Genetics and Genomics Commons^™

Pirna Expression In Regenerative Tissue Of Octopus Bimaculoides, Bailey Ervin

Honors Theses

Tissue regeneration is present in varying capacities across the animal kingdom. Animals such as Hydra and planarians have the capacity to regenerate entire bodies from extremely small sections of amputated tissue. Others, such as humans, have restricted capacities of regeneration, especially in terms of full appendages and specialized tissues such as cardiac and nervous tissue. One of the primary goals of studying regeneration in other organisms is to achieve the development of regenerative medicine. Interaction of P-element induced WImpy testis (PIWI) proteins and PIWI-interacting RNAs (piRNAs) have been implicated in germline genome maintenance, as well as transposable element silencing. Research …

Pirna Expression In The Tube Feet Of Lytechinus Variegatus, Reagan Milliet

Honors Theses

Tissue regeneration is an area of research with implications for medicine and animal health. While nearly all living multi-cellular organisms are capable of regeneration, there are major differences in the animal kingdom. Some organisms are capable of regenerating virtually every cell in their bodies. In hopes of engineering tissue regeneration for medical applications, the mechanisms by which organisms regenerate are being widely investigated. To better understand regeneration, the role of P-element Induced WImpy testis (PIWI) proteins are being evaluated. In collaboration with PIWIinteracting RNAs (piRNAs), PIWI proteins have been proven instrumental to transposon silencing and maintenance of the genome in …

Characterizing Endogenous Dicer Products To Unravel Novel Rnai Biogenesis Pathways, Jacob Oche Peter

Dissertations

ABSTRACT

RNA interference (RNAi) is a pervasive gene regulatory mechanism in eukaryotes based on the action of multiple classes of small RNA (sRNA). Exploiting RNAi pathways in non-model systems have great potential for creating potent RNAi technologies. Here, we accessed RNAi-mediated control of gene expression in the two-spotted spider mite, Tetranychus urticae (T. urticae) using engineered dsRNA designed to modulate the host RNAi pathway and increase RNAi efficacy. Analysis of Dicer (Dcr) generated fragments revealed how exogenous RNAs access the host RNAi pathway in this animal, opening avenues for designing RNAi technology for their control. Further, some organisms …

An Interaction Between Centrosome Scaffold Proteins And A Retrotransposon Nucleocapsid Protein May Alter Asymmetric Centrosome Inheritance, Lanilei Doctora

Legacy Theses & Dissertations (2009 - 2024)

Nearly all eukaryotic genomes harbor mobile genetic elements known as retrotransposons. The mRNA ofthese elements undergo reverse transcription, yielding cDNA that is inserted in a new location in the host genome. We study Saccharomyces cerevisiae Ty1 elements, an active family of retrovirus-like retrotransposons, and the mechanism behind its regulation of spindle pole body (SPB) inheritance. Ty1 retromobility is activated during growth at 20˚C. In a manuscript that includes my work (Murphy et al., 2022, manuscript in preparation), we report that essential SPB proteins Nud1 and Spc42 are sequestered in the Ty1 retrosome, the site of Ty1 nucleocapsid assembly, in a …

Investigating Pirna Expression And Function In Regenerating Tissue Of Segmented Annelid Capitella Teleta, Beatriz Schueng Zancanela

Honors Theses

Regeneration can be observed virtually in all animals and previous studies have identified numerous genes involved in this process. In some invertebrates, the P-element induced wimpy testis (PIWI) genes appear to have an essential role. One such organism is Capitella teleta, a widely accepted model for annelid development. PIWI proteins are associated with small non-coding RNA called PIWI-interacting RNAs or piRNAs, which are involved in transposon silencing in the germline cells of many animals. It was previously believed that these proteins were only expressed in germline cells, however, recent studies have shown expression in somatic tissues as well. The function …

Retrotransposon-Mediated Transduction Of An Environmental Cue To Regulate Centrosome Fate, Shawn Patrick Murphy

Legacy Theses & Dissertations (2009 - 2024)

In 1969, the enrichment of mobile element repeat sequences led Britton and Davidson to propose the hypothesis that gene expression in higher eukaryotes is regulated through the exaptation of mobile elements. In this work, I have explored the hypothesis that mobile elements can also be harnessed by the host to regulate asymmetric cell division, thereby determining cell fate. Retrotransposons are ubiquitous eukaryotic mobile elements that transpose through an RNA intermediate. They are often active in cell types that divide asymmetrically to yield daughter cells with different fates, such as embryonic stem cells, germline stem cells, neuronal stem cells and the …

Identification Of Novel Mites (Miniature Inverted-Repeat Transposable Elements) In Coxiella Burnetii: Implications For Protein And Small Rna Evolution, Shaun Wachter, Rahul Raghavan, Jenny Wachter, Michael F. Minnick

Biology Faculty Publications and Presentations

Background: Coxiella burnetii is a Gram-negative gammaproteobacterium and zoonotic agent of Q fever. C. burnetii’s genome contains an abundance of pseudogenes and numerous selfish genetic elements. MITEs (miniature invertedrepeat transposable elements) are non-autonomous transposons that occur in all domains of life and are thought to be insertion sequences (ISs) that have lost their transposase function. Like most transposable elements (TEs), MITEs are thought to play an active role in evolution by altering gene function and expression through insertion and deletion activities. However, information regarding bacterial MITEs is limited. Results: We describe two MITE families discovered during research on small non-coding …

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 …

Drosophila Muller F Elements Maintain A Distinct Set Of Genomic Properties Over 40 Million Years Of Evolution, Wilson Leung, William Dirkes, Matthew Dothager, Paul Lee, Jeanette Wong, David Xiong, Han Yuan, James E J Bedard, Joshua F. Machone, Seantay D. Patterson, Amber L. Price, Bryce A. Turner, Srebenka Robic, Erin K. Luippold, Shannon R. Mccartha, Tezin A. Walji, Chelsea A. Walker, Kenneth Saville, Marita K. Abrams, Andrew R. Armstrong, William Armstrong, Robert J. Bailey, Chelsea R. Barberi, Lauren R. Beck, Amanda L. Blaker, Christopher E. Blunden, Jordan P. Brand, Ethan J. Brock, Dana W. Brooks, Marie Brown, Sarah C. Butzler, Eric M. Clark, Nicole B. Clark, Ashley A. Collins, Rebecca J. Cotteleer, Peterson R. Cullimore, Seth G. Dawson, Carter T. Docking, Sasha L. Dorsett, Grace A. Dougherty, Kaitlyn A. Downey, Andrew P. Drake, Erica K. Earl, Trevor G. Floyd, Joshua D. Forsyth, Jonathan D. Foust, Spencer L. Franchi, James F. Geary, Cynthia K. Hanson, Taylor S. Harding, Cameron B. Harris, Jonathan M. Heckman, Heather L. Holderness, Nicole A. Howey, Dontae A. Jacobs, Elizabeth S. Jewell, Maria Kaisler, Elizabeth A. Karaska, James L. Kehoe, Hannah C. Koaches, Jessica Koehler, Dana Koenig, Alexander J. Kujawski, Jordan E. Kus, Jennifer A. Lammers, Rachel R. Leads, Emily C. Leatherman, Rachel N. Lippert, Gregory S. Messenger, Adam T. Morrow, Victoria Newcomb, Haley J. Plasman, Stephanie J. Potocny, Michelle K. Powers, Rachel M. Reem, Jonathan P. Rennhack, Katherine R. Reynolds, Lyndsey A. Reynolds, Dong K. Rhee, Allyson B. Rivard, Adam J. Ronk, Meghan B. Rooney, Lainey S. Rubin, Luke R. Salbert, Rasleen K. Saluja, Taylor Schauder, Allison R. Schneiter, Robert W. Schulz, Karl E. Smith, Sarah Spencer, Bryant R. Swanson, Melissa A. Tache, Ashley A. Tewilliager, Amanda K. Tilot, Eve Vaneck, Matthew M. Villerot, Megan B. Vylonis, David T. Watson, Juliana A. Wurzler, Lauren M. Wysocki, Monica Yalamanchili, Matthew A. Zaborowicz, Julia A. Emerson, Carlos Ortiz, Frederic J. Deuschle, Lauren A. Dilorenzo, Katie L. Goeller, Christopher R. Macchi, Sarah E. Muller, Brittany D. Pasierb, Joseph E. Sable, Jessica M. Tucci, Marykathryn Tynon, David A. Dunbar, Levent H. Beken, Alaina C. Conturso, Benjamin L. Danner, Gabriella A. Demichele, Justin A. Gonzales, Maureen S. Hammond, Colleen V. Kelley, Elisabeth A. Kelly, Danielle Kulich, Catherine M. Mageeney, Nikie L. Mccabe, Alyssa M. Newman, Lindsay A. Spaeder, Richard A. Tumminello, Dennis Revie, Jonathon M. Benson, Michael C. Cristostomo, Paolo A. Dasilva, Katherine S. Harker, Jenifer N. Jarrell, Luis A. Jimenez, Brandon M. Katz, William R. Kennedy, Kimberly S. Kolibas, Mark T. Leblanc, Trung T. Nguyen, Daniel S. Nicolas, Melissa D. Patao, Shane M. Patao, Bryan J. Rupley, Bridget J. Sessions, Jennifer A. Weaver, Anya L. Goodman, Erica L. Alvendia, Shane M. Baldassari, Ashley S. Brown, Ian O. Chase, Maida Chen, Scott Chiang, Avery B. Cromwell, Ashley F. Custer, Tia M. Ditommaso, Jad El-Adaimi, Nora C. Goscinski, Ryan A. Grove, Nestor Gutierrez, Raechel S. Harnoto, Heather Hedeen, Emily L. Hong, Barbara L. Hopkins, Vilma F. Huerta, Colin Khoshabian, Kristin M. Laforge, Cassidy T. Lee, Benjamin M. Lewis, Anniken M. Lydon, Brian J. Maniaci, Ryan D. Mitchell, Elaine V. Morlock, William M. Morris, Priyanka Naik, Nicole C. Olson, Jeanette M. Osterloh, Marcos A. Perez, Jonathan D. Presley, Matt J. Randazzo, Melanie K. Regan, Franca G. Rossi, Melanie A. Smith, Eugenia A. Soliterman, Ciani J. Sparks, Danny L. Tran, Tiffany Wan, Anne A. Welker, Jeremy N. Wong, Aparna Sreenivasan, Jim Youngblom, Andrew Adams, Justin Alldredge, Ashley Bryant, David Carranza, Alyssa Cifelli, Kevin Coulson, Calise Debow, Noelle Delacruz, Charlene Emerson, Cassandra Farrar, Don Foret, Edgar Garibay, John Gooch, Michelle Heslop, Sukhjit Kaur, Ambreen Khan, Van Kim, Travis Lamb, Peter Lindbeck, Gabi Lucas, Elizabeth Macias, Daniela Martiniuc, Lissett Mayorga, Joseph Medina, Nelson Membreno, Shady Messiah, Lacey Neufeld, San Francisco Nguyen, Zachary Nichols, George Odisho, Daymon Peterson, Laura Rodela, Priscilla Rodriguez, Vanessa Rodriguez, Jorge Ruiz, Will Sherrill, Valeria Silva, Jeri Sparks, Geeta Statton, Ashley Townsend, Isabel Valdez, Mary Waters, Kyle Westphal, Stacey Winkler, Joannee Zumkehr, Randall J. Dejong, Arlene J. Hoogewerf, Cheri M. Ackerman, Isaac O. Armistead, Lara Baatenberg, Matthew J. Bor, Lindsay K. Brouwer, Brandon J. Burkhart, Kelsey T. Bushhouse, Lejla Cesko, Tiffany Y Y Choi, Heather Cohen, Amanda M. Damsteegt, Jess M. Darusz, Cory M. Dauphin, Yelena P. Davis, Emily J. Diekema, Melissa Drewry, Michelle E M Eisen, Hayley M. Faber, Katherine J. Faber, Elizabeth Feenstra, Isabella T. Felzer-Kim, Brandy L. Hammond, Jesse Hendricksma, Milton R. Herrold, Julia A. Hilbrands, Emily J. Howell, Sarah A. Jelgerhuis, Timothy R. Jelsema, Benjamin K. Johnson, Kelly K. Jones, Anna Kim, Ross D. Kooienga, Erika E. Menyes, Eric A. Nollet, Brittany E. Plescher, Lindsay Rios, Jenny L. Rose, Allison J. Schepers, Geoff Scott, Joshua R. Smith, Allison M. Sterling, Jenna C. Tenney, Chris Uitvlugt, Rachel E. Vandyken, Marielle Vandervennen, Samantha Vue, Nighat P. Kokan, Kwabea Agbley, Sampson K. Boham, Daniel Broomfield, Kayla Chapman, Ali Dobbe, Ian Dobbe, William Harrington, Marwan Ibrahem, Andre Kennedy, Chad A. Koplinsky, Cassandra Kubricky, Danielle Ladzekpo, Claire Pattison, Roman E. Ramirez Jr., Lucia Wande, Sarah Woehlke, Matthew Wawersik, Elizabeth Kiernan, Jeffrey S. Thompson, Roxanne Banker, Justina R. Bartling, Chinmoy I. Bhatiya, Anna L. Boudoures, Lena Christiansen, Daniel S. Fosselman, Kristin M. French, Ishwar S. Gill, Jessen T. Havill, Jaelyn L. Johnson, Lauren J. Keny, John M. Kerber, Bethany M. Klett, Christina N. Kufel, Francis J. May, Jonathan P. Mecoli, Callie R. Merry, Lauren R. Meyer, Emily G. Miller, Gregory J. Mullen, Katherine C. Palozola, Jacob J. Pfeil, Jessica G. Thomas, Evan M. Verbofsky, Eric P. Spana, Anant Agarwalla, Julia Chapman, Ben Chlebina, Insun Chong, I N. Falk, John D. Fitzgibbons, Harrison Friedman, Osagie Ighile, Andrew J. Kim, Kristin A. Knouse, Faith Kung, Danny Mammo, Chun Leung Ng, Vinyak S. Nikam, Diana Norton, Philip Pham, Jessica W. Polk, Shreya Prasad, Helen Rankin, Camille D. Ratliff, Victoria Scala, Nicholas U. Schwartz, Jessica A. Shuen, Amy Xu, Thomas Q. Xu, Yi Zhang, Anne G. Rosenwald, Martin G. Burg, Stephanie J. Adams, Morgan Baker, Bobbi Botsford, Briana Brinkley, Carter Brown, Shadie Emiah, Erica Enoch, Chad Gier, Alyson Greenwell, Lindsay Hoogenboom, Jordan E. Matthews, Mitchell Mcdonald, Amanda Mercer, Nicholaus Monsma, Kristine Ostby, Alen Ramic, Devon Shallman, Matthew Simon, Eric Spencer, Trisha Tomkins, Pete Wendland, Anna Wylie, Michael J. Wolyniak, Gregory M. Robertson, Samuel I. Smith, Justin R. Diangelo, Eric D. Sassu, Satish C. Bhalla, Karim A. Sharif, Tenzin Choeying, Jason S. Macias, Fareed Sanusi, Karvyn Torchon, April E. Bednarski, Consuelo J. Alvarez, Kristen C. Davis, Carrie A. Dunham, Alaina J. Grantham, Amber N. Hare, Jennifer Schottler, Zachary W. Scott, Gary A. Kuleck, Nicole S. Yu, Marian M. Kaehler, Jacob Jipp, Paul J. Overvoorde, Elizabeth Shoop, Olivia Cyranowski, Betsy Hoover, Matt Kusner, Devry Lin, Tijana Martinov, Jonathan Misch, Garrett Salzman, Holly Schiedermeyer, Michael Snavely, Stephanie Zarrasola, Susan Parrish, Atlee Baker, Alissa Beckett, Carissa Belella, Julie Bryant, Turner Conrad, Adam Fearnow, Carolina Gomez, Robert A. Herbstsomer, Sarah Hirsch, Cristen Johnson, Melissa Jones, Rita Kabaso, Eric Lemmon, Carolina Marques Dos Santos Vieira, Darryl Mcfarland, Christopher Mclaughlin, Abbie Morgan, Sepo Musokotwane, William Neutzling, Jana Nietmann, Christina Paluskievicz, Jessica Penn, Emily Peoples, Caitlin Pozmanter, Emily Reed, Nichole Rigby, Lasse Schmidt, Micah Shelton, Rebecca Shuford, Tiara Tirasawasdichai, Blair Undem, Damian Urick, Kayla Vondy, Bryan Yarrington, Todd T. Eckdahl, Jeffrey L. Poet, Alicia B. Allen, John E. Anderson, Jason M. Barnett, Jordan S. Baumgardner, Adam D. Brown, Jordan E. Carney, Ramiro A. Chavez, Shelbi L. Christgen, Jordan S. Christie, Andrea N. Clary, Michael A. Conn, Kristen M. Cooper, Matt J. Crowley, Samuel T. Crowley, Jennifer S. Doty, Brian A. Dow, Curtis R. Edwards, Darcie D. Elder, John P. Fanning, Bridget M. Janssen, Anthony K. Lambright, Curtiss E. Lane, Austin B. Limle, Tammy Mazur, Marly R. Mccracken, Alexa M. Mcdonough, Amy D. Melton, Phillip J. Minnick, Adam E. Musick, William H. Newhart, Joseph W. Noynaert, Bradley J. Ogden, Michael W. Sandusky, Samantha M. Schmuecker, Anna L. Shipman, Anna L. Smith, Kristen M. Thomsen, Matthew R. Unzicker, William B. Vernon, Wesley W. Winn, Dustin S. Woyski, Xiao Zhu, Chunguang Du, Caitlin Ament, Soham Aso, Laura Simone Bisogno, Jason Caronna, Nadezhda Fefelova, Lenin Lopez, Lorraine Malkowitz, Jonathan Marra, Daniella Menillo, Ifeanyi Obiorah, Eric Nyabeta Onsarigo, Shekerah Primus, Mahdi Soos, Archana Tare, Ameer Zidan, Christopher J. Jones, Todd Aronhalt, James M. Bellush, Christa Burke, Steve Defazio, Benjamin R. Does, Todd D. Johnson, Nicholas Keysock, Nelson H. Knudsen, James Messler, Kevin Myirski, Jade Lea Rekai, Ryan Michael Rempe, Michael S. Salgado, Erica Stagaard, Justin R. Starcher, Andrew W. Waggoner, Anastasia K. Yemelyanova, Amy T. Hark, Anne Bertolet, Cyrus E. Kuschner, Kesley Parry, Michael Quach, Lindsey Shantzer, Mary E. Shaw, Mary A. Smith, Omolara Glenn, Portia Mason, Charlotte Williams, S Catherine Silver Key, Tyneshia C P Henry, Ashlee G. Johnson, Jackie X. White, Adam Haberman, Sam Asinof, Kelly Drumm, Trip Freeburg, Nadia Safa, Darrin Schultz, Yakov Shevin, Petros Svoronos, Tam Vuong, Jules Wellinghoff, Laura L M Hoopes, Kim M. Chau, Alyssa Ward, E Gloria C. Regisford, Lajerald Augustine, Brionna Davis-Reyes, Vivienne Echendu, Jasmine Hales, Sharon Ibarra, Lauriaun Johnson, Steven Ovu, John M. Braverman, Thomas J. Bahr, Nicole M. Caesar, Christopher Campana, Daniel W. Cassidy, Peter A. Cognetti, Johnathan D. English, Matthew C. Fadus, Cameron N. Fick, Philip J. Freda, Bryan M. Hennessy, Kelsey Hockenberger, Jennifer K. Jones, Jessica E. King, Christopher R. Knob, Karen J. Kraftmann, Linghui Li, Lena N. Lupey, Carl J. Minniti, Thomas F. Minton, Joseph V. Moran, Krishna Mudumbi, Elizabeth C. Nordman, William J. Puetz, Lauren M. Robinson, Thomas J. Rose, Edward P. Sweeney, Ashley S. Timko, Don W. Paetkau, Heather L. Eisler, Megan E. Aldrup, Jessica M. Bodenberg, Mara G. Cole, Kelly M. Deranek, Megan Deshetler, Rose M. Dowd, Alexandra K. Eckardt, Sharon C. Ehret, Jessica Fese, Amanda D. Garrett, Anna Kammrath, Michelle L. Kappes, Morgan R. Light, Anne C. Meier, Allison O'Rouke, Mallory Perella, Kimberley Ramsey, Jennifer R. Ramthun, Mary T. Reilly, Deirdre Robinett, Nadine L. Rossi, Mary Grace Schueler, Emma Shoemaker, Kristin M. Starkey, Ashley Vetor, Abby Vrable, Vidya Chandrasekaran, Christopher Beck, Kristen R. Hatfield, Douglas A. Herrick, Christopher B. Khoury, Charlotte Lea, Christopher A. Louie, Shannon M. Lowell, Thomas J. Reynolds, Jeanine Schibler, Alexandra H. Scoma, Maxwell T. Smith-Gee, Sarah Tuberty, Christopher D. Smith, Jane E. Lopilato, Jeanette Hauke, Jennifer A. Roecklein-Canfield, Maureen Corrielus, Hannah Gilman, Stephanie Intriago, Amanda Maffa, Sabya A. Rauf, Katrina Thistle, Melissa Trieu, Jenifer Winters, Bib Yang, Charles R. Hauser, Tariq Abusheikh, Yara Ashrawi, Pedro Benitez, Lauren R. Boudreaux, Megan Bourland, Miranda Chavez, Samantha Cruz, Ginell Elliott, Jesse R. Farek, Sarah Flohr, Amanda H. Flores, Chelsey Friedrichs, Zach Fusco, Zane Goodwin, Eric Helmreich, John Kiley, John Mark Knepper, Christine Langner, Megan Martinez, Carlos Mendoza, Monal Naik, Andrea Ochoa, Nicolas Ragland, England Raimey, Sunil Rathore, Evangelina Reza, Griffin Sadovsky, Marie-Isabelle B. Seydoux, Jonathan E. Smith, Anna K. Unruh, Vicente Velasquez, Matthew W. Wolski, Yuying Gosser, Shubha Govind, Nicole Clarke-Medley, Leslie Guadron, Dawn Lau, Alvin Lu, Cheryl Mazzeo, Mariam Meghdari, Simon Ng, Brad Pamnani, Olivia Plante, Yuki Kwan Wa Shum, Roy Song, Diana E. Johnson, Mai Abdelnabi, Alexi Archambault, Norma Chamma, Shailly Gaur, Deborah Hammett, Adrese Kandahari, Guzal Khayrullina

Peer Reviewed Articles

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F …

Drosophila Muller F Elements Maintain A Distinct Set Of Genomic Properties Over 40 Million Years Of Evolution, Wilson Leung, Christopher D. Shaffer, Laura K. Reed, Sheryl T. Smith, Randall J. Dejong, Arlene J. Hoogewerf

University Faculty Publications and Creative Works

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25-50%) than euchromatic reference regions (3-11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11-27%). F element genes have …