Genetics and Genomics Commons^™

Identifying Genes Downstream Of Mef2 That Influence Ethanol Sedation In Drosophila Melanogaster, Ananya Talikoti

Theses and Dissertations

Alcohol use disorder is a global public health issue that affects millions across the world. It can result in negative physical and mental health outcomes, and currently treatment options are limited and rates of relapse are high. Identifying genes that affect aspects of ethanol behaviors in model organisms, such as Drosophila melanogaster, can serve to eventually develop more robust therapeutic interventions for those experiencing alcohol dependence. Previous studies have identified a relationship between a person's initial sensitivity to alcohol and their abuse potential for the drug in later life. Therefore, we can study sedation behaviors in Drosophila melanogaster to …

Regulation Of A Messenger: Raising Oskar, It Takes A Village, Livia V. Bayer

Dissertations, Theses, and Capstone Projects

D. melanogaster oogenesis serves as an excellent system to study the life of an mRNA. Tremendous work has been done to understand the numerous complex mechanisms of mRNA regulation, still there is still so much that is yet to be discovered. In this thesis, I present studies I carried out to address several aspects of oskar mRNA post-transcriptional regulation. Leading me to extend our current understanding of the carefully controlled regulation of oskar mRNA life cycle via a myriad of proteins. I found that a specific NPC component, Nup154 is necessary not only for its export from the nucleus, but …

Genetic And Metabolomic Architecture Of Variation In Diet Restriction-Mediated Lifespan Extension In Drosophila., Kelly Jin, Kenneth A. Wilson, Jennifer N. Beck, Christopher S. Nelson, George W. Brownridge Iii, Benjamin R. Harrison, Danijel Djukovic, Daniel Raftery, Rachel B. Brem, Shiqing Yu, Mathias Drton, Ali Shojaie, Pankaj Kapahi, Daniel Promislow

Natural Sciences and Mathematics | Student Professional Publications

In most organisms, dietary restriction (DR) increases lifespan. However, several studies have found that genotypes within the same species vary widely in how they respond to DR. To explore the mechanisms underlying this variation, we exposed 178 inbred Drosophila melanogaster lines to a DR or ad libitum (AL) diet, and measured a panel of 105 metabolites under both diets. Twenty four out of 105 metabolites were associated with the magnitude of the lifespan response. These included proteinogenic amino acids and metabolites involved in α-ketoglutarate (α-KG)/glutamine metabolism. We confirm the role of α-KG/glutamine synthesis pathways in the DR response through genetic …

Phospholipases D: Making Sense Of Redundancy And Duplication, Andrew J. Morris

Internal Medicine Faculty Publications

Why have two genes when one would suffice? Evolutionary pressure means that biology, unlike government, is generally intolerant of wasted effort. Therefore, when multiple genes exist presumably they are there to provide some benefit to the organism even if that benefit is not immediately obvious to us scientists. A recent report from Raghu and colleagues (Biosci. Rep. (2018) 38, pii: BSR20181690) [1] sheds some light on one possible reason for the existence of two Phospholipases D genes in chordates when only one is present in invertebrates.

Detecting The Cold: Do Innexins Function In Cold Nociception?, Rachel Barborek

Senior Honors Projects, 2010-2019

Nociception is the perception of and response to harmful stimuli. Nociception is essential for minimizing tissue damage, but aberrant nociceptive pathways can result in chronic pain. Chronic pain in the U.S. is commonly managed with wide-acting opioids, and precisely defining the components of nociceptive pathways could uncover novel targets for pain therapies. I hypothesize that the vitally quick process of nociception would utilize electrical synapses because they transmit signals between neurons more quickly than chemical synapses do. This study, therefore, aims to uncover the potential role of the eight Drosophila melanogaster gap junction proteins, the Innexins, in cold nociception. Wild …

Investigating The Role Of Free Radicals In Huntington's Disease Using Drosophila Melanogaster, Jennifer Libov

Honors Program: Senior Projects (Public)

During normal cell metabolism, reactive oxygen species (ROS) are produced as a byproduct of oxidative phosphorylation. ROS are utilized in the cell as a signaling molecule and can be maintained at healthy levels by cellular antioxidants. However, when the cell experiences oxidative stress due to environmental or genetic conditions, levels of ROS can exceed healthy levels and inhibit necessary life functions by damaging biomolecules and cellular structures. This loss of function can lead to physiological decline and neurodegeneration, such as in diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and, potentially, Huntington’s disease. The following experiments use the model genetic organism …

Effect Of Larval Starvation On Lipid Content Of Drosophila Melanogaster Over 15 Days, Fabian Leija, Allen Gibbs

LSAMP Poster Presentations

Starvation-resistant Drosophila melanogaster, common fruit flies, deriving from 121 generations of starvation selection, have resulted in genetically, behaviorally, and physiologically different individuals compared to non-resistant counterparts. Starvation-resistant Drosophila are more obese, containing twice as much lipids as control flies.This is a result of starvation-resistant fly larva feeding for 5 days and then entering the pupa stage while non-resistant flies only feed for 4 days.

In this experiment, we hope to answer the question of whether the starvation-resistant flies are genetically predisposed to be substantially more obese than wild populations or if it is a result of this alternate behavior …

Genetic Basis Of Larval Crystal Cell Quantity Variation In The Drosophila Genetic Reference Panel (Dgrp), Brian Tang

Student Theses and Dissertations

Crystal cells are one of three requisite hemocytes that take part in fighting infection and wound healing in Drosophila melanogaster (common fruit flies). The developmental genetics of crystal cell formation is only beginning to be discovered. To address this question, we performed a Genome-Wide Association Study (GWAS) on larval crystal cell number from 78 isolines of the Drosophila Genetic Reference Panel (DGRP) collection. The DGRP consists of naturally caught fruit flies that are inbred to near homozygosity with completely sequenced genomes. By placing the wandering third instar larvae under heatshock, a process that induces the melanization of crystal cells, …

R1 Retrotransposons In Drosophila Melanogaster Are Transcribed By Rna Polymerase I Upon Heat Shock, Himanshu Shekhar Raje

LSU Doctoral Dissertations

The ribosomal RNA genes of Drosophila melanogaster reside within centromere-proximal nucleolar organizers on both the X and Y chromosomes. Each locus contains between 200-300 tandem repeat rDNA units that encode 18S, 5.8S, and 28S ribosomal RNAs (rRNAs) for ribosome biogenesis. In arthropods like Drosophila, about 60% of rDNA genes are inserted with R1 and/or R2 retrotransposons at specific sites within the 28S regions; these units likely fail to produce functional 28S rRNA. We showed previously that R2 expression increases upon nucleolar stress caused by the loss of a ribosome assembly factor, the Nucleolar Phosphoprotein of 140 kDa (Nopp140). Here …

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 …

Gene Expression Profiling In The Larval Fat Body Of Desiccation Selected Drosophila Melanogaster, Adriana Michelle Charles

UNLV Theses, Dissertations, Professional Papers, and Capstones

Drosophila melanogaster selected for resistance to desiccation (no food or water) display slower development and a higher body mass compared to fed controls due to an extended third larval instar. I hypothesize that desiccation selected D. melanogaster larvae will have a different gene expression profile compared to fed controls. Separate populations of D. melanogaster were subjected to desiccation (no food or water), starvation (no food) until 80-85% mortality, for 75 generations. mRNA from the larval fat body was collected at 88 hours, 96 hours, 112 hours and 120 hours post-hatching. Four replicate samples were used for each condition and time …

An Undergraduate Cell Biology Lab: Western Blotting To Detect Proteins From Drosophila Eye, Neha Gogia, Ankita Sarkar, Amit Singh

Biology Faculty Publications

We have developed an undergraduate laboratory to allow detection and localization of proteins in the compound eye of Drosophila melanogaster, a.k.a fruit fly. This lab was a part of the undergraduate curriculum of the cell biology laboratory course aimed to demonstrate the use of Western Blotting technique to study protein localization in the adult eye of Drosophila. Western blotting, a two-day laboratory exercise, can be used to detect the presence of proteins of interests from total protein isolated from a tissue. The first day involves isolation of proteins from the tissue and SDS-PAGE (sodium dodecyl sulfate-polyacrylamide) gel …

Real-Time Quantitative Pcr To Demonstrate Gene Expression In An Undergraduate Lab, Abijeet Singh Mehta, Amit Singh

Biology Faculty Publications

The objective of this teaching note is to develop a laboratory exercise, which allows students to get a hands-on experience of a molecular biology technique to analyze gene expression. The short duration of the biology laboratory for an undergraduate curriculum is the biggest challenge with the development of new labs. An important part of cell biology or molecular biology undergraduate curriculum is to study gene expression. There are many labs to study gene expression in qualitative manner. The commonly used reporter gene expression studies are primarily qualitative. However, there is no hands-on experience exercise to quantitatively determine gene expression. Therefore, …

Ubr3, A Novel Modulator Of Hh Signaling Affects The Degradation Of Costal-2 And Kif7 Through Poly-Ubiquitination, Tongchao Li, Junkai Fan, Bernardo Blanco-Sánchez, Nikolaos Giagtzoglou, Guang Lin, Shinya Yamamoto, Manish Jaiswal, Kuchuan Chen, Jie Zhang, Wei Wei, Michael T. Lewis, Andrew K. Groves, Monte Westerfield, Jianhang Jia, Hugo J. Bellen

Markey Cancer Center Faculty Publications

Hedgehog (Hh) signaling regulates multiple aspects of metazoan development and tissue homeostasis, and is constitutively active in numerous cancers. We identified Ubr3, an E3 ubiquitin ligase, as a novel, positive regulator of Hh signaling in Drosophila and vertebrates. Hh signaling regulates the Ubr3-mediated poly-ubiquitination and degradation of Cos2, a central component of Hh signaling. In developing Drosophila eye discs, loss of ubr3 leads to a delayed differentiation of photoreceptors and a reduction in Hh signaling. In zebrafish, loss of Ubr3 causes a decrease in Shh signaling in the developing eyes, somites, and sensory neurons. However, not all tissues that require …

Rac1 And Ire1 Are Required To Prevent Early Loss Of Intestinal Homeostasis In Drosophila Melanogaster, Mauricio M. Ortega

Dissertations, Masters Theses, Capstones, and Culminating Projects

No abstract available

The Uas-Gal4 System In D. Melanogaster: An Insight Into The Influence Of Micrornas On The Developmental Pathways Of The Wing, Emily R. Wilson

Honors Theses

By examining genetic pathways in D. melanogaster, a better understanding of the homologous regulatory mechanisms in humans can be utilized to further enhance knowledge of the roles of microRNA within development. This study utilizes the UAS-Gal4 system in order to produce a mutant phenotype capable of being visually studied and analyzed, focusing on the developmental pathway of the wing in D. melanogaster. Dissections of the wandering third instar larvae yielded wing disc tissue expressing the downregulation of loquacious and CG17386.

The Adp-Ribose Polymerase Tankyrase Regulates Adult Intestinal Stem Cell Proliferation During Homeostasis In Drosophila, Zhenghan Wang, Ai Tian, Hassina Benchabane, Ofelia Tacchelly-Benites, Eungi Yang, Hisashi Nojima, Yashi Ahmed

Dartmouth Scholarship

Wnt/β-catenin signaling controls intestinal stem cell (ISC) proliferation, and is aberrantly activated in colorectal cancer. Inhibitors of the ADP-ribose polymerase Tankyrase (Tnks) have become lead therapeutic candidates for Wnt-driven cancers, following the recent discovery that Tnks targets Axin, a negative regulator of Wnt signaling, for proteolysis. Initial reports indicated that Tnks is important for Wnt pathway activation in cultured human cell lines. However, the requirement for Tnks in physiological settings has been less clear, as subsequent studies in mice, fish and flies suggested that Tnks was either entirely dispensable for Wnt-dependent processes in vivo, or alternatively, had tissue-specific roles. Here, …

The Role Of Rapgap1 In Sxl Activation In Drosophila Melanogaster, Katherine M. Barnes

Lewis Honors College Capstone Collection

The master switch of the sexual differentiation and dosage compensation pathway in Drosophila is the sex lethal gene, Sxl. The early promoter, SxlPe, is activated in females, resulting in female-specific splicing of later transcripts (notably the late Sxl transcript SxlPm), while inactive in males. Chromatin immunoprecipitation (ChIP) assays have previously shown association of two conventionally heterochromatin-localized proteins, HOAP and HP1, at SxlPe, and in situ hybridization as well as RT-PCR assays have confirmed a repressive role for HOAP and both repressive and activating roles for HP1. The mechanism for the activity shift of HP1 is currently unknown. Deletions in the …

Highly Constrained Intergenic Drosophila Ultraconserved Elements Are Candidate Ncrnas, Andrew D. Kern, Daniel A. Barbash, Joshua Chang Mell, Daniel Hupalo, Amanda Jensen

Dartmouth Scholarship

Eukaryotes contain short (∼80–200 bp) regions that have few or no substitutions among species that represent hundreds of millions of years of evolutionary divergence. These ultraconserved elements (UCEs) are candidates for containing essential functions, but their biological roles remain largely unknown. Here, we report the discovery and characterization of UCEs from 12 sequenced Drosophilaspecies. We identified 98 elements ≥80 bp long with very high conservation across the Drosophila phylogeny. Population genetic analyses reveal that these UCEs are not present in mutational cold spots. Instead we infer that they experience a level of selective constraint almost 10-fold higher compared with …

The Mechanisms Of Α-Amanitin Resistance In The Fruit Fly Drosophila Melanogaster, Chelsea L. Mitchell

Dissertations, Master's Theses and Master's Reports

Insect pesticide resistance has become a costly problem in the US. To make things more problematic, resistance to one pesticide is often associated with cross-resistance to other toxins, including pesticides that have not yet even been developed. In this study, we investigated a possible type of cross-resistance in the model fruit fly Drosophila melanogaster, some stocks of which are resistant to the very potent mushroom toxin α-amanitin. Because α-amanitin is solely produced by mushrooms, and because D. melanogaster does not feed on mushrooms in nature, the fruit flies should not be resistant to this toxin. In order to understand …

Large-Scale Identification Of Chemically Induced Mutations In Drosophila Melanogaster, Nele A Haelterman, Lichun Jiang, Yumei Li, Vafa Bayat, Hector Sandoval, Berrak Ugur, Kai Li Tan, Ke Zhang, Danqing Bei, Bo Xiong, Wu-Lin Charng, Theodore Busby, Adeel Jawaid, Gabriela David, Manish Jaiswal, Koen J T Venken, Shinya Yamamoto, Rui Chen, Hugo J Bellen

Faculty, Staff and Students Publications

Forward genetic screens using chemical mutagens have been successful in defining the function of thousands of genes in eukaryotic model organisms. The main drawback of this strategy is the time-consuming identification of the molecular lesions causative of the phenotypes of interest. With whole-genome sequencing (WGS), it is now possible to sequence hundreds of strains, but determining which mutations are causative among thousands of polymorphisms remains challenging. We have sequenced 394 mutant strains, generated in a chemical mutagenesis screen, for essential genes on the Drosophila X chromosome and describe strategies to reduce the number of candidate mutations from an average of …

Orthoclust: An Orthology-Based Network Framework For Clustering Data Across Multiple Species, Koon-Kiu Yan, Daifeng Wang, Joel Rozowsky, Henry Zheng, Chao Cheng, Mark Gerstein Gerstein

Dartmouth Scholarship

Increasingly, high-dimensional genomics data are becoming available for many organisms.Here, we develop OrthoClust for simultaneously clustering data across multiple species. OrthoClust is a computational framework that integrates the co-association networks of individual species by utilizing the orthology relationships of genes between species. It outputs optimized modules that are fundamentally cross-species, which can either be conserved or species-specific. We demonstrate the application of OrthoClust using the RNA-Seq expression profiles of Caenorhabditis elegans and Drosophila melanogaster from the modENCODE consortium. A potential application of cross-species modules is to infer putative analogous functions of uncharacterized elements like non-coding RNAs based on guilt-by-association.

Stress Responses And Energy Storage In Drosophila Melanogaster Selected For Resistance To A Gram-Positive Bacillus Cereus Spores, Zhen Hu

School of Biological Sciences: Dissertations, Theses, and Student Research

A survival response study was carried out by using D. melanogaster and the opportunistic pathogen B. cereus as the agent of selection. The spores of B. cereus, a gram-positive bacteria that can cause the human pathogen disease, were applied in our artificial laboratory selection. Selected lines were treated with B. cereus spores. Wound control lines were punctured with a needle dipped into sterile H₂O. Control lines did not apply any treatment. Three different environmental treatments were used within each line type (autoclaved spores of B.cereus, sterile H₂O and no treatment). The autoclaved spores were …

Drosophila Snap-29 Is An Essential Snare That Binds Multiple Proteins Involved In Membrane Traffic, Hao Xu, Mahmood Mohtashami, Bryan Stewart, Gabrielle Boulianne, William S. Trimble

Faculty Publications

Each membrane fusion event along the secretory and endocytic pathways requires a specific set of SNAREs to assemble into a 4-helical coiled-coil, the so-called trans-SNARE complex. Although most SNAREs contribute one helix to the trans-SNARE complex, members of the SNAP-25 family contribute two helixes. We report the characterization of the Drosophila homologue of SNAP-29 (dSNAP-29), which is expressed throughout development. Unlike the other SNAP-25 like proteins in fruit fly (i.e., dSNAP-25 and dSNAP-24), which form SDS-resistant SNARE complexes with their cognate SNAREs, dSNAP-29 does not participate in any SDS-resistant complexes, despite its interaction with dsyntaxin1 and dsyntaxin 16 in vitro. …

Trip/Nopo E3 Ubiquitin Ligase Promotes Ubiquitylation Of Dna Polymerase Η, Heather A. Wallace, Julie A. Merkle, Michael C. Yu, Taloa G. Berg, Ethan Lee, Giovanni Bosco, Laura A. Lee

Dartmouth Scholarship

We previously identified a Drosophila maternal effect-lethal mutant named ‘no poles’ (nopo). Embryos from nopo females undergo mitotic arrest with barrel-shaped, acentrosomal spindles during the rapid cycles of syncytial embryogenesis because of activation of a Chk2-mediated DNA checkpoint. NOPO is the Drosophila homolog of human TNF receptor associated factor (TRAF)-interacting protein (TRIP), which has been implicated in TNF signaling. NOPO and TRIP contain RING domains closely resembling those of known E3 ubiquitin ligases. We herein sought to elucidate the mechanism by which TRIP/NOPO promotes genomic stability by performing a yeast two-hybrid screen to identify potential substrates/interactors. We identified members of …

The Role Of Body Size On The Outcome Of Mating Interactions In Drosophila Melanogaster, Adam C. Lounsbury

Theses and Dissertations (Comprehensive)

Sexual selection is the process by which some individuals produce more and/or better quality offspring than others because they are better at securing mates. While this may be accomplished by defeating same-sex rivals (intrasexual selection), individuals of one sex (typically females) may also “decide” on the suitability of individuals of the opposite sex (typically males), resulting in intersexual selection on attractive traits. While a great deal of scrutiny has focused on how sexual selection influences male display traits, much less scrutiny has been directed toward the factors underlying female preference, including genetic variation, as well as the extent to which …

Causes And Consequences Of Female Mate Choice In Drosophila Melanogaster: A Hemiclonal Analysis, Hannah Me Tennant

Theses and Dissertations (Comprehensive)

One of Darwin’s greatest questions, the reason why females prefer elaborate sexually selected male traits and displays, was elucidated by the Fisherian coevolution of male traits and female preferences. While variation in male attractiveness and ornamentation has received much attention, there has been little attempt to evaluate the causes and consequences of intraspecific variation in components of female preference. Furthermore, demonstrating a genetic basis to female preference does not answer the question of how within-population genetic variation is maintained.

Understanding the sources of variation in potential mating interactions between males and females is important because this variation determines the strength …

A Genetic, Transgenic, And Transcriptomic Analysis Of Larval Salivary Gland Physiology In Drosophila Melanogaster, Elana A. Paladino

UNLV Theses, Dissertations, Professional Papers, and Capstones

Cholesterol is the precursor to a unique class of lipophilic signaling molecules called steroid hormones that initiate the development of sexual characteristics, reactions to stress, and maintenance of metabolism, among many other functions. Although much progress has been made in understanding the function of these signaling hormones, we do not fully understand how a single steroid can cause many distinct, tissue-specific responses. Drosophila melanogaster is an effective model for understanding steroid hormone action because of its simplicity. The steroid molting hormone 20-hydroxyecdysone (hereafter, 20E) is the primary active steroid in Drosophila and mediates not only larval molts and the emergence …

Condensin Ii Promotes The Formation Of Chromosome Territories By Inducing Axial Compaction Of Polyploid Interphase Chromosomes, Christopher R. R. Bauer, Tom A. Hartl, Giovanni Bosco

Dartmouth Scholarship

The eukaryotic nucleus is both spatially and functionally partitioned. This organization contributes to the maintenance, expression, and transmission of genetic information. Though our ability to probe the physical structure of the genome within the nucleus has improved substantially in recent years, relatively little is known about the factors that regulate its organization or the mechanisms through which specific organizational states are achieved. Here, we show that Drosophila melanogaster Condensin II induces axial compaction of interphase chromosomes, globally disrupts interchromosomal interactions, and promotes the dispersal of peri-centric heterochromatin. These Condensin II activities compartmentalize the nucleus into discrete chromosome territories and indicate …

Abd-A Regulation By The Iab-8 Noncoding Rna, Maheshwar Gummalla, Robert K. Maeda, Javier J. Castro Alvarez, Henrik Gyurkovics, Kevin A. Edwards, Swetha Singari, Welcome Bender

Faculty Publications – Biological Sciences

The homeotic genes in Drosophila melanogaster are aligned on the chromosome in the order of the body segments that they affect. The genes affecting the more posterior segments repress the more anterior genes. This posterior dominance rule must be qualified in the case of abdominal-A (abd-A) repression by Abdominal-B (Abd-B). Animals lacking Abd-B show ectopic expression of abd-A in the epidermis of the eighth abdominal segment, but not in the central nervous system. Repression in these neuronal cells is accomplished by a 92 kb noncoding RNA. This "iab-8 RNA" produces a micro RNA to repress abd-A, but also has a …