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1. Introduction and Spread of Dengue Virus 3, Florida, USA, May 2022-April 2023

Author

Jones, Forrest K., Morrison, Andrea M., Santiago, Gilberto A., Rysava, Kristyna, Zimler, Rebecca A., Heberlein, Lea A., Kopp, Edgar, Team, Florida Department of Health Bureau of Public Health Laboratory, Saunders, Katharine E., Baudin, Samantha, Rico, Edhelene, Mejia-Echeverri, Alvaro, Taylor-Salmon, Emma, Hill, Verity, Breban, Mallery I., Vogels, Chantal B.F., Grubaugh, Nathan D., Paul, Lauren M., Michael, Scott F., Johansson, Michael A., Adams, Laura E., Munoz-Jordan, Jorge, Paz-Bailey, Gabriela, and Stanek, Danielle R.

Subjects
United States. Centers for Disease Control and Prevention, Genomics -- Health aspects, Infection -- Health aspects, Travelers -- Health aspects, Dengue viruses -- Health aspects, Health
Abstract

Dengue virus (DENV) is not endemic in the continental United States (1); most cases occur among travelers to DENV-endemic areas (2). In Florida, USA, DENV infections are primarily reported among [...]

Published
2024
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2. Instructional Models for Course-Based Research Experience (CRE) Teaching

Author

Hanauer, David I, Graham, Mark J, Arnold, Rachel J, Ayuk, Mary A, Balish, Mitchell F, Beyer, Andrea R, Butela, Kristen A, Byrum, Christine A, Chia, Catherine P, Chung, Hui-Min, Clase, Kari L, Conant, Stephanie, Coomans, Roy J, D’Elia, Tom, Diaz, Jason, Diaz, Arturo, Doty, Jean A, Edgington, Nicholas P, Edwards, Dustin C, Eivazova, Elvira, Emmons, Christine B, Fast, Kayla M, Fisher, Emily J, Fleischacker, Christine L, Frederick, Gregory D, Freise, Amanda C, Gainey, Maria D, Gissendanner, Chris R, Golebiewska, Urszula P, Guild, Nancy A, Hendrickson, Heather L, Herren, Christopher D, Hopson-Fernandes, Margaret S, Hughes, Lee E, Jacobs-Sera, Deborah, Johnson, Allison A, Kirkpatrick, Bridgette L, Klyczek, Karen K, Koga, Ann P, Kotturi, Hari, LeBlanc-Straceski, Janine, Lee-Soety, Julia Y, Leonard, Justin E, Mastropaolo, Matthew D, Merkhofer, Evan C, Michael, Scott F, Mitchell, Jon C, Mohan, Swarna, Monti, Denise L, Noutsos, Christos, Nsa, Imade Y, Peters, Nick T, Plymale, Ruth, Pollenz, Richard S, Porter, Megan L, Rinehart, Claire A, Rosas-Acosta, German, Ross, Joseph F, Rubin, Michael R, Scherer, Anne E, Schroeder, Stephanie C, Shaffer, Christopher D, Sprenkle, Amy B, Sunnen, C Nicole, Swerdlow, Sarah J, Tobiason, Deborah, Tolsma, Sara S, Tsourkas, Philippos K, Ward, Robert E, Ware, Vassie C, Warner, Marcie H, Washington, Jacqueline M, Westover, Kristi M, White, Simon J, Whitefleet-Smith, JoAnn L, Williams, Daniel C, Wolyniak, Michael J, Zeilstra-Ryalls, Jill H, Asai, David J, Hatfull, Graham F, and Sivanathan, Viknesh

Subjects
Curriculum and Pedagogy, Education Systems, Education, Quality Education, Engineering, Faculty, Humans, Mathematics, Models, Educational, Students, Teaching, Curriculum and pedagogy
Abstract

The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: 1) being a scientist and generating data; 2) teaching procedural knowledge; and 3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching.

Published
2022

3. Instructional Models for Course-Based Research Experience (CRE) Teaching

Author

Hanauer, David I., Graham, Mark J., Arnold, Rachel J., Ayuk, Mary A., Balish, Mitchell F., Beyer, Andrea R., Butela, Kristen A., Byrum, Christine A., Chia, Catherine P., Chung, Hui-Min, Clase, Kari L., Conant, Stephanie, Coomans, Roy J., D'Elia, Tom, Diaz, Jason, Diaz, Arturo, Doty, Jean A., Edgington, Nicholas P., Edwards, Dustin C., Eivazova, Elvira, Emmons, Christine B., Fast, Kayla M., Fisher, Emily J., Fleischacker, Christine L., Frederick, Gregory D., Freise, Amanda C., Gainey, Maria D., Gissendanner, Chris R., Golebiewska, Urszula P., Guild, Nancy A., Hendrickson, Heather L., Herren, Christopher D., Hopson-Fernandes, Margaret S., Hughes, Lee E., Jacobs-Sera, Deborah, Johnson, Allison A., Kirkpatrick, Bridgette L., Klyczek, Karen K., Koga, Ann P., Kotturi, Hari, LeBlanc-Straceski, Janine, Lee-Soety, Julia Y., Leonard, Justin E., Mastropaolo, Matthew D., Merkhofer, Evan C., Michael, Scott F., Mitchell, Jon C., Mohan, Swarna, Monti, Denise L., Noutsos, Christos, Nsa, Imade Y., Peters, Nick T., Plymale, Ruth, Pollenz, Richard S., Porter, Megan L., Rinehart, Claire A., Rosas-Acosta, German, Ross, Joseph F., Rubin, Michael R., Scherer, Anne E., Schroeder, Stephanie C., Shaffer, Christopher D., Sprenkle, Amy B., Sunnen, C. Nicole, Swerdlow, Sarah J., Tobiason, Deborah, Tolsma, Sara S., Tsourkas, Philippos K., Ward, Robert E., Ware, Vassie C., Warner, Marcie H., Washington, Jacqueline M., Westover, Kristi M., White, Simon J., Whitefleet-Smith, JoAnn L., Williams, Daniel C., Wolyniak, Michael J., Zeilstra-Ryalls, Jill H., Asai, David J., Hatfull, Graham F., and Sivanathan, Viknesh

Abstract

The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: (1) being a scientist and generating data; (2) teaching procedural knowledge; and (3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching.

Published
2022
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4. DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus

Author

Vogels, Chantal B. F., Hill, Verity, Breban, Mallery I., Chaguza, Chrispin, Paul, Lauren M., Sodeinde, Afeez, Taylor-Salmon, Emma, Ott, Isabel M., Petrone, Mary E., Dijk, Dennis, Jonges, Marcel, Welkers, Matthijs R. A., Locksmith, Timothy, Dong, Yibo, Tarigopula, Namratha, Tekin, Omer, Schmedes, Sarah, Bunch, Sylvia, Cano, Natalia, Jaber, Rayah, Panzera, Charles, Stryker, Ian, Vergara, Julieta, Zimler, Rebecca, Kopp, Edgar, Heberlein, Lea, Herzog, Kaylee S., Fauver, Joseph R., Morrison, Andrea M., Michael, Scott F., and Grubaugh, Nathan D.

Published
2024
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5. Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean

Author

Taylor-Salmon, Emma, Hill, Verity, Paul, Lauren M., Koch, Robert T., Breban, Mallery I., Chaguza, Chrispin, Sodeinde, Afeez, Warren, Joshua L., Bunch, Sylvia, Cano, Natalia, Cone, Marshall, Eysoldt, Sarah, Garcia, Alezaundra, Gilles, Nicadia, Hagy, Andrew, Heberlein, Lea, Jaber, Rayah, Kassens, Elizabeth, Colarusso, Pamela, Davis, Amanda, Baudin, Samantha, Rico, Edhelene, Mejía-Echeverri, Álvaro, Scott, Blake, Stanek, Danielle, Zimler, Rebecca, Muñoz-Jordán, Jorge L., Santiago, Gilberto A., Adams, Laura E., Paz-Bailey, Gabriela, Spillane, Melanie, Katebi, Volha, Paulino-Ramírez, Robert, Mueses, Sayira, Peguero, Armando, Sánchez, Nelissa, Norman, Francesca F., Galán, Juan-Carlos, Huits, Ralph, Hamer, Davidson H., Vogels, Chantal B. F., Morrison, Andrea, Michael, Scott F., and Grubaugh, Nathan D.

Published
2024
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6. Models of classroom assessment for course-based research experiences

Author

Hanauer, David I., primary, Zhang, Tong, additional, Graham, Mark J., additional, Adams, Sandra D., additional, Ahumada-Santos, Yesmi Patricia, additional, Alvey, Richard M., additional, Antunes, Mauricio S., additional, Ayuk, Mary A., additional, Elena Báez-Flores, María, additional, Bancroft, Christa T., additional, Bates, Tonya C., additional, Bechman, Meghan J., additional, Behr, Elizabeth, additional, Beyer, Andrea R., additional, Bortz, Rebecca L., additional, Bowder, Dane M., additional, Briggs, Laura A., additional, Brown-Kennerly, Victoria, additional, Buckholt, Michael A., additional, Bullock, Sharon K., additional, Butela, Kristen A., additional, Byrum, Christine A., additional, Caruso, Steven M., additional, Chia, Catherine P., additional, Chong, Rebecca A., additional, Chung, Hui-Min, additional, Clase, Kari L., additional, Coleman, Sean T., additional, Parks Collins, D., additional, Conant, Stephanie B., additional, Condon, Brett M., additional, Connerly, Pamela L., additional, Connors, Bernadette J., additional, Cook-Easterwood, Jennifer E., additional, Crump, Katie E., additional, D’Elia, Tom, additional, Dennis, Megan K., additional, DeVeaux, Linda C., additional, Diacovich, Lautaro, additional, Duffy, Iain, additional, Edgington, Nicholas P., additional, Edwards, Dustin C., additional, Egwuatu, Tenny O. G., additional, Eivazova, Elvira R., additional, Fallest-Strobl, Patricia C., additional, Fillman, Christy L., additional, Findley, Ann M., additional, Fisher, Emily, additional, Fisher, Matthew R., additional, Fogarty, Marie P., additional, Freise, Amanda C., additional, Frost, Victoria J., additional, Gainey, Maria D., additional, Garcia Costas, Amaya M., additional, Garza, Atenea A., additional, Gavin, Hannah E., additional, Ghittoni, Raffaella, additional, Gibb, Bryan, additional, Golebiewska, Urszula P., additional, Grinath, Anna S., additional, Gurney, Susan M. R., additional, Hare, Rebekah F., additional, Heninger, Steven G., additional, Hinz, John M., additional, Hughes, Lee E., additional, Jayachandran, Pradeepa, additional, Johnson, Kristen C., additional, Johnson, Allison A., additional, Kanther, Michelle, additional, Kenna, Margaret, additional, Kirkpatrick, Bridgette L., additional, Klyczek, Karen K., additional, Kohl, Kathryn P., additional, Kuchka, Michael, additional, LaPeruta, Amber J., additional, Lee-Soety, Julia Y., additional, Lewis, Lynn O., additional, Lindberg, Heather M., additional, Madden, Jaclyn A., additional, Markov, Sergei A., additional, Mastropaolo, Matthew D., additional, Mathur, Vinayak, additional, McClory, Sean P., additional, Merkhofer, Evan C., additional, Merkle, Julie A., additional, Michael, Scott F., additional, Mitchell, Jon C., additional, Molloy, Sally D., additional, Monti, Denise L., additional, Mussi, María Alejandra, additional, Nance, Holly, additional, Nieto-Fernandez, Fernando E., additional, Nissen, Jillian C., additional, Nsa, Imade Y., additional, O’Donnell, Mary G., additional, Page, Shallee T., additional, Panagakis, Andrea, additional, Parra-Unda, Jesús Ricardo, additional, Pelletier, Tara A., additional, Perez Morales, Tiara G., additional, Peters, Nick T., additional, Phuntumart, Vipaporn, additional, Pollenz, Richard S., additional, Preuss, Mary L., additional, Puthoff, David P., additional, Raifu, Muideen K., additional, Reyna, Nathan S., additional, Rinehart, Claire A., additional, Rocheleau, Jessica M., additional, Rossier, Ombeline, additional, Rudner, Adam D., additional, Rueschhoff, Elizabeth E., additional, Ryan, Amy, additional, Saha, Sanghamitra, additional, Shaffer, Christopher D., additional, Smith, Mary Ann V., additional, Sprenkle, Amy B., additional, Strong, Christy L., additional, Sunnen, C. Nicole, additional, Tarbox, Brian P., additional, Temple, Louise, additional, Thoemke, Kara R., additional, Thomas, Michael A., additional, Tobiason, Deborah M., additional, Tolsma, Sara S., additional, Garcia, Julie Torruellas, additional, Valentine, Megan S., additional, Vazquez, Edwin, additional, Ward, Robert E., additional, Ward, Catherine M., additional, Ware, Vassie C., additional, Warner, Marcie H., additional, Washington, Jacqueline M., additional, Westholm, Daniel E., additional, Wheaton, Keith A., additional, Wilkes, Beth M., additional, Williams, Elizabeth C., additional, Biederman, William H., additional, Cresawn, Steven G., additional, Heller, Danielle M., additional, Jacobs-Sera, Deborah, additional, Hatfull, Graham F., additional, Asai, David J., additional, and Sivanathan, Viknesh, additional

Published
2023
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7. Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean

Author

Taylor-Salmon, Emma, primary, Hill, Verity, additional, Paul, Lauren M., additional, Koch, Robert T., additional, Breban, Mallery I., additional, Chaguza, Chrispin, additional, Sodeinde, Afeez, additional, Warren, Joshua L., additional, Bunch, Sylvia, additional, Cano, Natalia, additional, Cone, Marshall, additional, Eysoldt, Sarah, additional, Garcia, Alezaundra, additional, Gilles, Nicadia, additional, Hagy, Andrew, additional, Heberlein, Lea, additional, Jaber, Rayah, additional, Kassens, Elizabeth, additional, Colarusso, Pamela, additional, Davis, Amanda, additional, Baudin, Samantha, additional, Rico, Edhelene, additional, Mejia-Echeverri, Alvaro, additional, Scott, Blake, additional, Stanek, Danielle, additional, Zimler, Rebecca, additional, Munoz-Jordan, Jorge L., additional, Santiago, Gilberto A., additional, Adams, Laura E., additional, Paz-Bailey, Gabriela, additional, Spillane, Melanie, additional, Katebi, Volha, additional, Paulino-Ramirez, Robert, additional, Mueses, Sayira, additional, Peguero, Armando, additional, Sanchez, Nelissa, additional, Norman, Francesca F., additional, Galan, Juan-Carlos Galan, additional, Huits, Ralph Huits, additional, Hamer, Davidison H., additional, Vogels, Chantal B.F., additional, Morrison, Andrea Morrison, additional, Michael, Scott F., additional, and Grubaugh, Nathan D., additional

Published
2023
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9. DengueSeq: A pan-serotype whole genome amplicon sequencing protocol for dengue virus

Author

Vogels, Chantal B.F., primary, Hill, Verity, additional, Breban, Mallery I., additional, Chaguza, Chrispin, additional, Paul, Lauren M., additional, Sodeinde, Afeez, additional, Taylor-Salmon, Emma, additional, Ott, Isabel M., additional, Petrone, Mary E., additional, Dijk, Dennis, additional, Jonges, Marcel, additional, Welkers, Matthijs R.A., additional, Locksmith, Timothy, additional, Dong, Yibo, additional, Tarigopula, Namratha, additional, Tekin, Omer, additional, Schmedes, Sarah, additional, Bunch, Sylvia, additional, Cano, Natalia, additional, Jaber, Rayah, additional, Panzera, Charles, additional, Stryker, Ian, additional, Vergara, Julieta, additional, Zimler, Rebecca, additional, Kopp, Edgar, additional, Heberlein, Lea, additional, Morrison, Andrea M., additional, Michael, Scott F., additional, and Grubaugh, Nathan D., additional

Published
2023
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10. Field-deployable viral diagnostics using CRISPR-Cas13

Author

Myhrvold, Cameron, Freije, Catherine A., Gootenberg, Jonathan S., Abudayyeh, Omar O., Metsky, Hayden C., Durbin, Ann F., Kellner, Max J., Tan, Amanda L., Paul, Lauren M., Parham, Leda A., Garcia, Kimberly F., Barnes, Kayla G., Chak, Bridget, Mondini, Adriano, Nogueira, Mauricio L., Isern, Sharon, Michael, Scott F., Lorenzana, Ivette, Yozwiak, Nathan L., MacInnis, Bronwyn L., Bosch, Irene, Gehrke, Lee, Zhang, Feng, and Sabeti, Pardis C.

Published
2018

11. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

Author

Grubaugh, Nathan D., Gangavarapu, Karthik, Quick, Joshua, Matteson, Nathaniel L., De Jesus, Jaqueline Goes, Main, Bradley J., Tan, Amanda L., Paul, Lauren M., Brackney, Doug E., Grewal, Saran, Gurfield, Nikos, Van Rompay, Koen K. A., Isern, Sharon, Michael, Scott F., Coffey, Lark L., Loman, Nicholas J., and Andersen, Kristian G.

Published
2019
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16. Design Principles of Lipid-like Ionic Liquids for Gene Delivery

Author

Siegel, David J., primary, Anderson, Grace I., additional, Paul, Lauren M., additional, Seibert, Philipp J., additional, Hillesheim, Patrick C., additional, Sheng, Yinghong, additional, Zeller, Matthias, additional, Taubert, Andreas, additional, Werner, Peter, additional, Balischewski, Christian, additional, Michael, Scott F., additional, and Mirjafari, Arsalan, additional

Published
2021
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20. Zika virus evolution and spread in the Americas

Author

Metsky, Hayden C., Matranga, Christian B., Wohl, Shirlee, Schaffner, Stephen F., Freije, Catherine A., Winnicki, Sarah M., West, Kendra, Qu, James, Baniecki, Mary Lynn, Gladden-Young, Adrianne, Lin, Aaron E., Tomkins-Tinch, Christopher H., Ye, Simon H., Park, Daniel J., Luo, Cynthia Y., Barnes, Kayla G., Shah, Rickey R., Chak, Bridget, Barbosa-Lima, Giselle, Delatorre, Edson, Vieira, Yasmine R., Paul, Lauren M., Tan, Amanda L., Barcellona, Carolyn M., Porcelli, Mario C., Vasquez, Chalmers, Cannons, Andrew C., Cone, Marshall R., Hogan, Kelly N., Kopp, Edgar W., Anzinger, Joshua J., Garcia, Kimberly F., Parham, Leda A., Ramrez, Rosa M. Glvez, Montoya, Maria C. Miranda, Rojas, Diana P., Brown, Catherine M., Hennigan, Scott, Sabina, Brandon, Scotland, Sarah, Gangavarapu, Karthik, Grubaugh, Nathan D., Oliveira, Glenn, Robles-Sikisaka, Refugio, Rambaut, Andrew, Gehrke, Lee, Smole, Sandra, Halloran, M. Elizabeth, Villar, Luis, Mattar, Salim, Lorenzana, Ivette, Cerbino-Neto, Jose, Valim, Clarissa, Degrave, Wim, Bozza, Patricia T., Gnirke, Andreas, Andersen, Kristian G., Isern, Sharon, Michael, Scott F., Bozza, Fernando A., Souza, Thiago M. L., Bosch, Irene, Yozwiak, Nathan L., MacInnis, Bronwyn L., and Sabeti, Pardis C.

Subjects
America -- Health aspects, Zika virus -- Natural history, Zika virus infection -- Distribution, Company distribution practices, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Hayden C. Metsky [1, 2]; Christian B. Matranga [1]; Shirlee Wohl [1, 3]; Stephen F. Schaffner [1, 3, 4]; Catherine A. Freije [1, 3]; Sarah M. Winnicki [1]; Kendra [...]

Published
2017
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21. Genomic epidemiology reveals multiple introductions of Zika virus into the United States

Author

Grubaugh, Nathan D., Ladner, Jason T., Kraemer, Moritz U. G., Dudas, Gytis, Tan, Amanda L., Gangavarapu, Karthik, Wiley, Michael R., White, Stephen, Thz, Julien, Magnani, Diogo M., Prieto, Karla, Reyes, Daniel, Bingham, Andrea M., Paul, Lauren M., Robles-Sikisaka, Refugio, Oliveira, Glenn, Pronty, Darryl, Barcellona, Carolyn M., Metsky, Hayden C., Baniecki, Mary Lynn, Barnes, Kayla G., Chak, Bridget, Freije, Catherine A., Gladden-Young, Adrianne, Gnirke, Andreas, Luo, Cynthia, MacInnis, Bronwyn, Matranga, Christian B., Park, Daniel J., Qu, James, Schaffner, Stephen F., Tomkins-Tinch, Christopher, West, Kendra L., Winnicki, Sarah M., Wohl, Shirlee, Yozwiak, Nathan L., Quick, Joshua, Fauver, Joseph R., Khan, Kamran, Brent, Shannon E., Reiner, Robert C., Jr, Lichtenberger, Paola N., Ricciardi, Michael J., Bailey, Varian K., Watkins, David I., Cone, Marshall R., Kopp, Edgar W., IV, Hogan, Kelly N., Cannons, Andrew C., Jean, Reynald, Monaghan, Andrew J., Garry, Robert F., Loman, Nicholas J., Faria, Nuno R., Porcelli, Mario C., Vasquez, Chalmers, Nagle, Elyse R., Cummings, Derek A. T., Stanek, Danielle, Rambaut, Andrew, Sanchez-Lockhart, Mariano, Sabeti, Pardis C., Gillis, Leah D., Michael, Scott F., Bedford, Trevor, Pybus, Oliver G., Isern, Sharon, Palacios, Gustavo, and Andersen, Kristian G.

Subjects
Zika virus -- Health aspects -- Genetic aspects, Gene expression -- Health aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Nathan D. Grubaugh [1]; Jason T. Ladner [2]; Moritz U. G. Kraemer [3, 4, 5]; Gytis Dudas [6]; Amanda L. Tan [7]; Karthik Gangavarapu [1]; Michael R. Wiley [2, [...]

Published
2017
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24. Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic

Author

Grubaugh, Nathan D., primary, Saraf, Sharada, additional, Gangavarapu, Karthik, additional, Watts, Alexander, additional, Tan, Amanda L., additional, Oidtman, Rachel J., additional, Ladner, Jason T., additional, Oliveira, Glenn, additional, Matteson, Nathaniel L., additional, Kraemer, Moritz U.G., additional, Vogels, Chantal B.F., additional, Hentoff, Aaron, additional, Bhatia, Deepit, additional, Stanek, Danielle, additional, Scott, Blake, additional, Landis, Vanessa, additional, Stryker, Ian, additional, Cone, Marshall R., additional, Kopp, Edgar W., additional, Cannons, Andrew C., additional, Heberlein-Larson, Lea, additional, White, Stephen, additional, Gillis, Leah D., additional, Ricciardi, Michael J., additional, Kwal, Jaclyn, additional, Lichtenberger, Paola K., additional, Magnani, Diogo M., additional, Watkins, David I., additional, Palacios, Gustavo, additional, Hamer, Davidson H., additional, Gardner, Lauren M., additional, Perkins, T. Alex, additional, Baele, Guy, additional, Khan, Kamran, additional, Morrison, Andrea, additional, Isern, Sharon, additional, Michael, Scott F., additional, and Andersen, Kristian G., additional

Published
2019
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25. Capturing sequence diversity in metagenomes with comprehensive and scalable probe design

Author

Metsky, Hayden C, Siddle, Katherine J, Gladden-Young, Adrianne, Qu, James, Yang, David K, Brehio, Patrick, Goldfarb, Andrew, Piantadosi, Anne, Wohl, Shirlee, Carter, Amber, Lin, Aaron E, Barnes, Kayla G, Tully, Damien C, Corleis, Bjӧrn, Hennigan, Scott, Barbosa-Lima, Giselle, Vieira, Yasmine R, Paul, Lauren M, Tan, Amanda L, Garcia, Kimberly F, Parham, Leda A, Odia, Ikponmwosa, Eromon, Philomena, Folarin, Onikepe A, Goba, Augustine, Viral Hemorrhagic Fever Consortium, Simon-Lorière, Etienne, Hensley, Lisa, Balmaseda, Angel, Harris, Eva, Kwon, Douglas S, Allen, Todd M, Runstadler, Jonathan A, Smole, Sandra, Bozza, Fernando A, Souza, Thiago ML, Isern, Sharon, Michael, Scott F, Lorenzana, Ivette, Gehrke, Lee, Bosch, Irene, Ebel, Gregory, Grant, Donald S, Happi, Christian T, Park, Daniel J, Gnirke, Andreas, Sabeti, Pardis C, and Matranga, Christian B

Abstract

Metagenomic sequencing has the potential to transform microbial detection and characterization, but new tools are needed to improve its sensitivity. Here we present CATCH, a computational method to enhance nucleic acid capture for enrichment of diverse microbial taxa. CATCH designs optimal probe sets, with a specified number of oligonucleotides, that achieve full coverage of, and scale well with, known sequence diversity. We focus on applying CATCH to capture viral genomes in complex metagenomic samples. We design, synthesize, and validate multiple probe sets, including one that targets the whole genomes of the 356 viral species known to infect humans. Capture with these probe sets enriches unique viral content on average 18-fold, allowing us to assemble genomes that could not be recovered without enrichment, and accurately preserves within-sample diversity. We also use these probe sets to recover genomes from the 2018 Lassa fever outbreak in Nigeria and to improve detection of uncharacterized viral infections in human and mosquito samples. The results demonstrate that CATCH enables more sensitive and cost-effective metagenomic sequencing.

Published
2019

27. Metal binding and folding properties of a minimalist Cys2His2 zinc finger peptide

Author

Michael, Scott F., Kilfoil, Valda J., Schmidt, Michael H, Amann, Barbara T., and Berg, Jeremy M.

Subjects
Peptides -- Synthesis, Protein folding -- Research, Amino acid sequence -- Research, Science and technology
Abstract

A polyanine 26- amino acid peptide characteristic of the TFIIIA-type zinc finger domains has been synthesized and characterized using its metal binding and structural properties. Results show that the peptide folds in the presence of appropriate metal ions to form a complex that has a three-dimensional structure similar to zinc finger domains with more natural sequences. The sequences form a 2:1 peptide/metal complex in which the cysteinate ligands are coordinated to the metal ion but not to histidine.

Published
1992

28. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

Author

Grubaugh, Nathan D, primary, Gangavarapu, Karthik, additional, Quick, Joshua, additional, Matteson, Nathaniel L., additional, De Jesus, Jaqueline Goes, additional, Main, Bradley J, additional, Tan, Amanda L, additional, Paul, Lauren M, additional, Brackney, Doug E, additional, Grewal, Saran, additional, Gurfield, Nikos, additional, Van Rompay, Koen KA, additional, Isern, Sharon, additional, Michael, Scott F, additional, Coffey, Lark L, additional, Loman, Nicholas J, additional, and Andersen, Kristian G, additional

Published
2018
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29. Neutralizing and non-neutralizing monoclonal antibodies against dengue virus E protein derived from a naturally infected patient

Author

Isern Sharon, Fontaine Krystal A, Orgeron Nicole M, Nicholson Cindo O, Costin Joshua M, Schieffelin John S, Michael Scott F, and Robinson James E

Subjects
Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background Antibodies produced in response to infection with any of the four serotypes of dengue virus generally provide homotypic immunity. However, prior infection or circulating maternal antibodies can also mediate a non-protective antibody response that can enhance the course of disease in a subsequent heterotypic infection. Naturally occurring human monoclonal antibodies can help us understand the protective and pathogenic roles of the humoral immune system in dengue virus infection. Results Epstein-Barr Virus (EBV) transformation of B cells isolated from the peripheral blood of a human subject with previous dengue infection was performed. B cell cultures were screened by ELISA for antibodies to dengue (DENV) envelope (E) protein. ELISA positive cultures were cloned by limiting dilution. Three IgG1 human monoclonal antibodies (HMAbs) were purified and their binding specificity to E protein was verified by ELISA and biolayer interferometry. Neutralization and enhancement assays were conducted in epithelial and macrophage-like cell lines, respectively. All three HMAbs bound to E from at least two of the four DENV serotypes, one of the HMAbs was neutralizing, and all were able to enhance DENV infection. Conclusions HMAbs against DENV can be successfully generated by EBV transformation of B cells from patients at least two years after naturally acquired DENV infections. These antibodies show different patterns of cross-reactivity, neutralizing, and enhancement activity.

Published
2010
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30. Peptide inhibitors of dengue virus and West Nile virus infectivity

Author

Garry Robert F, Hrobowski Yancey M, and Michael Scott F

Subjects
Infectious and parasitic diseases, RC109-216
Abstract

Abstract Viral fusion proteins mediate cell entry by undergoing a series of conformational changes that result in virion-target cell membrane fusion. Class I viral fusion proteins, such as those encoded by influenza virus and human immunodeficiency virus (HIV), contain two prominent alpha helices. Peptides that mimic portions of these alpha helices inhibit structural rearrangements of the fusion proteins and prevent viral infection. The envelope glycoprotein (E) of flaviviruses, such as West Nile virus (WNV) and dengue virus (DENV), are class II viral fusion proteins comprised predominantly of beta sheets. We used a physio-chemical algorithm, the Wimley-White interfacial hydrophobicity scale (WWIHS) 1 in combination with known structural data to identify potential peptide inhibitors of WNV and DENV infectivity that target the viral E protein. Viral inhibition assays confirm that several of these peptides specifically interfere with target virus entry with 50% inhibitory concentration (IC50) in the 10 μM range. Inhibitory peptides similar in sequence to domains with a significant WWIHS scores, including domain II (IIb), and the stem domain, were detected. DN59, a peptide corresponding to the stem domain of DENV, inhibited infection by DENV (>99% inhibition of plaque formation at a concentrations of 99% inhibition at

Published
2005
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31. Seroprevalence of simian immunodeficiency virus in wild and captive born Sykes' monkeys (Cercopithecus mitis) in Kenya

Author

Otsyula Moses G, Robinson James, Elliott Debra, Munene Elephas, Ellis Brett R, and Michael Scott F

Subjects
Immunologic diseases. Allergy, RC581-607
Abstract

Abstract Background The Sykes' monkey and related forms (Cercopithecus mitis) make up an abundant, widespread and morphologically diverse species complex in eastern Africa that naturally harbors a distinct simian immunodeficiency virus (SIVsyk). We carried out a retrospective serological survey of SIV infection from both wild and captive Sykes' monkeys from Kenya. We compared two commercially available, cross-reactive ELISA tests using HIV antigens with a novel SIVsyk antigen-specific Western blot assay and analyzed the data by origin, subspecies, age and sex. Results The SIVsyk antigen-specific Western blot assay detected more serum samples as positive than either of the cross-reactive ELISA assays. Using this assay, we found that seroprevalence is higher than previously reported, but extremely variable in wild populations (from 0.0 to 90.9%). Females were infected more often than males in both wild and captive populations. Seropositive infants were common. However, no seropositive juveniles were identified. Conclusion We have developed a specific and sensitive Western blot assay for anti-SIVsyk antibody detection. Sykes' monkeys are commonly infected with SIVsyk, but with extremely variable prevalence in the wild. Higher infection prevalence in females suggests predominantly sexual transmission. High infection prevalence in infants, but none in juveniles, suggests maternal antibodies, but little or no vertical transmission.

Published
2004
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32. In vitro fertilization and artificial activation of eggs of the direct-developing anuran Eleutherodactylus coqui

Author

Toro Esteban and Michael Scott F

Subjects
Gynecology and obstetrics, RG1-991, Reproduction, QH471-489
Abstract

Abstract Although much is known about the reproductive biology of pond-breeding frogs, there is comparatively little information about terrestrial-breeding anurans, a highly successful and diverse group. This study investigates the activation and in vitro fertilization of eggs of the Puerto Rican coqui frog obtained by hormonally induced ovulation. We report that spontaneous activation occurs in 34% of eggs, probably in response to mechanical stress during oviposition. Artificial activation, as evidenced by the slow block to polyspermy and the onset of zygote division, was elicited both by mechanical stimulation and calcium ionophore exposure in 64% and 83% of the cases, respectively. Finally, one in vitro fertilization protocol showed a 27% success rate, despite the fact that about one third of all unfertilized eggs obtained by hormone injection auto-activate. We expect these findings to aid in the conservation effort of Eleutherodactylus frogs, the largest vertebrate genus.

Published
2004
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33. Induced ovulation and egg deposition in the direct developing anuran Eleutherodactylus coqui

Author

Estrada Alberto R, Toro Esteban, Buckley Christine, Michael Scott F, and Vincent Shawn

Subjects
Gynecology and obstetrics, RG1-991, Reproduction, QH471-489
Abstract

Abstract This study investigates ovulation and egg deposition behaviors in the anuran Eleutherodactylus coqui from Puerto Rico in response to stimulation with gonadotropin and gonadotropin releasing hormones. Five hormones were tested by injection over a range of doses, including mammalian LHRH, avian LHRH, fish LHRH, D-Ala6, des-Gly10 ethylamide LHRH and hCG. We report a low level of ovulation and egg deposition in response to all hormones, with the most complete and consistent results from the non-natural D-Ala6, des-Gly10 ethylamide LHRH derivative. To confirm the viability of eggs produced in this manner we performed in vitro fertilization experiments that resulted in the development of normal frogs. Reproductive behaviors in E. coqui are apparently not controlled by a mammalian form of LHRH as reported in other common laboratory anuran species. D-Ala6, des-Gly10 ethylamide LHRH induces ovulation and deposition of mature and fertilizable eggs in E. coqui.

Published
2004
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35. Multiple introductions of Zika virus into the United States revealed through genomic epidemiology

Author

Grubaugh, Nathan D, primary, Ladner, Jason T, additional, Kraemer, Moritz UG, additional, Dudas, Gytis, additional, Tan, Amanda L, additional, Gangavarapu, Karthik, additional, Wiley, Michael R, additional, White, Stephen, additional, Thézé, Julien, additional, Magnani, Diogo M, additional, Prieto, Karla, additional, Reyes, Daniel, additional, Bingham, Andrea, additional, Paul, Lauren M, additional, Robles-Sikisaka, Refugio, additional, Oliveira, Glenn, additional, Pronty, Darryl, additional, Metsky, Hayden C, additional, Baniecki, Mary Lynn, additional, Barnes, Kayla G, additional, Chak, Bridget, additional, Freije, Catherine A, additional, Gladden-Young, Adrianne, additional, Gnirke, Andreas, additional, Luo, Cynthia, additional, MacInnis, Bronwyn, additional, Matranga, Christian B, additional, Park, Daniel J, additional, Qu, James, additional, Schaffner, Stephen F, additional, Tomkins-Tinch, Christopher, additional, West, Kendra L, additional, Winnicki, Sarah M, additional, Wohl, Shirlee, additional, Yozwiak, Nathan L, additional, Quick, Joshua, additional, Fauver, Joseph R, additional, Khan, Kamran, additional, Brent, Shannon E, additional, Reiner, Robert C, additional, Lichtenberger, Paola N, additional, Ricciardi, Michael, additional, Bailey, Varian K, additional, Watkins, David I, additional, Cone, Marshall R, additional, Kopp, Edgar W, additional, Hogan, Kelly N, additional, Cannons, Andrew C, additional, Jean, Reynald, additional, Garry, Robert F, additional, Loman, Nicholas J, additional, Faria, Nuno R, additional, Porcelli, Mario C, additional, Vasquez, Chalmers, additional, Nagle, Elyse R, additional, Cummings, Derek AT, additional, Stanek, Danielle, additional, Rambaut, Andrew, additional, Sanchez-Lockhart, Mariano, additional, Sabeti, Pardis C, additional, Gillis, Leah D, additional, Michael, Scott F, additional, Bedford, Trevor, additional, Pybus, Oliver G, additional, Isern, Sharon, additional, Palacios, Gustavo, additional, and Andersen, Kristian G, additional

Published
2017
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36. Prophage-mediated defence against viral attack and viral counter-defence

Author

Dedrick, Rebekah M., primary, Jacobs-Sera, Deborah, additional, Bustamante, Carlos A. Guerrero, additional, Garlena, Rebecca A., additional, Mavrich, Travis N., additional, Pope, Welkin H., additional, Reyes, Juan C. Cervantes, additional, Russell, Daniel A., additional, Adair, Tamarah, additional, Alvey, Richard, additional, Bonilla, J. Alfred, additional, Bricker, Jerald S., additional, Brown, Bryony R., additional, Byrnes, Deanna, additional, Cresawn, Steven G., additional, Davis, William B., additional, Dickson, Leon A., additional, Edgington, Nicholas P., additional, Findley, Ann M., additional, Golebiewska, Urszula, additional, Grose, Julianne H., additional, Hayes, Cory F., additional, Hughes, Lee E., additional, Hutchison, Keith W., additional, Isern, Sharon, additional, Johnson, Allison A., additional, Kenna, Margaret A., additional, Klyczek, Karen K., additional, Mageeney, Catherine M., additional, Michael, Scott F., additional, Molloy, Sally D., additional, Montgomery, Matthew T., additional, Neitzel, James, additional, Page, Shallee T., additional, Pizzorno, Marie C., additional, Poxleitner, Marianne K., additional, Rinehart, Claire A., additional, Robinson, Courtney J., additional, Rubin, Michael R., additional, Teyim, Joseph N., additional, Vazquez, Edwin, additional, Ware, Vassie C., additional, Washington, Jacqueline, additional, and Hatfull, Graham F., additional

Published
2017
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38. Dengue virus antibodies enhance Zika virus infection

Author

Paul, Lauren M, primary, Carlin, Eric R, additional, Jenkins, Meagan M, additional, Tan, Amanda L, additional, Barcellona, Carolyn M, additional, Nicholson, Cindo O, additional, Michael, Scott F, additional, and Isern, Sharon, additional

Published
2016
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39. Dengue Virus Antibodies Enhance Zika Virus Infection

Author

Paul, Lauren M., primary, Carlin, Eric R., additional, Jenkins, Meagan M., additional, Tan, Amanda L., additional, Barcellona, Carolyn M., additional, Nicholson, Cindo O., additional, Trautmann, Lydie, additional, Michael, Scott F., additional, and Isern, Sharon, additional

Published
2016
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40. Correction: Biomimetic design of protic lipidic ionic liquids with enhanced fluidity

Author

O'Brien, Richard A., primary, Zayas, Manuel Sanchez, additional, Nestor, Stephen T., additional, Gaitor, Jamie C., additional, Paul, Lauren M., additional, Edhegard, Forrest A., additional, Minkowicz, Samuel, additional, Sykora, Richard E., additional, Sheng, Yinghong, additional, Michael, Scott F., additional, Isern, Sharon, additional, and Mirjafari, Arsalan, additional

Published
2016
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41. Biomimetic design of protic lipidic ionic liquids with enhanced fluidity

Author

O'Brien, Richard A., primary, Zayas, Manuel Sanchez, additional, Nestor, Stephen T., additional, Gaitor, Jamie C., additional, Paul, Lauran M., additional, Edhegard, Forrest A., additional, Minkowicz, Samuel, additional, Sykora, Richard E., additional, Sheng, Yinghong, additional, Michael, Scott F., additional, Isern, Sharon, additional, and Mirjafari, Arsalan, additional

Published
2016
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42. Mosquito-associated dengue virus, Key West, Florida, USA, 2010

Author

Graham, Amanda S., Pruszynski, Catherine A., Hribar, Lawrence J., DeMay, David J., Tambasco, Adriane N., Hartley, Anne E., Fussell, Edsel M., Michael, Scott F., and Isern, Sharon

Subjects
Disease transmission -- Research, Dengue viruses -- Research -- Diagnosis -- Genetic aspects, Health
Abstract

To the Editor: Except for sporadic cases along the Texas-Mexico border, local transmission of dengue virus (DENV) has not occurred in the contiguous United States since 1946. In 2009, DENV [...]

Published
2011
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45. Induced ovulation and egg deposition in the direct developing anuran Eleutherodactylus coqui

Author

Estrada Alberto R, Toro Esteban, Buckley Christine, Michael Scott F, and Vincent Shawn

Subjects
Ovulation, endocrine system, lcsh:QH471-489, Behavior, Animal, Oviposition, Research, Puerto Rico, lcsh:Gynecology and obstetrics, Gonadotropin-Releasing Hormone, Oocytes, lcsh:Reproduction, Animals, Female, Anura, lcsh:RG1-991, hormones, hormone substitutes, and hormone antagonists, Gonadotropins
Abstract

This study investigates ovulation and egg deposition behaviors in the anuran Eleutherodactylus coqui from Puerto Rico in response to stimulation with gonadotropin and gonadotropin releasing hormones. Five hormones were tested by injection over a range of doses, including mammalian LHRH, avian LHRH, fish LHRH, D-Ala6, des-Gly10 ethylamide LHRH and hCG. We report a low level of ovulation and egg deposition in response to all hormones, with the most complete and consistent results from the non-natural D-Ala6, des-Gly10 ethylamide LHRH derivative. To confirm the viability of eggs produced in this manner we performed in vitro fertilization experiments that resulted in the development of normal frogs. Reproductive behaviors in E. coqui are apparently not controlled by a mammalian form of LHRH as reported in other common laboratory anuran species. D-Ala6, des-Gly10 ethylamide LHRH induces ovulation and deposition of mature and fertilizable eggs in E. coqui.

Published
2003

46. Mechanistic Study of Broadly Neutralizing Human Monoclonal Antibodies against Dengue Virus That Target the Fusion Loop

Author

Costin, Joshua M., primary, Zaitseva, Elena, additional, Kahle, Kristen M., additional, Nicholson, Cindo O., additional, Rowe, Dawne K., additional, Graham, Amanda S., additional, Bazzone, Lindsey E., additional, Hogancamp, Greg, additional, Figueroa Sierra, Marielys, additional, Fong, Rachel H., additional, Yang, Sung-Tae, additional, Lin, Li, additional, Robinson, James E., additional, Doranz, Benjamin J., additional, Chernomordik, Leonid V., additional, Michael, Scott F., additional, Schieffelin, John S., additional, and Isern, Sharon, additional

Published
2013
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47. Release of Dengue Virus Genome Induced by a Peptide Inhibitor

Author

Lok, Shee-Mei, primary, Costin, Joshua M., additional, Hrobowski, Yancey M., additional, Hoffmann, Andrew R., additional, Rowe, Dawne K., additional, Kukkaro, Petra, additional, Holdaway, Heather, additional, Chipman, Paul, additional, Fontaine, Krystal A., additional, Holbrook, Michael R., additional, Garry, Robert F., additional, Kostyuchenko, Victor, additional, Wimley, William C., additional, Isern, Sharon, additional, Rossmann, Michael G., additional, and Michael, Scott F., additional

Published
2012
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