Molecular Genetics Commons^™

Coordination Of Rna Polymerase Ii Pausing And 3' End Processing Factor Recruitment With Alternative Polyadenylation, Becky Fusby, Soojin Kim, Benjamin Erickson, Hyunmin Kim, Martha L. Peterson, David L Bentley

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Most mammalian genes produce transcripts whose 3' ends are processed at multiple alternative positions by cleavage/polyadenylation (CPA). Poly(A) site cleavage frequently occurs cotranscriptionally and is facilitated by CPA factor binding to the RNA polymerase II (Pol II) C-terminal domain (CTD) phosphorylated on Ser2 residues of its heptad repeats (YS₂PTSPS). The function of cotranscriptional events in the selection of alternative poly(A) sites is poorly understood. We investigated Pol II pausing, CTD Ser2 phosphorylation, and processing factor CstF recruitment at wild-type and mutant IgM transgenes that use alternative poly(A) sites to produce mRNAs encoding the secreted and membrane-bound forms of …

The Role Of Capillaries In The Lesser Ailments Of Old Age And In Alzheimer's Disease And Vascular Dementia: The Potential Of Pro-Therapeutic Angiogenesis, Charles T. Ambrose

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Apart from chronic diseases (arthritis, diabetes, etc.), old age is generally characterized by three lesser ailments: muscle weakness, minor memory lapses, and cold intolerance. This trio of complaints may have a common, underlying cause, namely, the age-associated reduced microcirculation in muscles, brain, skin, and elsewhere in the body. The Angiogenesis Hypothesis proposes that old age is in part a deficiency disease due to the decline in angiogenic (AG) factors, resulting in a reduced capillary density (CD) throughout the body. Over fifty published papers document waning levels of AG factors and/or decreased CD in various organ systems of aged animals and …

Nucleosome Distortion As A Possible Mechanism Of Transcription Activation Domain Function, Tamara Y. Erkina, Alexandre M. Erkine

Scholarship and Professional Work – COPHS

After more than three decades since the discovery of transcription activation domains (ADs) in gene-specific activators, the mechanism of their function remains enigmatic. The widely accepted model of direct recruitment by ADs of co-activators and basal transcriptional machinery components, however, is not always compatible with the short size yet very high degree of sequence randomness and intrinsic structural disorder of natural and synthetic ADs. In this review, we formulate the basis for an alternative and complementary model, whereby sequence randomness and intrinsic structural disorder of ADs are necessary for transient distorting interactions with promoter nucleosomes, triggering promoter nucleosome translocation and …

Functional Significance Of Mtdna Cytosine Modification Tested By Genome Editing, Jason M. Robinson

Theses and Dissertations

The field of epigenetics is gaining popularity and speed, due in part to its capability to answer lingering questions about the root cause of certain diseases. Epigenetics plays a crucial role in regulation of the cell and cell survival, particularly by cytosine methylation. It remains controversial if DNMT’s which facilitate methylation are present in mammalian mitochondria and what the functional significance they may have on modification of mitochondrial DNA. CRISPR-Cas9 technology enabled genome editing to remove the MTS (mitochondrial targeting sequence) from DNMT1 of HCT116 cells, purposefully minimizing effects on nuclear cytosine methylation, while exclusively impacting mitochondrial modification. Removal of …

And-1 Is Required For Homologous Recombination Repair By Regulating Dna End Resection, Yongming Li, Zongzhu Li, Zhiyong Han, Wenge Zhu

Biochemistry and Molecular Medicine Faculty Publications

Homologous recombination (HR) is a major mechanism to repair DNA double-strand breaks (DSBs). Although tumor suppressor CtIP is critical for DSB end resection, a key initial event of HR repair, the mechanism regulating the recruitment of CtIP to DSB sites remains largely unknown. Here, we show that acidic nucleoplasmic DNA‐binding protein 1 (And‐1) forms complexes with CtIP as well as other repair proteins, and is essential for HR repair by regulating DSB end resection. Furthermore, And-1 is recruited to DNA DSB sites in a manner dependent on MDC1, BRCA1 and ATM, down-regulation of And-1 impairs end resection by reducing the …

Evidence For The Fixation Of Gene Duplications By Positive Selection In Drosophila, Margarida Cardoso-Moreira, J. Roman Arguello, Srikanth Gottipati, Lawrence G. Harshman, Jennifer K. Grenier, Andrew G. Clark

Lawrence G. Harshman Publications

Gene duplications play a key role in the emergence of novel traits and in adaptation. But despite their centrality to evolutionary processes, it is still largely unknown how new gene duplicates are initially fixed within populations and later maintained in genomes. Long-standing debates on the evolution of gene duplications could be settled by determining the relative importance of genetic drift vs. positive selection in the fixation of new gene duplicates. Using the Drosophila Global Diversity Lines (GDL), we have combined genome-wide SNP polymorphism data with a novel set of copy number variant calls and gene expression profiles to characterize the …

The Impact Of Oxygen On Bacterial Enteric Pathogens, Nathan Wallace, Ashley N. Zani, Elizabeth A. Abrams, Yvonne Sun

Biology Faculty Publications

Bacterial enteric pathogens are responsible for a tremendous amount of foodborne illnesses every year through the consumption of contaminated food products. During their transit from contaminated food sources to the host gastrointestinal tract, these pathogens are exposed and must adapt to fluctuating oxygen levels to successfully colonize the host and cause diseases. However, the majority of enteric infection research has been conducted under aerobic conditions. To raise awareness of the importance in understanding the impact of oxygen, or lack of oxygen, on enteric pathogenesis, we describe in this review the metabolic and physiological responses of nine bacterial enteric pathogens exposed …

Can The Insertion Of An E. Coli Shine-Dalgarno Sequence Upstream Of M. Ruber Proa Of The Proba Operon Enhance Its Expression, As Measured By A Complementation Assay Using E. Coli Null Strains?, Matthew D. Murphy, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

The process by which the thermophilic bacteria Meiothermus ruber (M. ruber) synthesizes the amino acid proline is examined in this paper. In the well-studied E. coli system, proline biosynthesis involves three enzymes ProA, ProB and ProC; proA and proB form the proBA operon and both proA and proB possess an upstream Shine-Delgarno sequence; and ProB is functionally dependent on ProA as components of a ProBA complex. In previous studies in Dr. Scott’s lab, the putative M. ruber proA (locus tag Mrub1079), proB (Mrub1080) and proC (Mrub1345) genes were cloned into the pKt1 expression vector, transformed into the corresponding …

The Role Of E-Cadherin Force In The Maintenance Of Homeostasis In Epithelial Acini, Fnu Vani Narayanan

Theses and Dissertations

Numerous three-dimensional model systems have emerged for emulating the biochemical and physiological states of native tissue. Yet little is known about the effects of mechanical forces on cell behavior in the context of an organized tissue structure in three-dimensional cell-culture. Epithelial cells cultured in a three-dimensional environment comprised of extracellular matrix proteins form spheroids of polarized cells. Cellular responses to mechanical cues, generated from dynamic interactions with the extracellular matrix and neighboring cells, are known to influence cellular behavior to a great extent. Previous studies have shown that tumorigenic progression has been frequently linked to the down regulation of E-cadherin, …

Adducins Are Negative Regulators Of Migration And Invasion Of Normal Lung Epithelial Cells And Lung Cancer Cells, Parth Hitenbhai Amin, Parth Amin

Theses and Dissertations

Cell migration is an important component of many physiological and pathological processes such as tissue and organ morphogenesis during development, wound healing, inflammatory immune response, and tumor metastasis. The actin cytoskeleton is the basic engine driving cell migration. In the present study, we elucidate the role of an important actin interacting proteins, Adducins, in motility of normal lung epithelium and lung cancer cells. Adducins are the family of cytoskeleton protein capping the fast growing end and facilitating the bundling of actin filaments. Adducins are encoded by the three closely related genes namely alpha (ADD1), beta (ADD2) and gamma (ADD3) Adducin. …

Ecology Of Two Reintroduced Black Bear Populations In The Central Appalachians, Sean Mccarthy Murphy

Theses and Dissertations--Animal and Food Sciences

Reintroduced populations are vulnerable to demographic and environmental stochasticity, deleterious genetic effects, and reduced population fitness, all of which can increase extinction probability. Population viability is principle to determining the status of reintroduced populations and for guiding management decisions. To attempt to reestablish black bear (Ursus americanus) populations in the central Appalachians, two reintroductions using small founder groups occurred during the 1990s in the Big South Fork area along the Kentucky-Tennessee border (BSF) and in the Jefferson National Forest along the Kentucky-Virginia border (KVP). My objectives were to estimate demographic and genetic parameters, and to evaluate long-term viability …

Independent Origination Of Floral Zygomorphy, A Predicted Adaptive Response To Pollinators: Developmental And Genetic Mechanisms, Ghadeer Bukhari, Wenheng Zhang

Theses and Dissertations

Observations of floral development indicate that floral organ initiation in pentapetalous flowers more commonly results in a medially positioned abaxial petal (MAB) than in a medially positioned adaxial petal (MAD), where the medial plane is defined by the stem and the bract during early floral development. It was proposed that the dominant MAB petal initiation might impose a developmental constraint that leads to the evolution of limited patterns of floral zygomorphy in Asteridae, a family in which the floral zygomorphy develops along the medial plane and results in a central ventral (CV) petal in mature flowers. Here, I investigate whether …

Resolving Gnetum Evolutionary History, Angela Mcfadden

All Master's Theses

Gnetum are non-flowering seed plants of the tropics, indigenous to South America, Africa, and Asia. This group of about 40 species is fascinating to botanists because it shares distinctive morphological characteristics with flowering plants, such as broad leaves, woody stems, and flower-like strobili. There are still questions surrounding the relationships within the genus of Gnetum. With that in mind, I focused my work on generating phylogenetic hypotheses, using two molecular data sets: a concatenation of over 60 different chloroplast genes (66,815 base pairs), and the whole chloroplast genome (128,772 base pairs). This allowed me to compare the two phylogenies …

Functional Consequences Of Mtdna Methylation On Mitochondrial Transcription Factor Binding And Transcription Initiation, Elliot N. Burton

Theses and Dissertations

The role of cytosine modifications on nuclear transcription has been well characterized, but the function of DNA methylation in the mitochondrial genome has not been determined. Previous studies conducted by the Taylor laboratory have shown overexpression of the mitochondrial isoform of DNMT1 leads to strand-specific changes in gene expression. Here, we show that increased mtDNMT1 expression leads to an increase in the polycistronic transcript encoding the ND1 and Cox1 sequences. In order to understand the mechanistic basis of these changes, we investigated the effects of CpG methylation in the heavy strand promoter on transcription initiation and TFAM binding. Methylation was …

Molecular Mechanism Of The Priming By Jasmonic Acid Of Specific Dehydration Stress Response Genes In Arabidopsis, Ning Liu, Zoya Avramova

School of Biological Sciences: Faculty Publications

Background: Plant genes that provide a different response to a similar dehydration stress illustrate the concept of transcriptional ‘dehydration stress memory’. Pre-exposing a plant to a biotic stress or a stress-signaling hormone may increase transcription from response genes in a future stress, a phenomenon known as ‘gene priming’. Although known that primed transcription is preceded by accumulation of H3K4me3 marks at primed genes, what mechanism provides for their appearance before the transcription was unclear. How augmented transcription is achieved, whether/how the two memory phenomena are connected at the transcriptional level, and whether similar molecular and/or epigenetic mechanisms regulate them are …

Investigating The Molecular Etiologies Of Sporadic Als (Sals) Using Rna-Sequencing, David G. Brohawn

Theses and Dissertations

ALS is an often lethal disease involving degeneration of motor neurons in the brain and spinal cord. Current treatments only extend life by several months, and novel therapies are needed. We combined RNA-Sequencing, systems biology analyses, and molecular biology assays to elucidate sporadic ALS group-specific differences in postmortem cervical spinal sections (7 sALS and 8 control samples) that may be relevant to disease pathology. >55 million 2X150 RNA-sequencing reads per sample were generated and processed.

In Chapter 2, we used bioinformatics tools to identify nuclear differentially expressed genes (DEGs) between our two groups. Further, we used Weighted Gene Co-Expression Network …

High Diversity Of Trypanosoma Cruzi Discrete Typing Units Circulating In Triatoma In Western Mexico, Uyen T. Nguyen

All Master's Theses

Chagas disease is caused by the protozoan parasite Trypanosoma cruzi, which is transmitted to domestic and sylvatic mammals via the feces of hematophagous hemiptera of the subfamily Triatominae (Reduviidae). Trypanosoma cruzi is found only in the Americas and displays remarkable genetic diversity. Seven discrete typing units (DTUs) are currently recognized (TcI–TcVI and TcBat). In Jalisco, Mexico, where Chagas disease has a high prevalence rate, TcI has historically been the only DTU reported. This study focused on the molecular identification of T. cruzi DTUs circulating in Triatoma near the Estación de Biología Chamela, on the southwest coast of Jalisco, Mexico. …

Understanding The Molecular Mechanisms Underlying Rsv1 Mediated Resistance To Smv In Soybean, Mohammed Ali Ahmed Eid

Theses and Dissertations--Plant Pathology

Like humans, viral diseases also affect plants. Of these, viruses belonging to the potyvirus genus are the most prolific. The potyvirus soybean mosaic virus (SMV) is an important pathogen of the crop plant soybean. SMV causes mosaic symptoms (yellow areas alternate with dark green areas on the leaves of the plant) and can affect yield by reducing seed quality. Few cultivars from soybean can resist different SMV strains. To understand soybean defense mechanisms to SMV, I identified soybean proteins that interact with the helper component protease (HC-Pro) of SMV, which also functions as the suppressor of host RNA silencing and …

Genome Wide Epigenetic Analyses Of Araptus Attenuatus, A Bark Beetle, Chitra Seshadri

Theses and Dissertations

Phylogeographic studies have relied on surveying neutral genetic variation in natural populations as a way of gaining better insights into the evolutionary processes shaping present day population demography. Recent emphasis on understanding putative adaptive variation have brought to light the role of epigenetic variation in influencing phenotypes and the mechanisms underlying local adaptation. While much is known about how methylation acts at specific loci to influence known phenotypes, there is little information on the spatial genetic structure of genome-wide patterns of methylation and the extent to which it can extend our understanding of both neutral and putatively adaptive processes. This …

Biogeographical Patterns In The Hard-Tick Genus Amblyomma Koch 1844 (Acari: Ixodidae), Matthew H. Seabolt

Electronic Theses and Dissertations

Amblyomma Koch is a genus of hard-ticks with approximately 130 species. Its geographical range is typical for organisms with a Gondwanan origin. A majority of these species are endemic to the Neo- and Afrotropical regions, with the remaining taxa dispersed throughout Southeast Asia, Australia and the Pacific islands. Based on this distribution, we hypothesize that the genus dispersal patterns will mirror the fragmentation and continental drift of the Gondwanan supercontinent. Maximum parsimony, maximum likelihood, Bayesian inference and node-dating analyses of nuclear 18S rDNA gene sequences reveal a more recent origin and radiation patterns within the genus and suggest that Amblyomma …