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1. Student Attitudes Contribute to the Effectiveness of a Genomics CURE

Author

David Lopatto, Anne G. Rosenwald, Rebecca C. Burgess, Catherine Silver Key, Melanie Van Stry, Matthew Wawersik, Justin R. DiAngelo, Amy T. Hark, Matthew Skerritt, Anna K. Allen, Consuelo Alvarez, Sara Anderson, Cindy Arrigo, Andrew Arsham, Daron Barnard, James E. J. Bedard, Indrani Bose, John M. Braverman, Martin G. Burg, Paula Croonquist, Chunguang Du, Sondra Dubowsky, Heather Eisler, Matthew A. Escobar, Michael Foulk, Thomas Giarla, Rivka L. Glaser, Anya L. Goodman, Yuying Gosser, Adam Haberman, Charles Hauser, Shan Hays, Carina E. Howell, Jennifer Jemc, Christopher J. Jones, Lisa Kadlec, Jacob D. Kagey, Kimberly L. Keller, Jennifer Kennell, Adam J. Kleinschmit, Melissa Kleinschmit, Nighat P. Kokan, Olga Ruiz Kopp, Meg M. Laakso, Judith Leatherman, Lindsey J. Long, Mollie Manier, Juan C. Martinez-Cruzado, Luis F. Matos, Amie Jo McClellan, Gerard McNeil, Evan Merkhofer, Vida Mingo, Hemlata Mistry, Elizabeth Mitchell, Nathan T. Mortimer, Jennifer Leigh Myka, Alexis Nagengast, Paul Overvoorde, Don Paetkau, Leocadia Paliulis, Susan Parrish, Stephanie Toering Peters, Mary Lai Preuss, James V. Price, Nicholas A. Pullen, Catherine Reinke, Dennis Revie, Srebrenka Robic, Jennifer A. Roecklein-Canfield, Michael R. Rubin, Takrima Sadikot, Jamie Siders Sanford, Maria Santisteban, Kenneth Saville, Stephanie Schroeder, Christopher D. Shaffer, Karim A. Sharif, Diane E. Sklensky, Chiyedza Small, Sheryl Smith, Rebecca Spokony, Aparna Sreenivasan, Joyce Stamm, Rachel Sterne-Marr, Katherine C. Teeter, Justin Thackeray, Jeffrey S. Thompson, Norma Velazquez-Ulloa, Cindy Wolfe, James Youngblom, Brian Yowler, Leming Zhou, Janie Brennan, Jeremy Buhler, Wilson Leung, Sarah C. R. Elgin, and Laura K. Reed

Subjects
active learning, bioinformatics, CUREs, genomics, undergraduate education, Special aspects of education, LC8-6691, Biology (General), QH301-705.5
Abstract

ABSTRACT The Genomics Education Partnership (GEP) engages students in a course-based undergraduate research experience (CURE). To better understand the student attributes that support success in this CURE, we asked students about their attitudes using previously published scales that measure epistemic beliefs about work and science, interest in science, and grit. We found, in general, that the attitudes students bring with them into the classroom contribute to two outcome measures, namely, learning as assessed by a pre- and postquiz and perceived self-reported benefits. While the GEP CURE produces positive outcomes overall, the students with more positive attitudes toward science, particularly with respect to epistemic beliefs, showed greater gains. The findings indicate the importance of a student’s epistemic beliefs to achieving positive learning outcomes.

Published
2022
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2. Facilitating Growth through Frustration: Using Genomics Research in a Course-Based Undergraduate Research Experience

Author

David Lopatto, Anne G. Rosenwald, Justin R. DiAngelo, Amy T. Hark, Matthew Skerritt, Matthew Wawersik, Anna K. Allen, Consuelo Alvarez, Sara Anderson, Cindy Arrigo, Andrew Arsham, Daron Barnard, Christopher Bazinet, James E. J. Bedard, Indrani Bose, John M. Braverman, Martin G. Burg, Rebecca C. Burgess, Paula Croonquist, Chunguang Du, Sondra Dubowsky, Heather Eisler, Matthew A. Escobar, Michael Foulk, Emily Furbee, Thomas Giarla, Rivka L. Glaser, Anya L. Goodman, Yuying Gosser, Adam Haberman, Charles Hauser, Shan Hays, Carina E. Howell, Jennifer Jemc, M. Logan Johnson, Christopher J. Jones, Lisa Kadlec, Jacob D. Kagey, Kimberly L. Keller, Jennifer Kennell, S. Catherine Silver Key, Adam J. Kleinschmit, Melissa Kleinschmit, Nighat P. Kokan, Olga Ruiz Kopp, Meg M. Laakso, Judith Leatherman, Lindsey J. Long, Mollie Manier, Juan C. Martinez-Cruzado, Luis F. Matos, Amie Jo McClellan, Gerard McNeil, Evan Merkhofer, Vida Mingo, Hemlata Mistry, Elizabeth Mitchell, Nathan T. Mortimer, Debaditya Mukhopadhyay, Jennifer Leigh Myka, Alexis Nagengast, Paul Overvoorde, Don Paetkau, Leocadia Paliulis, Susan Parrish, Mary Lai Preuss, James V. Price, Nicholas A. Pullen, Catherine Reinke, Dennis Revie, Srebrenka Robic, Jennifer A. Roecklein-Canfield, Michael R. Rubin, Takrima Sadikot, Jamie Siders Sanford, Maria Santisteban, Kenneth Saville, Stephanie Schroeder, Christopher D. Shaffer, Karim A. Sharif, Diane E. Sklensky, Chiyedza Small, Mary Smith, Sheryl Smith, Rebecca Spokony, Aparna Sreenivasan, Joyce Stamm, Rachel Sterne-Marr, Katherine C. Teeter, Justin Thackeray, Jeffrey S. Thompson, Stephanie Toering Peters, Melanie Van Stry, Norma Velazquez-Ulloa, Cindy Wolfe, James Youngblom, Brian Yowler, Leming Zhou, Janie Brennan, Jeremy Buhler, Wilson Leung, Laura K. Reed, and Sarah C. R. Elgin

Subjects
Special aspects of education, LC8-6691, Biology (General), QH301-705.5
Abstract

A hallmark of the research experience is encountering difficulty and working through those challenges to achieve success. This ability is essential to being a successful scientist, but replicating such challenges in a teaching setting can be difficult. The Genomics Education Partnership (GEP) is a consortium of faculty who engage their students in a genomics Course-Based Undergraduate Research Experience (CURE). Students participate in genome annotation, generating gene models using multiple lines of experimental evidence. Our observations suggested that the students’ learning experience is continuous and recursive, frequently beginning with frustration but eventually leading to success as they come up with defendable gene models. In order to explore our “formative frustration” hypothesis, we gathered data from faculty via a survey, and from students via both a general survey and a set of student focus groups. Upon analyzing these data, we found that all three datasets mentioned frustration and struggle, as well as learning and better understanding of the scientific process. Bioinformatics projects are particularly well suited to the process of iteration and refinement because iterations can be performed quickly and are inexpensive in both time and money. Based on these findings, we suggest that a dynamic of “formative frustration” is an important aspect for a successful CURE.

Published
2020
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3. Student Attitudes Contribute to the Effectiveness of a Genomics CURE

Author

David Lopatto, Anne G. Rosenwald, Rebecca C. Burgess, Catherine Silver Key, Melanie Van Stry, Matthew Wawersik, Justin R. DiAngelo, Amy T. Hark, Matthew Skerritt, Anna K. Allen, Consuelo Alvarez, Sara Anderson, Cindy Arrigo, Andrew Arsham, Daron Barnard, James E. J. Bedard, Indrani Bose, John M. Braverman, Martin G. Burg, Paula Croonquist, Chunguang Du, Sondra Dubowsky, Heather Eisler, Matthew A. Escobar, Michael Foulk, Thomas Giarla, Rivka L. Glaser, Anya L. Goodman, Yuying Gosser, Adam Haberman, Charles Hauser, Shan Hays, Carina E. Howell, Jennifer Jemc, Christopher J. Jones, Lisa Kadlec, Jacob D. Kagey, Kimberly L. Keller, Jennifer Kennell, Adam J. Kleinschmit, Melissa Kleinschmit, Nighat P. Kokan, Olga Ruiz Kopp, Meg M. Laakso, Judith Leatherman, Lindsey J. Long, Mollie Manier, Juan C. Martinez-Cruzado, Luis F. Matos, Amie Jo McClellan, Gerard McNeil, Evan Merkhofer, Vida Mingo, Hemlata Mistry, Elizabeth Mitchell, Nathan T. Mortimer, Jennifer Leigh Myka, Alexis Nagengast, Paul Overvoorde, Don Paetkau, Leocadia Paliulis, Susan Parrish, Stephanie Toering Peters, Mary Lai Preuss, James V. Price, Nicholas A. Pullen, Catherine Reinke, Dennis Revie, Srebrenka Robic, Jennifer A. Roecklein-Canfield, Michael R. Rubin, Takrima Sadikot, Jamie Siders Sanford, Maria Santisteban, Kenneth Saville, Stephanie Schroeder, Christopher D. Shaffer, Karim A. Sharif, Diane E. Sklensky, Chiyedza Small, Sheryl Smith, Rebecca Spokony, Aparna Sreenivasan, Joyce Stamm, Rachel Sterne-Marr, Katherine C. Teeter, Justin Thackeray, Jeffrey S. Thompson, Norma Velazquez-Ulloa, Cindy Wolfe, James Youngblom, Brian Yowler, Leming Zhou, Janie Brennan, Jeremy Buhler, Wilson Leung, Sarah C. R. Elgin, and Laura K. Reed

Subjects
General Immunology and Microbiology, General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology, Education
Abstract

The Genomics Education Partnership (GEP) engages students in a course-based undergraduate research experience (CURE). To better understand the student attributes that support success in this CURE, we asked students about their attitudes using previously published scales that measure epistemic beliefs about work and science, interest in science, and grit. We found, in general, that the attitudes students bring with them into the classroom contribute to two outcome measures, namely, learning as assessed by a pre- and postquiz and perceived self-reported benefits. While the GEP CURE produces positive outcomes overall, the students with more positive attitudes toward science, particularly with respect to epistemic beliefs, showed greater gains. The findings indicate the importance of a student's epistemic beliefs to achieving positive learning outcomes.

Published
2021

4. Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

Author

Raechel Harnoto, Morgan C. Anderson, Amy Z. Xu, Heather Hedeen, Arnaldo J. Santiago-Sanabria, Brandy L. Hammond, Kenneth Saville, Ross D. Kooienga, Christopher Chesley, Robert W. Morris, Aubree T. Gillis, Brittney Offenbacker, Katherine C. Palozola, Trisha Tomkins, Nicole Yu, Matthew Kwong, Megan E. Aldrup, Jordan E. Kus, Chelsey Friedrichs, Kenneth Stapleton, Carly E. Pelchen, Norma Chamma, Joshua F. Machone, Danielle Kulich, Andre Kennedy, Matt J. Crowley, Daniel Broomfield, Adeola Adebayo, Nicolas Ragland, Shady Messiah, Jonathan Misch, Meghan B. Rooney, Eva N. Rubio-Marrero, Will Sherrill, Joyce Stamm, Rachel R. Leads, Lindsey Shantzer, Alexis J. Scott, Andrew W. Waggoner, Kristen M. Cooper, Adam Haberman, Carmen A. Watchinski, Marcos A. Perez, Lisa Kadlec, Kiara N. Medina-Ortega, Kayla Chapman, Cheryl Bailey, Nicholas Fazzio, Insun Chong, Lasse Schmidt, Darla M. Balthaser, Megan DeShetler, Jien Shim, Anna Rogers, Chris Uitvlugt, Bryan Yarrington, Ruth A. Howe, Andrea Ochoa, Gregory J. Mullen, Young Lu Kim, Olivia L Knowles, Kevin M. Levine, Matthew M. Villerot, Thomas J. Rose, Jonathan E. Smith, Sukhjit Kaur, Roshni Patel, Olivia Plante, Tenzin Choeying, Jennifer R. Ramthun, Tiffany Y. Y. Choi, Michael Rahimi, Guzal Khayrullina, Lauren R. Boudreaux, James E. J. Bedard, Brian A. Dow, Christopher A. Louie, Kenneth S. Smith, Joannee Zumkehr, Marcus Gostelow, Melissa A. Tache, Tiffany Dai, Joan D. Zambrana-Burgos, Lauren R. Meyer, Carter Brown, Adam Brown, Travis Lamb, Carissa Belella, Hannah Gilman, David DuPuis, Ramón E. Rivera-Vicéns, Priyanka Naik, Anna L. Shipman, Jad El-Adaimi, Eric Spencer, Jonathan D. Marra, Melissa D. Patao, Sharon Ibarra, Jiayu Zhang, Ashley Vetor, Bobbi Botsford, Jenifer Winters, Nelson A. Valentín-Feliciano, Lauren M. Robinson, Christopher R. Macchi, Jennifer Hernández-Muñiz, E. Gloria C. Regisford, Jaelyn L. Johnson, Cory M. Dauphin, Tezin A. Walji, Matthew A. Zaborowicz, Stacey Winkler, Shannon M. Lowell, Marly R. McCracken, Andrew Adams, Lindsay A. Spaeder, Matthew W. Wolski, Adrese Kandahari, Fabiola Robles-Juarbe, Bryce A. Turner, Ángel L. Laboy-Corales, David T. Watson, Elaine J. Durchholz, Vanessa Rodriguez, Emily J. Teepe, Alaina C. Conturso, Eric Nyabeta Onsarigo, Tijana Martinov, Rohit Venkat, Charles R. Hauser, Priya Srikanth, Marwan Ibrahem, Karl E. Smith, Jessica M. Tucci, Ethan J. Brock, Aparna Sreenivasan, Jasmine Hales, Brianna K. Barnard, Andrew P. Stein, Jessica G. Thomas, Mallory Perella, Lorraine Rodriguez-Bonilla, Shekerah Primus, Zachary D. Moore, Caitlin M. Ament, Amber N. Hare, Brad Pamnani, Eugenia A. Soliterman, Christina Paluskievicz, Yashira M. Valentín-Feliciano, Alexandra K. Eckardt, Anya Goodman, Joseph W. Noynaert, Ashlee G. Johnson, Tyneshia C. P. Henry, Camille D. Ratliff, Ian O. Chase, Michel A. Conn, Jessica Koehler, Daniela Martiniuc, Allison J. Schepers, Megan B. Vylonis, Chrystel Dol, William Dirkes, Michelle S. Rivera-Llovet, Susana Rodríguez-Santiago, Heather L. Eisler, Mary L. Preuss, Daymon Peterson, Martin G. Burg, Aaditya Khatri, John R. Woytanowski, Holly Schiedermayer, Dara Cohn, Leah E Waldman, William M. Morris, Sharon C. Ehret, Marianna Defendini-Ávila, Jessica Fese, Suzette M. Arias-Mejias, Anna Kammrath, William D. Barshop, Edwin G. Ramírez-Aponte, Luis A. Jimenez, Carolina Marques dos Santos Vieira, Cody D. Kern, Francheska M. Delgado-Peraza, Tiffany Wan, Janice L. Krumm, Osagie Ighile, Eric D. Sassu, Jess M. Darusz, Laura Rodela, Daniel S. Nicolas, Shubha Govind, Mary Miller, Joseph E Marcus, Jason Pollack, Rostislav Castillo, Daniel Coomes, Matthew J. Borr, Diana Pérez-Afanador, Lucas A. Watson, Hannah C. Koaches, Amber Quintana, Faith H. Kung, Cameron B. Harris, Bridget M. Janssen, Cristina Zambrana-Echevarría, Jennifer K. Jones, Ian Dobbe, Benjamin M. Lewis, Lena N. Lupey, Julia A. Hilbrands, Cristina Montero Diez, Jorge L. Santiago-Ortiz, Dustin S. Woyski, Sandy D. Mach, Joseph Perez-Otero, Karim A. Sharif, Carlos Mendoza, John D. Fitzgibbons, Nelson H. Knudsen, Christy MacKinnon, Hayley M. Faber, Kwabea Agbley, Michelle Heslop, Olivia Cyrankowski, Priscilla Rodriguez, Melissa Jones, Jean M. Strelitz, Ryan A. Grove, Rachel A Greenstein, Michael Murillo, Elizabeth Greiner-Sosanko, Ciani Jean Sparks, Darryl McFarland, Franca G. Rossi, Heran Gebreyesus, Chris Kay, Danielle Ladzekpo, Chris Harward, Jordan S. Christie, Consuelo J. Alvarez, Elaine V. Morlock, Geoff Scott, Kelsey Hockenberger, Sepo Musokotwane, Adam Fearnow, Lauren J. Keny, Alaina J. Grantham, Evangelina Reza, Mike Colgan, Melanie K. Regan, Stephanie J. Potocny, Sasha L. Dorsett, Tara Skorupa, Valerie M. Gónzalez-Pérez, Vinayak S. Nikam, Anne C. Meier, Varun Sundaram, Helen B. Rankin, Andrew B. Nylander, Mariela Gines-Rosario, Laurell MacMillian, Jeannette M. Osterloh, Robert H. Allen, Melanie A. Smith, Sarah J. Spencer, Cheri M. Ackerman, Jeffrey L. Poet, Amanda J. Hay, Isaac O. Armistead, Laura K. Reed, Don W. Paetkau, Bib Yang, Enid M. Quintana-Torres, Kathryn L. Golden, Lauren A. DiLorenzo, Alen Ramic, Mark T. LeBlanc, Carl J. Minniti, Robert J. Bailey, Kristen M. Thomsen, Ashley L. Adams, Chad A. Koplinsky, Eliezer O. Perez-Colomba, Nicole A. Howey, Katie A. TerMeer, Stephanie Intriago, Christina N. Kufel, Mary Waters, Bo Liu, Thomas J. Bahr, Ashley R. Miller, Claire Pattison, Morgan R. Light, Amy T. Hark, Jennifer S. Doty, Catherine M. Mageeney, Adam J. Ronk, Nadezhda Fefelova, Andrew R. Armstrong, Maida Chen, Elizabeth Macias, Kim M. Chau, Paul Bilinski, Trevor G. Floyd, Cassidy T. Lee, Jenna C. Tenney, Bob Gardner, Patricia Ortiz-Ortiz, Elizabeth S. Jewell, Gabi Lucas, Brandon Lee, Jenifer N. Jarrell, Jimmy Hsiang-Chun Chang, Lorraine Malkowitz, Ulises Marrero-Llerena, Gabriel Stancu, Matthew R. Unzicker, Andrea P. Burgos-Bula, Michelle L. Miller, Elisandra Rivera, Kate Bagaeva, Jessica W. Polk, Jordan E. Carney, Maureen Corrielus, Jana Nietmann, Jeff Howenstein, Elizabeth Kiernan, Sabya A. Rauf, Brandon M. Katz, Elizabeth C. Nordman, Devon Shallman, Eric M. Clark, Lenin Lopez, Karen J. Kraftmann, Leslie Guadron, Julia Kuhn, Allison R. Schneiter, Satish C. Bhalla, Emily J. Howell, Blair Undem, Jeffrey S. Thompson, Arelys Flores-Vazquez, John Kiley, Cody M. Morrow, Joseline Serrano-González, John Mark Knepper, Christopher Beck, Calise Debow, Anna L. Smith, Angelica Garcia, Shelbi Christgen, Shadie Emiah, Tammy Mazur, Rachel E. VanDyken, Frank R. Soto delValle, Zachary Nichols, William R. Kennedy, Ameer Zidan, Douglas A. Herrick, Thomas Q. Xu, Elizabeth Shoop, Jessica A. Kampmeier, John M. Kerber, Caitlin Pozmanter, Emily L. Hong, Frederic J. Deuschle, Allyson B. Rivard, William Neutzling, Joseph V. Moran, Benjamin K. Johnson, Jacob Jipp, Shannon R. McCartha, Abby Vrable, Z. Goodwin, Suchita Rastogi, Alyssa M. Newman, Lionel Ortiz-Fuentes, Arjun A. Anilkumar, Bryan M. Hennessy, Hui-Min Chung, Katie L. Goeller, Carlos E. Santos-Ramos, Adam Dillman, Christine D. Wilson, Sarah J. Peacock, Andrew J. Kim, Carol I. Morales-Caraballo, Briana Brinkley, Justin Alldredge, Rebecca Krock, Kristen C. Davis, David Dunbar, Joshua L. Manghelli, Erica K. Earl, Katherine Gavinski, Sheryl T. Smith, Portia Mason, Lindsay J. Hoogenboom, Jessen T. Havill, Sonya G. Méndez-Castellanos, Darrin T. Schultz, Katherine J. Faber, Allison O’Rouke, Emily G. Miller, Yara Ashrawi, Curtiss E. Lane, Saryleine Ortiz-DeChoudens, Michael W. Sandusky, Andrew Montgomery, Rita Kabaso, Todd Aronhalt, Jonathan D. Foust, Jorge Ruiz, Eric Helmreich, Todd T. Eckdahl, Charlotte Lea, Kevin Coulson, Kristin M. French, Kate A. Woodard, Brandon J. Burkhart, Kylie McNeil, Curtis R. Edwards, Jimmy Ma, Darcie D. Elder, Tia DiTommaso, Nicholaus Monsma, Sarah A. Jelgerhuis, Stephanie J. Adams, Nichole Rigby, Heather L. Holderness, Charlotte Williams, Megan Donegan, Taylor S. Harding, Javier O. Martinez-Rodriguez, Sandeep Venkataram, Tiffany Wong, Anika Toorie, Jenny L. Rose, Ashley S. Brown, Sarah A. Popelka, Matthew Williams, Julie Bryant, Sarah C. R. Elgin, Sonali Kumar, Joshua Burkhardt, William J. Puetz, Erica L. Alvendia, Richard A. Tumminello, Kesley Parry, Joshua R. Smith, Ashley F. Custer, Carlos E. Ortiz, Yedda Li, April E. Bednarski, Simon Ng, Max Mandelbaum, Arlene J. Hoogewerf, Chelsea A. Walker, Ryan S. Lee, Jeannette Wong, Isabella Theresa Felzer-Kim, Harrison Friedman, Megan Bourland, Luis R. Colón-Cruz, Lucy Liu, Nicole C. Olson, Yi Ren, Adam P Lousararian, José M. Cruz-García, Charlie Manchee, Kyle Zoll, Kristina M. Stemler, Juliana Belén-Rodríguez, Ashley S. Timko, Jane Lopilato, England Raimey, Amy D. Melton, Joshua D. Forsyth, Christopher D. Savell, Himabindu Reddy, Alica B. Allen, Amanda Maffa, Daniel W. Cassidy, Luciann Bracero-Quiñones, Eric Lemmon, Justina R. Bartling, Bradley J. Ogden, Petros Svoronos, Mary Spratt, Lisa Sudmeier, Héctor A. Martell-Martínez, James F. Geary, Bridget J. Sessions, Christopher Campana, Kaitlyn A. Downey, Seth G. Dawson, Daniella Menillo, Casey Hanson, James M. Bellush, Justin A. Gonzales, Roy Song, Karvyn Torchon, Betsy Hoover, Michael Closser, Lacey Neufeld, Micah Shelton, Benjamin R. Does, Juan Carlos Martínez-Cruzado, Jordan S. Baumgardner, Nicole Chichearo, Mary T. Reilly, Colleen V. Kelley, Monica Yalamanchili, Dawn Lau, Abbie Morgan, Alyssa Cifelli, Milton R. Herrold, Ambreen Khan, James Messler, Kyle Westphal, James L. Kehoe, Juliana A. Wurzler, Garrett Salzman, Tracy Wang, Charlene Emerson, Lyndsey A. Reynolds, Alysha Moretti, Marita K. Abrams, Mara G. Cole, Michael B. Schultz, Samantha Cruz, Natalie Ngai, Nadia Safa, Vicente Velasquez, Ashley Townsend, Jonathan L. Crooke-Rosado, Amber M. Gygi, Ishwar S. Gill, Christopher McLaughlin, Dorianmarie Vargas-Franco, Alissa Beckett, Samantha Vue, Nadine L. Rossi, Justina Chinwong, Ryan Michael Rempe, Trip Freeburg, Amy J. Johnson, Omolara Glenn, Jade Lea Rekai, Hashini Gunasinghe, Vivienne Echendu, Marshall Strother, Morgan Baker, Christopher D. Smith, Paolo A. DaSilva, Noelle Delacruz, Tiara Tirasawasdichai, Yakov Shevin, Wilfried Guiblet, Shane M. Patao, Peterson R. Cullimore, Giancarlo F. Garbagnati, Adam E. Musick, Sarah C. Butzler, Jonathan D. Presley, Ana I. Correa-Muller, Christopher D. Shaffer, Chunguang Du, Ryan D. Mitchell, Jonathan P. Rennhack, Barbara L. Hopkins, Mary E. Shaw, Jessica E. Hill, Jeremy N. Wong, Anna Kim, Christopher B. Khoury, Julia Chapman, Amanda T. Mercer, Jessica A. Shuen, Joyce H. Lau, I.N. Falk, Sunil Rathore, Christopher J. Jones, Laura Simone Bisogno, Nighat P. Kokan, Paul Yenerall, Amber L. Price, Kelsey T. Bushhouse, Stephen L. McDaniel, Andrew P. Drake, Johnathan D. English, Sampson K. Boham, Robert A. Herbstsomer, Daniel S. Fosselman, Kevin Babilonia-Figueroa, Matthew Simon, Anne G. Rosenwald, Bryan J. Rupley, Heather Cohen, Victoria Scala, Avery B. Cromwell, Christopher E. Blunden, Yelena P. Davis, William B. Armstrong, Kristine Ostby, Joanna Haye, Lauren M. Wysocki, Lena Christiansen, Allison A. Throm, Sarah Flohr, Matthew Wawersik, Rebecca J. Cotteleer, Kristen R Ramirez, Dontae A. Jacobs, Sarah Woehlke, Gregory S. Messenger, Soham Aso, Nicole Clarke-Medley, Bryant R. Swanson, Lindsay K. Brouwer, S. Catherine Silver Key, Stephanie Zarrasola, Michael S. Salgado, Dong K. Rhee, Mai Abdelnabi, Eve VanEck, Jeremy Buhler, Sarah Kong, Turner Conrad, Jennifer Roecklein-Canfield, Marykathryn Tynon, Brian J. Maniaci, Alexa M. McDonough, Ivan G. Llavona-Cartagena, J. Devin Spencer, Todd D. Johnson, Azita Bashiri, Kimberley Ramsey, Mike Polen, Hien P Nguyen, Seantay D. Patterson, Lucia Wande, Nicholas U. Schwartz, Han Yuan, Albeliz Santiago-Colón, Joseph Medina, Samuel Thomas Crowley, Emma Shoemaker, Alex J. Feliciano-Cancela, Alexander J. Kujawski, Lillyann Asencio-Zayas, Gentry L. Pickett, Matt J. Randazzo, Erica Stagaard, Kristin M. LaForge, Gabriela A. Llaurador-Caraballo, Anastasia K. Yemelyanova, Alan Tseng, Erika E. Menyes, Julie Azarewicz, Christa Burke, Samuel I. Smith, Nazanin Ghavam, Carolina Gomez, Cameron Fick, Anthony Pinto, Lindsay Rios, Gary A Kuleck, Ashley Rich, Kayla A. Florian, Martin N. Cheramie, Yuki Kwan Wa Shum, Atlee Baker, LaJerald Augustine, Alyson Greenwell, Rasleen K. Saluja, Jason S. Macias, Wesley W. Winn, Samantha M. Schmuecker, Michelle E. M. Eisen, Pedro Benitez, Jeanette Hauke, Nora C. Goscinski, Justin R. DiAngelo, Carter T. Docking, David D. Xiong, Brittany D. Pasierb, Matt Van Camp, Yin Zheng, Nikie L. McCabe, Emily Reed, Katie Homa, Kimberly S. Kolibas, Elizabeth A. Karaska, Grace A. Dougherty, John P. Fanning, Michael Fasano, Joseph E. Sable, Robert W. Schulz, San Francisco Nguyen, Michael L. Rojas-Vargas, Kierstin L. Naylor, Emily Peoples, Jessica Neely, Lejla Cesko, Brionna D. Davis-Reyes, Roxanne Banker, Amanda K. Tilot, Jordan P. Brand, William H. Newhart, Lauriaun Johnson, Michelle M. Giddens, Nicole B. Clark, Anant Agarwalla, Thomas F. Minton, Dana W. Brooks, Amanda D. Garrett, Bethany M. Klett, Kristin M. Starkey, Antoinette E. Fafara-Thompson, Michael R. Rubin, Jonathon M. Benson, Erica Enoch, Amanda M. Damsteegt, Zackary W. Scott, Elisabeth A. Kelly, Jason M. Barnett, Wilson Leung, Luke J. Rodriguez-Giron, Krishna C. Mudumbi, Francis J. May, Nadyan M. Vargas-Barreto, Geeta Statton, José L. Torres-Castillo, Sarah Hirsch, Rachel M. Reem, Linghui Li, Deirdre Robinett, Jason Caronna, Abneris E. Rodríguez-Laboy, Samantha Lawrence, Katherine R. Reynolds, Corinne Weeks, Allison M. Sterling, Chun Leung Ng, Roman E. Ramirez, Daron C. Barnard, Leming Zhou, Eric P. Spana, John A. Toth, Alvin Lu, Krizia C. Menéndez-Serrano, Jonathan M. Heckman, Ben Chlebina, Matthew C. Fadus, Helmet T. Karim, Shailly Gaur, Timothy R. Jelsema, Nicholas Keysock, Thomas J. Carr, Zach Fusco, Evan M. Verbofsky, Monal Naik, Amanda H. Flores, Kristin A. Knouse, Olga R. Kopp, Elizabeth Feenstra, Edward P. Sweeney, Christen Johnson, Justin Crawford, Damian Urick, Victor W. Mullen, Carrie A. Dunham, Gabriella A. DeMichele, Mengyang Sun, William Harrington, Jessica M. Bodenberg, Xavier A. Collado-Méndez, T. Aaron Wiles, Michelle K. Powers, Phillip J. Minnick, Lourdes N. Irizarry-González, Valeria Silva, Steven Ovu, Nik Kolba, Peter Lindbeck, Jerome M. Molleston, Ifeanyi Obiorah, David Carranza, Lauren R. Beck, Alina M. Tamayo-Figueroa, Elaine R. Mardis, Rachel N. Lippert, Ingrid T. Rivera-Pagán, Mahdi Soos, Trung T. Nguyen, Megan Martinez, Van Kim, Benjamin L. Danner, Randall J. DeJong, Melissa M. Trieu, Andrea M. Senquiz-Gonzalez, Mary Grace Schueler, Emily E. Magnuson, Lesley E. Jackson, Hendrick Pagán-Torres, Fareed Sanusi, Dana Koenig, Vidya Chandrasekaran, Chinmoy I. Bhatiya, Dongyeon Kim, Paul J. Overvoorde, Reece Watson, Jennifer Schottler, Devry Lin, Jim Youngblom, Taylor Schauder, Nigel Madden, Isabel Valdez, Thomas John Reynolds, Kelly M. Deranek, Anne A. Welker, Jackie X. White, Nicole C. Riddle, Jacob Pfeil, Aldo Heredia-Negrón, Christine Langner, Tao Jian He, Jonathan P. Mecoli, Lissett Mayorga, Scott Chiang, Rishi Singhal, Julia C. Peairs, Michael Quach, Anne M. Eime, GiNell Elliott, Meleah J. Gross, Melissa Drewry, Julia A. Emerson, Anthony K. Lambright, Isaac Appiah, Gregory M. Robertson, Nathaniel Regenold, Philip Pham, George Odisho, Alexi Archambault, Matthew Dothager, Shana M. Baldassari, Paul J. Lee, Callie R. Merry, Jesse R. Farek, Archana Tare, Srebrenka Robic, William Vernon, Tam Vuong, Bethany Grace Bonifield, Katrina Thistle, Rose M. Dowd, Noor Tazudeen, Jennifer Weaver, Manpreet Kaur, Nicole M. Caesar, Yi Zhang, Michael C. Cristostomo, Albert Tzeng, Kayla Vondy, Emily Perling, Ramiro A. Chavez, Lanor S. Horton, Matt Kroll, Levent H. Beken, Justin R. Starcher, Sam Asinof, Nathalia M. Cruz, Eunice George, Adam T. Morrow, Heather Milnthorp, Cheryl Mazzeo, Kristen R. Hatfield, Anna L. Boudoures, Ashley A. Tewilliager, Edna P. Tascón-Peñaranda, Vilma F. Huerta, Sarah Tuberty, Mallory A. Williams, Rachel E. Weber, Sarah Spencer, Emily C. Leatherman, Yuying Gosser, Steve DeFazio, Patrick Ng, Jeri Sparks, Pavan Bhat, Mindy E. Bower, Jordan E. Matthews, Cyrus E. Kuschner, Anne Bertolet, Matt Kusner, Thomas C. Giarla, Jessica Penn, Gerard P. McNeil, Mariam Meghdari, Michael J. Wolyniak, Matthew Juergens, Karla I. Velázquez-Soto, Maria Kaisler, Jeanine Schibler, Alexis Nagengast, Susan Parrish, Frances Marín-Maldonado, Shiv Mohini, Jessica King, Danny Mammo, Katherine S. Harker, Allyson P. Hawkins, Kelly Drumm, Jennifer A. Lammers, Allyson P Mallya, Ashley Bryant, Katie Weihbrecht, Pete Wendland, Gabriela V. Bernal-Vega, Nestor A. Gutierrez, Armando G. Bermudez-Capo, Luke R. Salbert, Kirk Haltaufderhyde, Michelle L. Kappes, Mary A. Smith, York Chen, Miguel Vélez-Vázquez, Brittany E. Plescher, Francis D. Beauchamp-Pérez, Alyssa Ward, Andrea N. Clary, Don Foret, Mitchell J McDonald, Mariela Colon-Vazquez, Amanda L. Blaker, Hao Yang, James Z. Liu, Austin B. Limle, Henry Huang, Luis Vilanova-Velez, Edgar Garibay, Philip J. Freda, Laura L. Mays Hoopes, Maureen S. Hammond, Marian M. Kaehler, Rebecca Shuford, Ray Sunjed, Cynthia K. Hanson, Marielle VanderVennen, Idaliz M. Martínez-Traverso, Jack Y. Yu, Spencer L. Franchi, Michael Snavely, John E. Anderson, Lainey S. Rubin, Kelly K. Jones, Stephanie F. Mel, Stacey Lytle, Danny L. Tran, Chelsea R. Barberi, Max Mian Liu, Eric A. Nollet, Sarah E. Muller, Diana Norton, John M. Braverman, Thu A. Phan, Nelson Membreno, Colin Khoshabian, John Gooch, Cassandra Kubricky, Priscila M. Rodríguez-García, Anna Wylie, Diana L. E. Johnson, Anna K. Unruh, Deborah Hammett, Jon Sarezky, Marie Brown, Carolina Riascos-Cuero, Emily J. Diekema, Emmy E. Ogawa, Miranda Chavez, Zuzana Kocsisova, Dennis Revie, Anniken M. Lydon, Peter A. Cognetti, Ashley A. Collins, Tariq Abusheikh, Erin K. Luippold, Kevin Myirski, Brian O. Rodríguez-Echevarría, Haley J. Plasman, Lara Baatenburg, Jesse Hendriksma, Christopher R. Knob, Max Semon, Cassandra Farrar, Xiao Zhu, Ali Dobbe, Marie-Isabelle B. Seydoux, Griffin Sadovsky, Shreya Prasad, Victoria Newcomb, Chad Gier, Dmitri Serjanov, Jules Wellinghoff, Maxwell T. Smith-Gee, and Alexandra H. Scoma

Subjects
Transposable element, Codon Adaptation Index, Euchromatin, Heterochromatin, transposons, evolution of heterochromatin, Investigations, Genome, Evolution, Molecular, 03 medical and health sciences, gene size, 0302 clinical medicine, melting characteristics, Species Specificity, codon bias, Genetics, Animals, Drosophila Proteins, Selection, Genetic, Codon, Molecular Biology, Genetics (clinical), 030304 developmental biology, Polytene Chromosomes, Repetitive Sequences, Nucleic Acid, Gene Rearrangement, 0303 health sciences, biology, Computational Biology, Molecular Sequence Annotation, Gene rearrangement, Exons, Genomics, biology.organism_classification, Introns, Drosophila melanogaster, Codon usage bias, DNA Transposable Elements, Drosophila, 030217 neurology & neurosurgery
Abstract

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 larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.

Published
2015

5. A Course-Based Research Experience: How Benefits Change with Increased Investment in Instructional Time

Author

Juan Carlos Martínez-Cruzado, Gary A Kuleck, Shubha Govind, Christopher D. Smith, Judith Leatherman, Jeffrey S. Thompson, Daron C. Barnard, Christopher J. Jones, Paul J. Overvoorde, Matthew Wawersik, Amy Frary, Randall J. DeJong, Dale L. Beach, Todd T. Eckdahl, Laura L. Mays Hoopes, Marian M. Kaehler, David Lopatto, Justin R. DiAngelo, Michael R. Rubin, Mary A. Smith, Carina E. Howell, Donald R. Frohlich, Chunguang Du, Leming Zhou, Eric P. Spana, Stephanie F. Mel, John M. Braverman, Karim A. Sharif, Consuelo J. Alvarez, Gary R. Skuse, Cheryl Bailey, Anya Goodman, Kari Clase, Laura K. Reed, Anne G. Rosenwald, Don W. Paetkau, James E. J. Bedard, Mary L. Preuss, Gerard P. McNeil, Michael J. Wolyniak, Martin G. Burg, Lisa Kadlec, Alexis Nagengast, Susan Parrish, Hemlata Mistry, Hui-Min Chung, Joyce Stamm, April E. Bednarski, Sheryl T. Smith, Aparna Sreenivasan, Paul Szauter, Celeste Peterson, Stephanie Schroeder, Nighat P. Kokan, Satish C. Bhalla, Arlene J. Hoogewerf, Heather L. Eisler, Christy MacKinnon, Mary Spratt, Christopher Bazinet, Amy T. Hark, Wilson Leung, Olga R. Kopp, Diana S Johnson, Elaine R. Mardis, Mary E. Shaw, Catherine Reinke, David Dunbar, Yuying Gosser, Jane Lopilato, Vidya Chandrasekaran, Srebrenka Robic, Sarah C. R. Elgin, Kenneth Saville, Adam Haberman, Dennis Revie, Christopher D. Shaffer, Jennifer Roecklein-Canfield, Julia A. Emerson, Adam Kleinschmit, Jeremy Buhler, Charles R. Hauser, James J. Youngblom, S. Catherine Silver Key, and O'Dowd, Diane K

Subjects
Value (ethics), Program evaluation, Time Factors, General Biochemistry, Genetics and Molecular Biology, Information science, Education, Surveys and Questionnaires, Mathematics education, ComputingMilieux_COMPUTERSANDEDUCATION, Humans, Learning, Cooperative Behavior, Curriculum, Biology, Mathematics, Data collection, Genome, Data Collection, Research, Molecular Sequence Annotation, Articles, Genomics, Investment (macroeconomics), Faculty, Research Personnel, Variety (cybernetics), Knowledge, Undergraduate research, Attitude, Self Report, Curriculum and Pedagogy, Program Evaluation
Abstract

While course-based research in genomics can generate both knowledge gains and a greater appreciation for how science is done, a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. Nonetheless, this is a very cost-effective way to reach larger numbers of students., There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit.

Published
2014
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6. EFRI-REM at CCNY: Research experience and mentoring for underrepresented groups in cross-disciplinary research on assistive technology

Author

Yuying Gosser, Camille Santistevan, Yingli Tian, Edgardo Molina, Zhigang Zhu, Wai L. Khoo, Hao Tang, and Tony Ro

Subjects
Medical education, Research program, Academic year, Multimedia, Cross disciplinary, 05 social sciences, 02 engineering and technology, Research opportunities, computer.software_genre, 050105 experimental psychology, ComputingMilieux_GENERAL, Multidisciplinary approach, Assistive technology, ComputingMilieux_COMPUTERSANDEDUCATION, 0202 electrical engineering, electronic engineering, information engineering, 020201 artificial intelligence & image processing, 0501 psychology and cognitive sciences, Community college, Psychology, computer, Career development
Abstract

We have successfully run the NSF EFRI-REM program at The City College of The City University of New York (CUNY) for four years (2012 to 2015) with over 50 research participants (RPs), most of whom are from underrepresented groups, particularly individuals who are disabled, women, veterans and minorities. Each year we started with an 8 to 10-week summer research program and then mentored the participants' education and career paths in the following academic year. We have not only provided exciting cross-disciplinary, student initiated research opportunities in human and machine vision research and applications in assisting visually impaired people, but also shaped an innovative model to support career development of high school students, community and senior college students, graduate students (mentors), high school teachers, as well as community college professors. The EFRI-REM program provides a novel and effective platform to allow more underrepresented students in the greater NYC area to participate in our multidisciplinary research.

Published
2016
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7. The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

Author

E. Gloria C. Regisford, Jeremy Buhler, Christopher D. Smith, Cheryl Bailey, Laura L. Mays Hoopes, Marian M. Kaehler, Anne G. Rosenwald, Elizabeth Shoop, Satish C. Bhalla, Yuying Gosser, Mary Shaw, Donald R. Frohlich, Gary A Kuleck, Gerard P. McNeil, Barbara A. Wilson, Joyce Stamm, Daron C. Barnard, Alexis Nagengast, Susan Parrish, Stephanie Schroeder, Jeffrey S. Thompson, Jennifer Leigh Myka, Consuelo J. Alvarez, Chitra Chandrasekaran, Christopher D. Shaffer, Robert W. Morris, Jim Youngblom, Paul J. Overvoorde, Mary Spratt, Diana L. E. Johnson, Todd T. Eckdahl, Charles R. Hauser, Vidya Chandrasekaran, Christopher J. Jones, David Lopatto, Kelynne E. Reed, Mary A. Smith, Robert Moss, Gary R. Skuse, Anya Goodman, Sarah C. R. Elgin, Wilson Leung, Olga R. Kopp, Nighat P. Kokan, Chunguang Du, Jeff L Poet, Elaine R. Mardis, Dennis Revie, Matthew Wawersik, Ken Saville, Douglas R Dorer, Hui-Min Chung, and Eric P. Spana

Subjects
Genetic Research, Universities, Genomics, Science education, General Biochemistry, Genetics and Molecular Biology, Education, 03 medical and health sciences, Annotation, Pedagogy, ComputingMilieux_COMPUTERSANDEDUCATION, Animals, Students, Curriculum, 030304 developmental biology, 0303 health sciences, Medical education, 4. Education, 05 social sciences, Educational technology, 050301 education, Articles, Faculty, ComputingMethodologies_PATTERNRECOGNITION, Undergraduate research, General partnership, Active learning, Laboratories, 0503 education
Abstract

Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre- and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students.

Published
2010

8. Towards Structural Genomics of RNA: Rapid NMR Resonance Assignment and Simultaneous RNA Tertiary Structure Determination Using Residual Dipolar Couplings

Author

Andrey Gorin, Yuying Gosser, Ananya Majumdar, Dinshaw J. Patel, and Hashim M. Al-Hashimi

Subjects
Base Sequence, Sequence Analysis, RNA, Chemistry, Nucleic acid tertiary structure, RNA Conformation, RNA, Hydrogen Bonding, Context (language use), Genome, Viral, Genomics, Crystallography, X-Ray, Resonance (particle physics), Structural genomics, Ribonomics, Crystallography, Structural Biology, Residual dipolar coupling, HIV-1, Nucleic Acid Conformation, RNA, Viral, Nuclear Magnetic Resonance, Biomolecular, Molecular Biology, HIV Long Terminal Repeat
Abstract

We report a new residual dipolar couplings (RDCs) based NMR procedure for rapidly determining RNA tertiary structure demonstrated on a uniformly (15)N/(13)C-labeled 27 nt variant of the trans-activation response element (TAR) RNA from HIV-I. In this procedure, the time-consuming nuclear Overhauser enhancement (NOE)-based sequential assignment step is replaced by a fully automated RDC-based assignment strategy. This approach involves examination of all allowed sequence-specific resonance assignment permutations for best-fit agreement between measured RDCs and coordinates for sub-structures in a target RNA. Using idealized A-form geometries to model Watson-Crick helices and coordinates from a previous X-ray structure to model a hairpin loop in TAR, the best-fit RDC assignment solutions are determined very rapidly (

Published
2002
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9. Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings 1 1Edited by M. F. Summers

Author

Andrey Gorin, Yuying Gosser, Dinshaw J. Patel, Weidong Hu, Hashim M. Al-Hashimi, and Ananya Majumdar

Subjects
Chemistry, Dynamics (mechanics), Human immunodeficiency virus (HIV), RNA, Tar, medicine.disease_cause, Residual, Protein tertiary structure, Dipole, Crystallography, Structural Biology, Bound state, medicine, Molecular Biology
Abstract

Ground-state dynamics in RNA is a critical precursor for structural adaptation observed ubiquitously in protein-RNA recognition. A tertiary conformational analysis of the stem-loop structural element in the transactivation response element (TAR) from human immunodeficiency virus type 1 (HIV-I) RNA is presented using recently introduced NMR methods that rely on the measurement of residual dipolar couplings (RDC) in partially oriented systems. Order matrix analysis of RDC data provides evidence for inter-helical motions that are of amplitude 46(±4) °, of random directional character, and that are executed about an average conformation with an inter-helical angle between 44 ° and 54 °. The generated ensemble of TAR conformations have different organizations of functional groups responsible for interaction with the trans-activator protein Tat, including conformations similar to the previously characterized bound-state conformation. These results demonstrate the utility of RDC-NMR for simultaneously characterizing RNA tertiary dynamics and average conformation, and indicate an avenue for TAR complex formation involving tertiary structure capture.

Published
2002
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10. [Untitled]

Author

Weijun Xu, Weidong Hu, Yuying Gosser, Ronnie Frederick, Thomas Hermann, Dinshaw J. Patel, Ananya Majumdar, and Feng Jiang

Subjects
chemistry.chemical_classification, Oligonucleotide, Stereochemistry, viruses, RNA, Peptide, Peptide binding, Nuclear magnetic resonance spectroscopy, Biochemistry, Uridine, chemistry.chemical_compound, Crystallography, Protein structure, chemistry, Structural Biology, Genetics, Peptide sequence
Abstract

We have used NMR spectroscopy to determine the solution structure of a complex between an oligonucleotide derived from stem IIB of the Rev responsive element (RRE-IIB) of HIV-1 mRNA and an in vivo selected, high affinity binding Arg-rich peptide. The peptide binds in a partially alpha-helical conformation into a pocket within the RNA deep groove. Comparison with the structure of a complex between an alpha-helical Rev peptide and RRE-IIB reveals that the sequence of the bound peptide determines the local conformation of the RRE peptide binding site. A conformational switch of an unpaired uridine base was revealed; this points out into the solvent in the Rev peptide complex, but it is stabilized inside the RNA deep groove by stacking with an Arg side chain in the selected peptide complex. The conformational switch has been visualized by NMR chemical shift mapping of the uridine H5/H6 atoms during a competition experiment in which Rev peptide was displaced from RRE-IIB by the higher affinity binding selected peptide.

Published
2001
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11. [Untitled]

Author

Yuying Gosser, Weijun Xu, Dinshaw J. Patel, and Weidong Hu

Subjects
chemistry.chemical_classification, Base (chemistry), Proton, Pyrimidine, Chemical shift, RNA, Biochemistry, Isotopes of nitrogen, Crystallography, chemistry.chemical_compound, Magnetization, Nuclear magnetic resonance, chemistry, Ribose, Spectroscopy
Abstract

Multiple-quantum 2D and 3D bi-directional HCNCH experiments are presented for the correlation of base and ribose protons/carbons in 13C/15N labeled HIV-1 TAR RNA. In both 2D and 3D experiments, the magnetization of H1′ is transferred to H6/H8 and H1′ through H1′-C1′-N1/9-C6/8-H6/8 and H1′-C1′-N1/9-C1′-H1′ pathways, and the magnetization of H6/8 is transferred to H1′ and H6/8 through H6/8-C6/8-N1/9-C1′-H1′ and H6/8-C6/8-N1/9-C6/8-H6/8 pathways. Chemical shifts of four different nuclei (H1′, C1′, C6/8 and H6/8) are sampled in the 2D experiment. The correlation of base and ribose protons/carbons is established by the rectangular arrangement of crossover and out-and-back peaks in the proton/carbon correlated spectrum. The rectangular connections can be further resolved using the nitrogen dimension in a 1H/13C/15N 3D experiment. Furthermore, by taking advantage of the well separated chemical shifts of N1 (pyrimidine) and N9 (purine), the 2D spectrum can be simplified into two sub-spectra based on their base type. Both experiments were tested on a 13C/15N labeled 27-mer HIV-1 TAR RNA containing a UUCG hairpin loop.

Published
2001
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12. [Untitled]

Author

Ananya Majumdar, Yuying Gosser, and Dinshaw J. Patel

Subjects
chemistry.chemical_classification, Base pair, Stereochemistry, Hydrogen bond, RNA, Pulse sequence, Peptide, Biochemistry, Acceptor, chemistry.chemical_compound, Nuclear magnetic resonance, chemistry, Nucleic acid, Spectroscopy, DNA
Abstract

In 2HJNN-COSY experiments, which correlate protons with donor/acceptor nitrogens across Nd•••HNa bonds, the receptor nitrogen needs to be assigned in order to unambiguously identify the hydrogen bond. For many situations this is a non-trivial task which is further complicated by poor dispersion of (Na,Nd) resonances. To address these problems, we present pulse sequences to obtain direct, internucleotide correlations between protons in uniformly 13C/15N labeled nucleic acids containing Nd•••HNa hydrogen bonds. Specifically, the pulse sequence H2(N1N3)H3 correlates H2(A,ω1):H3(U,ω2) protons across Watson–Crick A–U and mismatched G•A base pairs, the sequences H5(N3N1)H1/H6(N3N1)H1 correlate H5(C,ω1)/H6(C,ω1):H1(G,ω2) protons across Watson–Crick G-C base pairs, and the H2(N2N7)H8 sequence correlates NH2(G,A,C;ω1):H8(G,A;ω2) protons across G•G, A•A, sheared G•A and other mismatch pairs. These 1H-1H connectivities circumvent the need for independent assignment of the donor/acceptor nitrogen and related degeneracy issues associated with poorly dispersed nitrogen resonances. The methodology is demonstrated on uniformly 13C/15N labeled samples of (a) an RNA regulatory element involving the HIV-1 TAR RNA fragment, (b) a multi-stranded DNA architecture involving a G•(C-A) triad-containing G-quadruplex and (c) a peptide-RNA complex involving an evolved peptide bound to the HIV-1 Rev response element (RRE) RNA fragment.

Published
2001
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13. Sensitivity-Enhanced MQ–HCN–CCH–TOCSY and MQ–HCN–CCH–COSY Pulse Schemes for 13C/15N Labeled RNA Oligonucleotides

Author

Yuying Gosser, Licong Jiang, and Weidong Hu

Subjects
Purine, chemistry.chemical_classification, Carbon Isotopes, Nuclear and High Energy Physics, Oligoribonucleotides, Nitrogen Isotopes, Pyrimidine, Chemistry, Oligonucleotide, Stereochemistry, Aptamer, Biophysics, Resonance, RNA, Peptide, Image Enhancement, Condensed Matter Physics, Sensitivity and Specificity, Biochemistry, chemistry.chemical_compound, Nuclear magnetic resonance, Ribose, Nuclear Magnetic Resonance, Biomolecular
Abstract

Sensitivity enhanced multiple-quantum 3D HCN–CCH–TOCSY and HCN–CCH–COSY experiments are presented for the ribose resonance assignment of 13 C/ 15 N-labeled RNA sample. The experiments make use of the chemical shift dispersion of N1/N9 of pyrimidine/purine to distinguish the ribose spin systems. They provide a complementary approach for the assignment of ribose resonance to the currently used HCCH–COSY and HCCH–TOCSY type experiments in which either 13 C or 1 H is utilized to separate the different ribose spin systems. The pulse schemes have been demonstrated on a 23-mer 13 C/ 15 N-labeled RNA aptamer complexed with neomycin and tested on a 32-mer RNA complexed with a 23-residue peptide.

Published
2000
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14. A central support system can facilitate implementation and sustainability of a Classroom-based Undergraduate Research Experience (CURE) in Genomics

Author

Lisa Kadlec, Vidya Chandrasekaran, Michael R. Rubin, Aparna Sreenivasan, Srebrenka Robic, David Dunbar, Christopher D. Shaffer, Amy Frary, Sarah C. R. Elgin, Charles R. Hauser, Gerard P. McNeil, Michael J. Wolyniak, Jane Lopilato, Shubha Govind, Chunguang Du, Gary A Kuleck, Martin G. Burg, Justin R. DiAngelo, Julia A. Emerson, Jennifer A Roecklien-Canfield, Kenneth Saville, Adam Haberman, Alexis Nagengast, Susan Parrish, David Lopatto, James J. Youngblom, Wilson Leung, Laura D Reed, Nighat P. Kokan, Olga R. Kopp, Amy T. Hark, Arlene J. Hoogewerf, Mary Spratt, Yuying Gosser, Elaine R. Mardis, James E. J. Bedard, John M. Braverman, April E. Bednarski, Christy MacKinnon, Karim A. Sharif, Christopher D. Smith, Diana L. E. Johnson, Satish C. Bhalla, Marian M. Kaehler, Daron C. Barnard, Jeremy Buhler, Donald R. Frohlich, S. Catherine Silver Key, Randall J. DeJong, Stephanie F. Mel, Paul J. Overvoorde, Consuelo J. Alvarez, Jeffrey S. Thompson, Don W. Paetkau, Dennis Revie, Mary A. Smith, Mary Shaw, Todd T. Eckdahl, Joyce Stamm, Hui-Min Chung, Juan Carlos Martínez-Cruzado, Christopher J. Jones, Gary R. Skuse, Anya Goodman, Mary L. Preuss, Leming Zhou, Eric P. Spana, Anne G. Rosenwald, Matthew Wawersik, Jennifer Mary Threlfall, Stephanie Schroeder, Sheryl T. Smith, E. Gloria C. Regisford, and Dolan, Erin

Subjects
Value (ethics), Models, Educational, Universities, Genomics, Articles, General Biochemistry, Genetics and Molecular Biology, United States, Education, Incentive, Undergraduate research, Models, Clinical Research, General partnership, Pedagogy, Sustainability, ComputingMilieux_COMPUTERSANDEDUCATION, Curriculum development, Engineering ethics, Educational, Curriculum, Program Development, Curriculum and Pedagogy
Abstract

There have been numerous calls to engage students in science as science is done. A survey of 90-plus faculty members explores barriers and incentives when developing a research-based genomics course. The results indicate that a central core supporting a national experiment can help overcome local obstacles., In their 2012 report, the President's Council of Advisors on Science and Technology advocated “replacing standard science laboratory courses with discovery-based research courses”—a challenging proposition that presents practical and pedagogical difficulties. In this paper, we describe our collective experiences working with the Genomics Education Partnership, a nationwide faculty consortium that aims to provide undergraduates with a research experience in genomics through a scheduled course (a classroom-based undergraduate research experience, or CURE). We examine the common barriers encountered in implementing a CURE, program elements of most value to faculty, ways in which a shared core support system can help, and the incentives for and rewards of establishing a CURE on our diverse campuses. While some of the barriers and rewards are specific to a research project utilizing a genomics approach, other lessons learned should be broadly applicable. We find that a central system that supports a shared investigation can mitigate some shortfalls in campus infrastructure (such as time for new curriculum development, availability of IT services) and provides collegial support for change. Our findings should be useful for designing similar supportive programs to facilitate change in the way we teach science for undergraduates.

Published
2014
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15. C-terminal binding domain of Rho GDP-dissociation inhibitor directs N-terminal inhibitory peptide to GTPases

Author

Behzad Aghazadeh, Michael K. Rosen, Danny Manor, Tyzoon K. Nomanbhoy, Richard A. Cerione, Yuying Gosser, and Carolyn Combs

Subjects
Models, Molecular, Protein Folding, Magnetic Resonance Spectroscopy, GTP', Protein Conformation, Molecular Sequence Data, Protein Prenylation, Cell Cycle Proteins, GTPase, CDC42, Guanosine Diphosphate, Protein Structure, Secondary, GTP Phosphohydrolases, GTP-Binding Proteins, Animals, Humans, rho-Specific Guanine Nucleotide Dissociation Inhibitors, ortho-Aminobenzoates, Nucleotide, Amino Acid Sequence, Guanine Nucleotide Dissociation Inhibitors, cdc42 GTP-Binding Protein, Saccharomyces cerevisiae, rho Guanine Nucleotide Dissociation Inhibitor alpha, chemistry.chemical_classification, Multidisciplinary, Chemistry, dGTPase, Hydrogen Bonding, Guanosine nucleotide dissociation inhibitors, Protein Structure, Tertiary, Molecular Weight, Biochemistry, Biophysics, Thermodynamics, Cattle, Sequence Alignment, Protein Binding, Binding domain
Abstract

The Rho GDP-dissociation inhibitors (GDIs) negatively regulate Rho-family GTPases1,2. The inhibitory activity of GDI derives both from an ability to bind the carboxy-terminal isoprene of Rho family members and extract them from membranes3,4, and from inhibition of GTPase cycling between the GTP- and GDP-bound states4,5. Here we demonstrate that these binding and inhibitory functions of rhoGDI can be attributed to two structurally distinct regions of the protein. A carboxy-terminal folded domain of relative molecular mass 16,000 (Mr 16K) binds strongly to the Rho-family member Cdc42, yet has little effect on the rate of nucleotide dissociation from the GTPase. The solution structure of this domain shows a β-sandwich motif with a narrow hydrophobic cleft that binds isoprenes, and an exposed surface that interacts with the protein portion of Cdc42. The amino-terminal region of rhoGDI is unstructured in the absence of target and contributes little to binding, but is necessary to inhibit nucleotide dissociation from Cdc42. These results lead to a model of rhoGDI function in which the carboxy-terminal binding domain targets the amino-terminal inhibitory region to GTPases, resulting in membrane extraction and inhibition of nucleotide cycling.

Published
1997
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16. Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings

Author

Hashim M, Al-Hashimi, Yuying, Gosser, Andrey, Gorin, Weidong, Hu, Ananya, Majumdar, and Dinshaw J, Patel

Subjects
Models, Molecular, Motion, Gene Products, tat, Static Electricity, HIV-1, Nucleic Acid Conformation, RNA, Viral, RNA-Binding Proteins, tat Gene Products, Human Immunodeficiency Virus, Nuclear Magnetic Resonance, Biomolecular, HIV Long Terminal Repeat, Protein Binding
Abstract

Ground-state dynamics in RNA is a critical precursor for structural adaptation observed ubiquitously in protein-RNA recognition. A tertiary conformational analysis of the stem-loop structural element in the transactivation response element (TAR) from human immunodeficiency virus type 1 (HIV-I) RNA is presented using recently introduced NMR methods that rely on the measurement of residual dipolar couplings (RDC) in partially oriented systems. Order matrix analysis of RDC data provides evidence for inter-helical motions that are of amplitude 46(+/-4) degrees, of random directional character, and that are executed about an average conformation with an inter-helical angle between 44 degrees and 54 degrees. The generated ensemble of TAR conformations have different organizations of functional groups responsible for interaction with the trans-activator protein Tat, including conformations similar to the previously characterized bound-state conformation. These results demonstrate the utility of RDC-NMR for simultaneously characterizing RNA tertiary dynamics and average conformation, and indicate an avenue for TAR complex formation involving tertiary structure capture.

Published
2002

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