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Full-Text Articles in Genetics and Genomics

Evolutionary Interpretations Of Mycobacteriophage Biodiversity And Host-Range Through The Analysis Of Codon Usage Bias, Laura A. Esposito, Swati Gupta, Fraida Streiter, Ashley Prasad, John J. Dennehy Oct 2016

Evolutionary Interpretations Of Mycobacteriophage Biodiversity And Host-Range Through The Analysis Of Codon Usage Bias, Laura A. Esposito, Swati Gupta, Fraida Streiter, Ashley Prasad, John J. Dennehy

Publications and Research

In an genomics course sponsored by the Howard Hughes Medical Institute (HHMI), undergraduate students have isolated and sequenced the genomes of more than 1,150 mycobacteriophages, creating the largest database of sequenced bacteriophages able to infect a single host, Mycobacterium smegmatis, a soil bacterium. Genomic analysis indicates that these mycobacteriophages can be grouped into 26 clusters based on genetic similarity. These clusters span a continuum of genetic diversity, with extensive genomic mosaicism among phages in different clusters. However, little is known regarding the primary hosts of these mycobacteriophages in their natural habitats, nor of their broader host ranges. As such, it …


Nuclear Architecture And Patterns Of Molecular Evolution Are Correlated In The Ciliate Chilodonella Uncinata, Xyrus X. X. Maurer-Alcala, Laura A. Katz Apr 2016

Nuclear Architecture And Patterns Of Molecular Evolution Are Correlated In The Ciliate Chilodonella Uncinata, Xyrus X. X. Maurer-Alcala, Laura A. Katz

Biological Sciences: Faculty Publications

The relationship between nuclear architecture and patterns of molecular evolution in lineages across the eukaryotic tree of life is not well understood, partly because molecular evolution is traditionally explored as changes in base pairs along a linear sequence without considering the context of nuclear position of chromosomes. The ciliate Chilodonella uncinata is an ideal system to address the relationship between nuclear architecture and patterns of molecular evolution as the somatic macronucleus of this ciliate is composed of a peripheral DNA-rich area (orthomere) and a DNA-poor central region (paramere) to form a “heteromeric” macronucleus. Moreover, because the somatic chromosomes of C. …


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 May 2015

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 Jan 2015

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 …


Functional Implication Of The Trna Genes Encoded In The Chlorella Virus Pbcv-L Genome, Da Young Lee, Michael V. Graves, James L. Van Etten, Tae-Jin Choi Jan 2005

Functional Implication Of The Trna Genes Encoded In The Chlorella Virus Pbcv-L Genome, Da Young Lee, Michael V. Graves, James L. Van Etten, Tae-Jin Choi

James Van Etten Publications

The prototype Chlorella virus PBCV-l encodes 11 tRNA genes and over 350 protein-encoding genes in its 330 kbp genome. Initial attempts to overexpress the recombinant A189/192R protein, a putative virus attachment protein, in E. coli strain BL21(DE3) SI were unsuccessful, and multiple protein bands were detected on Western blots. However, the full-length A189/192R recombinant protein or fragments derived from it were detected when they were expressed in E. coli BL21 CodonPlus (DE3) RIL, which contains extra tRNAs. Codon usage analysis of the a1891192r gene showed highly biased usage of the AGA and AUA codons compared to genes encoded by E. …