Genetics and Genomics Commons^™

Addressing The Black Box Phenomenon Of Genome Sequencing And Assembly, Brandon Carter

Senior Honors Projects, 2010-2019

Genomics, a study of all genetic material in an organism, is a new discipline having a great impact on medicine, agriculture, and environmental phenomena. Most undergraduate faculty members were not formally trained in genomics and must retool themselves in order to stay current with these evolving technologies. Advances in sequencing technology have resulted in an explosion of “big data” that can only be managed and analyzed using digital methods. Multiple complex computer programs are required to teach students the concepts using hands-on methods. These programs are challenging to use, especially since the same faculty members lacking genomics training were not …

Short Germ Insects Utilize Both The Ancestral And Derived Mode Of Polycomb Group-Mediated Epigenetic Silencing Of Hox Genes, Yuji Matsuoka, Tetsuya Bando, Takahito Watanabe, Yoshiyasu Ishimaru, Sumihare Noji, Aleksander Popadic, Taro Mito

Biological Sciences Faculty Research Publications

In insect species that undergo long germ segmentation, such as Drosophila, all segments are specified simultaneously at the early blastoderm stage. As embryogenesis progresses, the expression boundaries of Hox genes are established by repression of gap genes, which is subsequently replaced by Polycomb group (PcG) silencing. At present, however, it is not known whether patterning occurs this way in a more ancestral (short germ) mode of embryogenesis, where segments are added gradually during posterior elongation. In this study, two members of the PcG family, Enhancer of zeste (E(z)) and Suppressor of zeste 12 (Su(z)12), were analyzed in the …

Divergence Of Vertebrate And Insect Specific Toxin Genes Between Three Species Of Widow Spider, Shannon G. Kahn

Honors College Theses

The Brown widow spider, Latrodectus geometricus, is an introduced species to the southern United States (Brown 2008). The Brown widow is a member of the widow spider genus Latrodectus which includes the southern Black widow (L. mactans) and 29 other venomous species. All species of widow spiders produce venom which is used against both predator and prey. These venoms are composed of several different species-specific toxins, each encoded by a different gene (Graudins 2012). Previous research has shown that positive selection pressures affect the venom of snakes and snails, thus aiding in adaptive potential of the species …

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 …

Structural And Functional Interactions Between Bro1 Domain Of Human Alix Protein And Nucleocapsid Packaging Rna Complex From Hiv, Scott Gross

Graduate School of Biomedical Sciences Theses and Dissertations

A virus is only as powerful as its ability to spread. Enveloped retroviruses, namely HIV-1, use exocytosis pathways that normal host cells use to release particles from the plasma membrane. The main pathways of interest in this study are the Endosomal Sorting Complex Required for Transport (ESCRT) and adjacent ALIX pathways. The ESCRT pathway is especially important for degradation of receptor/cargo complexes that form Multi-Vesicular Bodies (MVBs). Currently, there is no known therapy that targets this endosomal pathway, which would prevent the spread of the virus to other cells. The virus has adapted to jump from pathway to pathway when …

Age-Dependent Breakdown Of The Blood Brain Barrier And Associated Changes In S100b Ko Mice, Eric V. Brown

Graduate School of Biomedical Sciences Theses and Dissertations

Autoantibodies play an important role in many autoimmune diseases. Recent research has shown that breakdown of the blood brain barrier (BBB) occurs concomitant to generation of brain reactive autoantibodies in many neurodegenerative diseases, which serve as biomarkers and drivers of pathology. SI00B, a calcium binding protein found most highly expressed in astrocytes which ensheathe the BBB, has many functions in neural development and signaling. Currently literature indicates that S100B KO mice develop normally, with no phenotypic abnormalities. Here, it is demonstrated that S100B KO mice seem to develop a chronic BBB breakdown similar to that seen in human neurodegenerative diseases. …

Evolution Of Sperm Activation In Nematodes, Qing Wei

Graduate School of Biomedical Sciences Theses and Dissertations

Three hermaphroditic species in the nematode genus Caenorhabditis - C. elegans, C. briggsae and C. tropicalis evolved independently from a male/female ancestor. Thus, the hermaphroditic reproductive system provides an ideal subject for studying the origin of new complex traits. Previous studies implied that this transition required two steps: a mutation that caused XY animals to make sperm, and a mutation that allowed XX spermatids to activate and fertilize oocytes. In this dissertation, I show how sperm activation is regulated in different hermaphroditic species.

First, I used TALENs to create genetic tools for C. briggsae and C. tropicalis. These tools were …

Investigation Of Sex Differences In The Expression Of Rora And Its Transcriptional Targets In The Brain As A Potential Contributor To The Sex Bias In Autism, Valerie W. Hu, Tewarit Sarachana, Rachel Sherrard, Kristen M. Kocher

Medicine Faculty Publications

Background

Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by significant impairment in reciprocal social interactions and communication coupled with stereotyped, repetitive behaviors and restricted interests. Although genomic and functional studies are beginning to reveal some of the genetic complexity and underlying pathobiology of ASD, the consistently reported male bias of ASD remains an enigma. We have recently proposed that retinoic acid-related orphan receptor alpha (RORA), which is reduced in the brain and lymphoblastoid cell lines of multiple cohorts of individuals with ASD and oppositely regulated by male and female hormones, might contribute to the sex bias …

Fisheries Management Paper No 274 - Finfish Resources Of The Peel-Harvey Estuary - Harvest Strategy 2015-2020 (Version 1.0), Department Of Fisheries, Western Australia

Fisheries Management Papers

WEST COAST ESTUARINE MANAGED FISHERY (AREA 2)

Harvest strategies for aquatic resources managed by the Western Australian Department of Fisheries (the Department) are formal documents prepared to support the decision-making processes required to ensure the management of these resources are consistent with the principles of Ecologically Sustainable Development (ESD). The objectives of ESD are reflected in the objects of the Fish Resources Management Act 1994 (FRMA), Section 3, and the draft Aquatic Resources Management Bill 2013 (ARMB), Clause 9, which will replace the FRMA once enacted.

The publication of these strategies is intended to make the decision-making considerations and processes …

Characterization Of A Novel Clade Of Transporters In Phytophthora, Stephanie Padula, Paul F. Morris Dr, Howard Casey Cromwell Dr., Menaka Ariyaratne, Andrew Wagner

Honors Projects

The oomycete Phytophthora parasitica has a worldwide distribution and is an economically important pathogen of more than 100 species⁴. RNA-seq analysis showed that one gene, PPTG_16698 has the 5^th highest level of expression of all transport proteins in the zoospore stage, and is highly conserved throughout Phytophthora species. This project attempts to characterize the important biological role that PPTG_16698 plays in P. parasitica and other oomycetes. Three strategies have been implemented to accomplish this goal: growth analysis by heterologous expression in yeast, metabolite analysis in yeast, and construction of a GFP fusion protein to enable localization of …

An Inquiry-Infused Introductory Biology Laboratory That Integrates Mendel's Pea Phenotypes With Molecular Mechanisms, Philip Kudish, E. Schlag, Nicholas J. Kaplinsky

Biology Faculty Works

We developed a multi-week laboratory in which college-level introductory biology students investigate Mendel's stem length phenotype in peas. Students collect, analyze and interpret convergent evidence from molecular and physiological techniques. In weeks 1 and 2, students treat control and experimental plants with Gibberellic Acid (GA) to determine whether uncharacterized short mutant lines are GA responsive. These data allow students to place the mutation in the GA signal transduction pathway. During weeks 2 and 3, plants are genotyped for Mendel's "le" mutation using a derived cleaved polymorphic sequences (dCAPS) PCR assay. This laboratory allows students to make a direct connection between …

Examination Of Polymorphism In The Serine Proteinase Inhibitor Gene In The Eastern Oyster, Crassostrea Virginica., Aine Lehane

Senior Honors Projects

Oysters are a keystone species; they are filter-feeders and reef-builders. Additionally, oysters are extremely important within the shellfish aquaculture industry; they are the second most widely produced species in world aquaculture production. Eastern oysters, Crassostrea virginica, are produced in aquaculture and are unfortunately susceptible to Dermo disease. Dermo is caused by a protozoan parasite, Perkinsus marinus, and infection is often fatal in oysters due to widespread tissue damage and blockage of blood vessels. Research in oyster disease is particularly needed because disease is one of the largest impediments faced by the aquaculture industry as entire oyster populations can …

Determination Of The Dermacentor Variabilis Ferritin Gene Exon And Intron Structure, Dana Sylvestre

Honors College Theses

The American dog tick Dermacentor variabilis is a hard body, 3-host tick that relies on the blood of small and large mammals to satisfy its metabolic demands. The excess iron consumed in its blood diet can cause cellular damage through oxidation. Ticks rely on the ferritin protein to metabolize iron. For this reason, it is important to further characterize the ferritin gene. After extracting DNA from D. variabilis ticks, the suspected ferritin gene was amplified through polymerase chain reaction (PCR) and purified. The putative ferritin DNA fragment was inserted into plasmids and isolated in a long PCR length gene cloning. …

Overexpression And Gene Profiling Of Asparagine Synthetase In Hybrid Poplar, Kristopher Murray

Renée Crown University Honors Thesis Projects - All

Plants with polysaccharide-rich secondary cell walls have great potential as a source of carbohydrates for bioethanol production. However, the presence of phenolic lignin inhibits the isolation of bioethanol precursors cellulose and hemicellulose from the secondary cell wall. Recent studies have linked nitrogen availability to secondary cell wall development and composition, making nitrogen metabolism genes an interesting target in the improvement of plant cell walls for biofuels production. Plants use a nitrogen assimilation pathway to convert inorganic nitrogen sources into organic sources, included amino acids, which play key roles in metabolism and cell wall development. Asparagine synthetase (AS), a key enzyme …

Bioinformatic Game Theory And Its Application To Cluster Multi-Domain Proteins, Brittney Keel

Department of Mathematics: Dissertations, Theses, and Student Research

The exact evolutionary history of any set of biological sequences is unknown, and all phylogenetic reconstructions are approximations. The problem becomes harder when one must consider a mix of vertical and lateral phylogenetic signals. In this dissertation we propose a game-theoretic approach to clustering biological sequences and analyzing their evolutionary histories. In this context we use the term evolution as a broad descriptor for the entire set of mechanisms driving the inherited characteristics of a population. The key assumption in our development is that evolution tries to accommodate the competing forces of selection, of which the conservation force seeks to …

Tracking Plastid Gene Migration In Karenia Brevis, Kelly E. Scott

Honors Theses

Karenia brevis is a marine dinoflagellate responsible for the harmful algal blooms (also known as red tides) in the Gulf of Mexico. K. brevis expresses antisense (AS) RNAs, each of which has a complementary region to the messenger RNA (mRNA) of a variety of genes. In dinoflagellates, many plastid (and mitochondrial) genes have migrated to the nuclear genome. It is unknown whether chloroplast genes, such as photosystem – D2, have migrated in K. brevis. It is also unknown where the gene that expresses the AS RNA for photosystem D2 resides. The protein-coding gene and the AS RNA-expressing gene could …

The Hippo Pathway Effector Yki Downregulates Wg Signaling To Promote Retinal Differentiation In The Drosophila Eye, Erika Lynn Wittkorn, Ankita Sarkar, Kristine Garcia, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

The evolutionarily conserved Hippo signaling pathway is known to regulate cell proliferation and maintain tissue homeostasis during development. We found that activation of Yorkie (Yki), the effector of the Hippo signaling pathway, causes separable effects on growth and differentiation of theDrosophila eye. We present evidence supporting a role for Yki in suppressing eye fate by downregulation of the core retinal determination genes. Other upstream regulators of the Hippo pathway mediate this effect of Yki on retinal differentiation. Here, we show that, in the developing eye, Yki can prevent retinal differentiation by blocking morphogenetic furrow (MF) progression and R8 specification. …

A Phylogenetic Analysis Of Dictyostelium Purpureum Based On Nuclear Rdna Sequences, Mahmoud Suliman

Graduate Theses and Dissertations

Dictyostelids (cellular slime molds) are eukaryotic microorganisms that have both unicellular and multicellular stages during their life cycle. In this study, a molecular phylogenetic analysis was conducted for isolates of one species (Dictyostelium purpureum) based DNA sequences of the ITS, 5.8S and SSU regions of nuclear rDNA. Moreover, a detailed morphological study was carried out using images obtained with both dissecting and compound microscopes. Mating experiments were carried out to assess macrocysts formation between each pair of isolates. The constructed molecular phylogenetic trees indicate that (1) D. purpureum isolates are more closely related to each other than to other species …

Development Of A Large Set Of Microsatellite Markers In Zapote Mamey (Pouteria Sapota (Jacq.) H.E. Moore & Stearn) And Their Potential Use In The Study Of The Species, Renee S. Arias, Jaime Martínez-Castillo, V. S. Sobolev, Nasib H. Blancarte-Jaso, S. A. Simpson, Linda L. Ballard, Mary V. Duke, Xiaofen F. Liu, Brian M. Irish, Brian E. Scheffler

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Pouteria sapota is known for its edible fruits that contain unique carotenoids, as well as for its fungitoxic, anti-inflammatory and anti-oxidant activity. However, its genetics is mostly unknown, including aspects about its genetic diversity and domestication process. We did high-throughput sequencing of microsatellite-enriched libraries of P. sapota, generated 5223 contig DNA sequences, 1.8 Mbp, developed 368 microsatellites markers and tested them on 29 individuals from 10 populations (seven wild, three cultivated) from Mexico, its putative domestication center. Gene ontology BLAST analysis of the DNA sequences containing microsatellites showed potential association to physiological functions. Genetic diversity was slightly higher in cultivated …

Physiological Response To Salinity Challenge Is Mediated By Na+, K+ - Atpase “Isoform Switching” In A Euryhaline Fish, The Alewife, Rebecca S. Colby

Honors Scholar Theses

Na⁺, K⁺-ATPase (NKA) a1a and a1b expression was investigated in Alewives in response to salinity challenge. Anadromous and landlocked Alewives were exposed to freshwater (0ppt) and seawater (30ppt) treatments and sampled at 2-, 5-, and 15-day time points. Anadromous alewives exhibit significant up-regulation of a1a in freshwater compared to seawater at all time points, and significant up-regulation of a1b in seawater compared to freshwater at all time points. In landlocked Alewives, a1a is significantly up regulated at the 5-day time point and a1b is significantly up regulated at all time points (in their respective salinities). Analysis …

Investigation Of Genetic Alterations In Emt Suppressor, Dear1, Through Pan-Cancer Analysis And Ultra-Deep Targeted Sequencing In Ductal Carcinoma In Situ, Jacquelyn Reuther

Dissertations and Theses (Open Access)

Ductal carcinoma in situ (DCIS) is thought to be one of the earliest pre-invasive form of and non-obligate precursor to invasive ductal carcinoma (IDC). There is an urgent need to identify predictive and prognostic biomarkers for breast cancers with a heightened risk of progression from DCIS to IDC. Our laboratory has previously discovered a novel TRIM family member, DEAR1 (Ductal Epithelium Associated Ring Chromosome 1, annotated as TRIM62) within chromosome 1p35.1, that is mutated and homozygously deleted in breast cancer and whose expression is downregulated/lost in DCIS. Previous work has shown that DEAR1 is a novel tumor suppressor …

Igfbp2 Potentiates Egfr-Stat3 Signaling In Glioma, Yingxuan Chua

Dissertations and Theses (Open Access)

Gliomas are clinically challenging brain tumors with dismal survival rates due to its infiltrative nature and ineffective standard therapy. Insulin-like growth factor binding protein 2 (IGFBP2) is a pleiotropic oncogenic protein that has both extracellular and intracellular functions. Despite a clear causal role in cancer development, the contributions of intracellular IGFBP2 to tumor development and progression are poorly understood. Here we present evidence that both exogenous IGFBP2 treatment and cellular IGFBP2 overexpression lead to aberrant activation of EGFR, which subsequently activates STAT3 signaling. Furthermore, we demonstrate that IGFBP2 augments the nuclear accumulation of EGFR to potentiate STAT3 transactivation activities, via …

Genetics Of Obesity In Starr County, Texas Mexican Americans, Heather M. Highland

Dissertations and Theses (Open Access)

Currently, over two-thirds of Americans are classified as over-weight or obese. Obesity increases risk for many other diseases including type 2 diabetes, heart disease, stroke, and cancer, making obesity the largest public health problem in America and most other Westernized nations. Hispanics have a higher rate of both obesity and type 2 diabetes, making them a particularly interesting population in which to study obesity. For the last 33 years, the Starr County Health Studies has collected an array of phenotypes and biological samples from residents of Starr County, along Texas-Mexico border. This study includes 825 subjects who were not known …

Elucidating The Role Of Rumi And O-Glucosylation In The Drosophila Eye, Amanda Haltom

Dissertations and Theses (Open Access)

Rumi is a protein O-glucosyltransferase that adds the sugar O-glucose onto the serine in the target sequence C-S-X-S-(P/A)-C found within properly folded EGF repeats. It was first discovered to modify the Drosophila Notch extracellular domain and to be required for Notch signaling in a temperature dependent manner, but other targets of Rumi remained unknown. Several other proteins in the Drosophila proteome harbor multiple consensus sequence highly predictive of O-glucose, including the transmembrane protein Crumbs and the secreted protein Eyes shut (Eys). Both of these proteins are required for proper eye development and mutations in their human homologs …

Dna Polymerase Θ (Polq) And The Cellular Defense Against Dna Damage, Matthew J. Yousefzadeh

Dissertations and Theses (Open Access)

In mammalian cells, DNA polymerase θ (POLQ) is an unusual specialized DNA polymerase whose in vivo function is under active investigation. The protein is comprised of an N-terminal helicase-like domain, a C-terminal DNA polymerase domain, and a large central domain that spans between the two. This arrangement is also found in the Drosophila Mus308 protein, which helps confer resistance to DNA interstrand crosslinking agents. Homologs of POLQ and Mus308 are found in eukaryotes, including plants, but a comparison of phenotypes suggests that not all of these genes are functional orthologs. Flies with defective Mus308 are sensitive to DNA interstrand crosslinking …

Spiritual Exploration In The Prenatal Genetic Counseling Session, Katelynn G. Sagaser

Dissertations and Theses (Open Access)

Religion and spirituality are important components of many individuals’ lives, and spiritual needs may present among persons receiving medical care. Spirituality has been demonstrated to be significant in the coping of women experiencing pregnancy complications (Breen et al. 2006; Price et al. 2007). To characterize the manner in which prenatal genetic counselors might address spiritual issues with their patients, we surveyed 283 patients receiving prenatal genetic counseling using the Brief RCope and a series of questions that examined interest in spiritual exploration. Counselors were concurrently surveyed to identify the spiritual language used within the session and the counselor’s perceived importance …

Investigating The Roles Of P63 And P73 Isoforms To Therapeutically Treat P53-Altered Cancers, Avinashnarayan Venkatanarayan

Dissertations and Theses (Open Access)

Investigating the roles of p63 & p73 isoforms to therapeutically treat

p53-altered cancers

Avinashnarayan Venkatanarayan, M.S.

Supervisory Professor: Elsa R. Flores, Ph.D.

The TP53 tumor suppressor is mutated in approximately 50% of human cancers rendering cancer therapies ineffective. p53 reactivation suppresses tumor formation in mice. However, this strategy has proven difficult to implement therapeutically. An alternate approach to overcome p53 loss is to manipulate the p53-family members, p63 and p73, which interact and share structural similarities to p53. p63 and p73, unlike p53 are less frequently mutated and have two major isoforms with distinct functions …

Evaluating The Nccn Clinical Criteria For Hereditary Breast And Ovarian Cancer Syndrome Genetic Testing, Caiqian Wu

Dissertations and Theses (Open Access)

Hereditary Breast and Ovarian Cancer (HBOC) syndrome predisposes females with a BRCA1 or BRCA2 mutation to an up to 85% lifetime risk for breast cancer and an up to 40% lifetime risk for ovarian cancer. It is crucial for individuals with HBOC to be identified to allow for proper screening, management, and identification of at-risk family members in order to reduce mortality. The National Comprehensive Cancer Network (NCCN) has established clinical guidelines for when to recommend BRCA1/2 testing. A retrospective chart review of 1123 M.D. Anderson Cancer Center breast cancer patients was performed in order to evaluate the positive predictive …

Impact Of Differentiation Status Of Kidney Progenitors In Wilms Tumor Development, Le Huang

Dissertations and Theses (Open Access)

Wilms tumor is one of the most common solid tumors in children. It is an embryonic cancer of the kidney and is thought to arise from undifferentiated renal mesenchyme. However, the differentiation status of cells in the mesenchyme that can give rise to Wilms tumors is unknown. Gene expression analysis of a large panel of Wilms tumor patients has identified different subsets of Wilms tumors that are distinct in their clinical outcomes and gene expression signatures. These subsets express specific genes that correspond to different stages of differentiation during renal development, suggesting that Wilms tumors may arise from transformed cells …

Characterization Of Putative Exbb And Exbd Leads To The Identification Of A Potential Tol-Pal System In Rhizobium Leguminosarum Atcc 14479, Valeria Barisic

Electronic Theses and Dissertations

Rhizobium leguminosarum is a Gram negative nitrogen-fixing soil bacterium. Due to the limited bioavailability of iron, bacteria utilize siderophores that scavenge and bind available iron. The transport of iron-siderophore complexes is achieved by the TonB-ExbB-ExbD complex. We have previously shown that a functional TonB protein is necessary for iron transport by creating ΔtonB mutants and assessing their growth and 55Fe-siderophore transport ability. We attempted to identify and characterize the roles of putative exbB and exbD genes using a similar approach. Growth curves and sequence analyses suggest putative exbB and exbD may be the tolpal-associated genes tolQ and tolR. Phenotypic and …