTV interactions, the changes in genome-wide gene expressions in response to wild-type and vaccine ILTV infections in primary chicken embryo lung cells were investigated using microarray analysis. Results provide crucial insights into host cell pathogenic and immunogenic responses against wild-type and vaccine ILTV infections. Using microarray method and Ingenuity Pathway Analysis (IPA) bioinformatics tool, 273 and 306 differentially expressed genes were identified …

Stability Of Nucleic Acid Secondary Structures And Their Contribution To Gene Expression, Maged A. Darwish

Seton Hall University Dissertations and Theses (ETDs)

Bacteriorhodopsin (bR) is a highly expressed transmembrane protein that acts as a light-driven proton pump converting light energy into a proton gradient. The extraordinary levels of expression achieved (15-30 mg per liter of culture) are a result of very efficient biogenesis that originates from molecular information encoded in the bacterio-opsin gene {bop) (1). DNA sequence analysis and predictive folding algorithms suggest that the first twenty-five bases of the bop gene mRNA can form a secondary structural element (a "stem-loop"). Using biophysical methods, the goal was to determine if the stem-loop structure exists in solution conditions that mimic the in vivo …

Ganglioside-Cytokine Interaction In The Induction Of Primary Brain Cell Death, John Charles Gorbet

Open Access Theses & Dissertations

Gangliosides have been implicated in multiple pathologies affecting the central nervous system (CNS) and recent research has implicated them in playing an active role in the pathogenesis of multiple sclerosis. Empirical studies and theoretical considerations have suggested the possibility of interactions between gangliosides, like GD3, and pro-inflammatory cytokines present in the nervous system. This study sought to investigate the possibility that either individual gangliosides acting alone or complexed with other species interact with the known immune response factor TNF&alpha to initiate or facilitate cell death in the CNS. I examined the cellular viability and gene expression in primary brain cell …