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  1. AU="Beach, Dale L"
  2. AU="Kunning, Sheryl R"
  3. AU="Durkan, Garrett C"
  4. AU="Barcelona, Laura"
  5. AU="McDonald, Bryan"
  6. AU="Martin, Jacqueline M"
  7. AU="Ingrisch, Doris"
  8. AU="Hanks, Ephraim M"
  9. AU="Ruiz-Narvaez, Edward A"
  10. AU="Krzysztof Kamiński"
  11. AU="Sharma, Ishna"
  12. AU="Warner, Brit"
  13. AU="JOCHEN SCHÖNGART"
  14. AU="Curdy, Nicolas"
  15. AU="Nkfusai, Claude Ngwayu"
  16. AU="Peng, Yonghan"
  17. AU="Decker, Miriam"
  18. AU="Campbell, Kerry"
  19. AU="Le Deley, Marie-Cécile" AU="Le Deley, Marie-Cécile"
  20. AU="Guan, Shu"

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  1. Artikel: Biotechnology by Design: An Introductory Level, Project-Based, Synthetic Biology Laboratory Program for Undergraduate Students.

    Beach, Dale L / Alvarez, Consuelo J

    Journal of microbiology & biology education

    2015  Band 16, Heft 2, Seite(n) 237–246

    Abstract: Synthetic biology offers an ideal opportunity to promote undergraduate laboratory courses with research-style projects, immersing students in an inquiry-based program that enhances the experience of the scientific process. We designed a semester-long, ... ...

    Abstract Synthetic biology offers an ideal opportunity to promote undergraduate laboratory courses with research-style projects, immersing students in an inquiry-based program that enhances the experience of the scientific process. We designed a semester-long, project-based laboratory curriculum using synthetic biology principles to develop a novel sensory device. Students develop subject matter knowledge of molecular genetics and practical skills relevant to molecular biology, recombinant DNA techniques, and information literacy. During the spring semesters of 2014 and 2015, the Synthetic Biology Laboratory Project was delivered to sophomore genetics courses. Using a cloning strategy based on standardized BioBrick genetic "parts," students construct a "reporter plasmid" expressing a reporter gene (GFP) controlled by a hybrid promoter regulated by the lac-repressor protein (lacI). In combination with a "sensor plasmid," the production of the reporter phenotype is inhibited in the presence of a target environmental agent, arabinose. When arabinose is absent, constitutive GFP expression makes cells glow green. But the presence of arabinose activates a second promoter (pBAD) to produce a lac-repressor protein that will inhibit GFP production. Student learning was assessed relative to five learning objectives, using a student survey administered at the beginning (pre-survey) and end (post-survey) of the course, and an additional 15 open-ended questions from five graded Progress Report assignments collected throughout the course. Students demonstrated significant learning gains (p < 0.05) for all learning outcomes. Ninety percent of students indicated that the Synthetic Biology Laboratory Project enhanced their understanding of molecular genetics. The laboratory project is highly adaptable for both introductory and advanced courses.
    Sprache Englisch
    Erscheinungsdatum 2015-12-01
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ISSN 1935-7877
    ISSN 1935-7877
    DOI 10.1128/jmbe.v16i2.971
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel: Ribotrap : targeted purification of RNA-specific RNPs from cell lysates through immunoaffinity precipitation to identify regulatory proteins and RNAs.

    Beach, Dale L / Keene, Jack D

    Methods in molecular biology (Clifton, N.J.)

    2008  Band 419, Seite(n) 69–91

    Abstract: Many elegant methodologies have been devised to explore RNA-protein as well as RNA-RNA interactions. Although the characterization of messages targeted by a specific RNA-binding protein (RBP) has been accelerated by the application of microarray ... ...

    Abstract Many elegant methodologies have been devised to explore RNA-protein as well as RNA-RNA interactions. Although the characterization of messages targeted by a specific RNA-binding protein (RBP) has been accelerated by the application of microarray technologies, reliable methods to describe the endogenous assembly of ribonucleoproteins (RNPs) are needed. However, this approach requires the targeted purification of a select mRNA under conditions favorable for the copurification of associated factors including RNA and protein components of the RNP. This chapter describes previous methods used to characterize RNPs in the context of in vitro approaches and presents the Ribotrap methodology, an in vivo protocol for message-specific purification of a target RNP. The method was developed in a yeast model system, yet is amenable to other in vivo cell systems including mammalian cell culture.
    Mesh-Begriff(e) 3' Untranslated Regions ; Affinity Labels ; Base Sequence ; Blotting, Western ; Electrophoresis, Polyacrylamide Gel ; Genes, Reporter ; Immunoprecipitation/methods ; Molecular Biology/methods ; RNA/genetics ; RNA/isolation & purification ; RNA/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Fungal/genetics ; RNA, Fungal/isolation & purification ; RNA, Fungal/metabolism ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/isolation & purification ; RNA-Binding Proteins/metabolism ; Ribonucleoproteins/genetics ; Ribonucleoproteins/isolation & purification ; Ribonucleoproteins/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/isolation & purification ; Saccharomyces cerevisiae Proteins/metabolism
    Chemische Substanzen 3' Untranslated Regions ; Affinity Labels ; RNA, Fungal ; RNA-Binding Proteins ; Ribonucleoproteins ; Saccharomyces cerevisiae Proteins ; RNA (63231-63-0)
    Sprache Englisch
    Erscheinungsdatum 2008
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1064-3745
    ISSN 1064-3745
    DOI 10.1007/978-1-59745-033-1_5
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel: Phylogeny of Pilobolaceae.

    Foos, K Michael / May, Nicole L / Beach, Dale L / Pomper, Markus / Sheehan, Kathy B / Ruch, Donald G

    Mycologia

    2011  Band 103, Heft 1, Seite(n) 36–44

    Abstract: The three genera traditionally classified as Pilobolaceae have been identified on the basis of morphological characteristics. In the absence of distinctive morphological differences phylogenetic techniques have proven to be superior for developing ... ...

    Abstract The three genera traditionally classified as Pilobolaceae have been identified on the basis of morphological characteristics. In the absence of distinctive morphological differences phylogenetic techniques have proven to be superior for developing phylogenies. Molecular techniques have been used primarily for studies of higher fungi; there are few investigations of the Zygomycota using genetic sequences for classification. DNA sequences coding for three regions of rRNA were used to investigate phylogenetic relationships of the three genera traditionally considered within the Pilobolaceae. Evidence indicates that Pilaira should be removed from Pilobolaceae and the family redescribed. Sporangiospore size is the morphological characteristic that most closely correlates with rDNA clades of phylogenetic trees. This study demonstrates that traditional morphological characteristics alone are not adequate to differentiate species of Pilobolus.
    Mesh-Begriff(e) Base Sequence ; DNA, Fungal/chemistry ; DNA, Fungal/genetics ; Fungi/classification ; Fungi/genetics ; Fungi/ultrastructure ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/chemistry ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 23S/genetics ; RNA, Ribosomal, 5.8S/chemistry ; RNA, Ribosomal, 5.8S/genetics ; Sequence Alignment
    Chemische Substanzen DNA, Fungal ; RNA, Ribosomal, 18S ; RNA, Ribosomal, 23S ; RNA, Ribosomal, 5.8S
    Sprache Englisch
    Erscheinungsdatum 2011-01
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 281335-x
    ISSN 1557-2536 ; 0027-5514
    ISSN (online) 1557-2536
    ISSN 0027-5514
    DOI 10.3852/09-314
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: A course-based research experience: how benefits change with increased investment in instructional time.

    Shaffer, Christopher D / Alvarez, Consuelo J / Bednarski, April E / Dunbar, David / Goodman, Anya L / Reinke, Catherine / Rosenwald, Anne G / Wolyniak, Michael J / Bailey, Cheryl / Barnard, Daron / Bazinet, Christopher / Beach, Dale L / Bedard, James E J / Bhalla, Satish / Braverman, John / Burg, Martin / Chandrasekaran, Vidya / Chung, Hui-Min / Clase, Kari /
    Dejong, Randall J / Diangelo, Justin R / Du, Chunguang / Eckdahl, Todd T / Eisler, Heather / Emerson, Julia A / Frary, Amy / Frohlich, Donald / Gosser, Yuying / Govind, Shubha / Haberman, Adam / Hark, Amy T / Hauser, Charles / Hoogewerf, Arlene / Hoopes, Laura L M / Howell, Carina E / Johnson, Diana / Jones, Christopher J / Kadlec, Lisa / Kaehler, Marian / Silver Key, S Catherine / Kleinschmit, Adam / Kokan, Nighat P / Kopp, Olga / Kuleck, Gary / Leatherman, Judith / Lopilato, Jane / Mackinnon, Christy / Martinez-Cruzado, Juan Carlos / McNeil, Gerard / Mel, Stephanie / Mistry, Hemlata / Nagengast, Alexis / Overvoorde, Paul / Paetkau, Don W / Parrish, Susan / Peterson, Celeste N / Preuss, Mary / Reed, Laura K / Revie, Dennis / Robic, Srebrenka / Roecklein-Canfield, Jennifer / Rubin, Michael R / Saville, Kenneth / Schroeder, Stephanie / Sharif, Karim / Shaw, Mary / Skuse, Gary / Smith, Christopher D / Smith, Mary A / Smith, Sheryl T / Spana, Eric / Spratt, Mary / Sreenivasan, Aparna / Stamm, Joyce / Szauter, Paul / Thompson, Jeffrey S / Wawersik, Matthew / Youngblom, James / Zhou, Leming / Mardis, Elaine R / Buhler, Jeremy / Leung, Wilson / Lopatto, David / Elgin, Sarah C R

    CBE life sciences education

    2013  Band 13, Heft 1, Seite(n) 111–130

    Abstract: 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 ... ...

    Abstract 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.
    Mesh-Begriff(e) Attitude ; Biology/education ; Cooperative Behavior ; Curriculum ; Data Collection ; Faculty ; Genome ; Genomics/education ; Humans ; Knowledge ; Learning ; Molecular Sequence Annotation ; Program Evaluation ; Research/education ; Research Personnel ; Self Report ; Surveys and Questionnaires ; Time Factors
    Sprache Englisch
    Erscheinungsdatum 2013-09-09
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2465176-X
    ISSN 1931-7913 ; 1931-7913
    ISSN (online) 1931-7913
    ISSN 1931-7913
    DOI 10.1187/cbe-13-08-0152
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: Retrotransposons Are the Major Contributors to the Expansion of the

    Leung, Wilson / Shaffer, Christopher D / Chen, Elizabeth J / Quisenberry, Thomas J / Ko, Kevin / Braverman, John M / Giarla, Thomas C / Mortimer, Nathan T / Reed, Laura K / Smith, Sheryl T / Robic, Srebrenka / McCartha, Shannon R / Perry, Danielle R / Prescod, Lindsay M / Sheppard, Zenyth A / Saville, Ken J / McClish, Allison / Morlock, Emily A / Sochor, Victoria R /
    Stanton, Brittney / Veysey-White, Isaac C / Revie, Dennis / Jimenez, Luis A / Palomino, Jennifer J / Patao, Melissa D / Patao, Shane M / Himelblau, Edward T / Campbell, Jaclyn D / Hertz, Alexandra L / McEvilly, Maddison F / Wagner, Allison R / Youngblom, James / Bedi, Baljit / Bettincourt, Jeffery / Duso, Erin / Her, Maiye / Hilton, William / House, Samantha / Karimi, Masud / Kumimoto, Kevin / Lee, Rebekah / Lopez, Darryl / Odisho, George / Prasad, Ricky / Robbins, Holly Lyn / Sandhu, Tanveer / Selfridge, Tracy / Tsukashima, Kara / Yosif, Hani / Kokan, Nighat P / Britt, Latia / Zoellner, Alycia / Spana, Eric P / Chlebina, Ben T / Chong, Insun / Friedman, Harrison / Mammo, Danny A / Ng, Chun L / Nikam, Vinayak S / Schwartz, Nicholas U / Xu, Thomas Q / Burg, Martin G / Batten, Spencer M / Corbeill, Lindsay M / Enoch, Erica / Ensign, Jesse J / Franks, Mary E / Haiker, Breanna / Ingles, Judith A / Kirkland, Lyndsay D / Lorenz-Guertin, Joshua M / Matthews, Jordan / Mittig, Cody M / Monsma, Nicholaus / Olson, Katherine J / Perez-Aragon, Guillermo / Ramic, Alen / Ramirez, Jordan R / Scheiber, Christopher / Schneider, Patrick A / Schultz, Devon E / Simon, Matthew / Spencer, Eric / Wernette, Adam C / Wykle, Maxine E / Zavala-Arellano, Elizabeth / McDonald, Mitchell J / Ostby, Kristine / Wendland, Peter / DiAngelo, Justin R / Ceasrine, Alexis M / Cox, Amanda H / Docherty, James E B / Gingras, Robert M / Grieb, Stephanie M / Pavia, Michael J / Personius, Casey L / Polak, Grzegorz L / Beach, Dale L / Cerritos, Heaven L / Horansky, Edward A / Sharif, Karim A / Moran, Ryan / Parrish, Susan / Bickford, Kirsten / Bland, Jennifer / Broussard, Juliana / Campbell, Kerry / Deibel, Katelynn E / Forka, Richard / Lemke, Monika C / Nelson, Marlee B / O'Keeffe, Catherine / Ramey, S Mariel / Schmidt, Luke / Villegas, Paola / Jones, Christopher J / Christ, Stephanie L / Mamari, Sami / Rinaldi, Adam S / Stity, Ghazal / Hark, Amy T / Scheuerman, Mark / Silver Key, S Catherine / McRae, Briana D / Haberman, Adam S / Asinof, Sam / Carrington, Harriette / Drumm, Kelly / Embry, Terrance / McGuire, Richard / Miller-Foreman, Drew / Rosen, Stella / Safa, Nadia / Schultz, Darrin / Segal, Matt / Shevin, Yakov / Svoronos, Petros / Vuong, Tam / Skuse, Gary / Paetkau, Don W / Bridgman, Rachael K / Brown, Charlotte M / Carroll, Alicia R / Gifford, Francesca M / Gillespie, Julie Beth / Herman, Susan E / Holtcamp, Krystal L / Host, Misha A / Hussey, Gabrielle / Kramer, Danielle M / Lawrence, Joan Q / Martin, Madeline M / Niemiec, Ellen N / O'Reilly, Ashleigh P / Pahl, Olivia A / Quintana, Guadalupe / Rettie, Elizabeth A S / Richardson, Torie L / Rodriguez, Arianne E / Rodriguez, Mona O / Schiraldi, Laura / Smith, Joanna J / Sugrue, Kelsey F / Suriano, Lindsey J / Takach, Kaitlyn E / Vasquez, Arielle M / Velez, Ximena / Villafuerte, Elizabeth J / Vives, Laura T / Zellmer, Victoria R / Hauke, Jeanette / Hauser, Charles R / Barker, Karolyn / Cannon, Laurie / Parsamian, Perouza / Parsons, Samantha / Wichman, Zachariah / Bazinet, Christopher W / Johnson, Diana E / Bangura, Abubakarr / Black, Jordan A / Chevee, Victoria / Einsteen, Sarah A / Hilton, Sarah K / Kollmer, Max / Nadendla, Rahul / Stamm, Joyce / Fafara-Thompson, Antoinette E / Gygi, Amber M / Ogawa, Emmy E / Van Camp, Matt / Kocsisova, Zuzana / Leatherman, Judith L / Modahl, Cassie M / Rubin, Michael R / Apiz-Saab, Susana S / Arias-Mejias, Suzette M / Carrion-Ortiz, Carlos F / Claudio-Vazquez, Patricia N / Espada-Green, Debbie M / Feliciano-Camacho, Marium / Gonzalez-Bonilla, Karina M / Taboas-Arroyo, Mariela / Vargas-Franco, Dorianmarie / Montañez-Gonzalez, Raquel / Perez-Otero, Joseph / Rivera-Burgos, Myrielis / Rivera-Rosario, Francisco J / Eisler, Heather L / Alexander, Jackie / Begley, Samatha K / Gabbard, Deana / Allen, Robert J / Aung, Wint Yan / Barshop, William D / Boozalis, Amanda / Chu, Vanessa P / Davis, Jeremy S / Duggal, Ryan N / Franklin, Robert / Gavinski, Katherine / Gebreyesus, Heran / Gong, Henry Z / Greenstein, Rachel A / Guo, Averill D / Hanson, Casey / Homa, Kaitlin E / Hsu, Simon C / Huang, Yi / Huo, Lucy / Jacobs, Sarah / Jia, Sasha / Jung, Kyle L / Wai-Chee Kong, Sarah / Kroll, Matthew R / Lee, Brandon M / Lee, Paul F / Levine, Kevin M / Li, Amy S / Liu, Chengyu / Liu, Max Mian / Lousararian, Adam P / Lowery, Peter B / Mallya, Allyson P / Marcus, Joseph E / Ng, Patrick C / Nguyen, Hien P / Patel, Ruchik / Precht, Hashini / Rastogi, Suchita / Sarezky, Jonathan M / Schefkind, Adam / Schultz, Michael B / Shen, Delia / Skorupa, Tara / Spies, Nicholas C / Stancu, Gabriel / Vivian Tsang, Hiu Man / Turski, Alice L / Venkat, Rohit / Waldman, Leah E / Wang, Kaidi / Wang, Tracy / Wei, Jeffrey W / Wu, Dennis Y / Xiong, David D / Yu, Jack / Zhou, Karen / McNeil, Gerard P / Fernandez, Robert W / Menzies, Patrick Gomez / Gu, Tingting / Buhler, Jeremy / Mardis, Elaine R / Elgin, Sarah C R

    G3 (Bethesda, Md.)

    2017  Band 7, Heft 8, Seite(n) 2439–2460

    Abstract: The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (∼5.2 Mb) is the smallest chromosome ... ...

    Abstract The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (∼5.2 Mb) is the smallest chromosome in
    Mesh-Begriff(e) Animals ; Base Composition/genetics ; Base Sequence ; Chromosomes/genetics ; Codon/genetics ; Drosophila/genetics ; Female ; Gene Expression Profiling ; Genes, Insect ; Histones/metabolism ; Protein Processing, Post-Translational/genetics ; Retroelements/genetics ; Wolbachia/genetics
    Chemische Substanzen Codon ; Histones ; Retroelements
    Sprache Englisch
    Erscheinungsdatum 2017-08-07
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2629978-1
    ISSN 2160-1836 ; 2160-1836
    ISSN (online) 2160-1836
    ISSN 2160-1836
    DOI 10.1534/g3.117.040907
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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