1
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Goodwin EC, Pais D, He J, Gin LE, Brownell SE. Perspectives from Undergraduate Life Sciences Faculty: Are We Equipped to Effectively Accommodate Students With Disabilities in Our Classrooms? CBE Life Sci Educ 2024; 23:ar18. [PMID: 38620006 DOI: 10.1187/cbe.23-05-0094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Higher education has evolved in ways that may increase the challenges life science faculty face in providing accommodations for students with disabilities. Guided by Expectancy-Value Theory, we interviewed 34 life sciences faculty instructors from institutions nationwide to explore faculty motivation to create disability-inclusive educational experiences. We found that faculty in our sample perceive that providing most standard accommodations is a manageable but often challenging task. Further, faculty in our sample feel that improving accommodations necessitates additional support from their institutions. Most faculty had high attainment value for providing accommodations, in that they strongly believed that supporting students with disabilities is the fair and right thing to do. However, faculty did not perceive much utility value or intrinsic value in their task of providing accommodations, and most reported that providing accommodations can be a substantial burden on faculty. These findings imply that current approaches to providing inclusive educational experiences for students with disabilities rely primarily on the personal belief that providing accommodations is the right thing to do, which likely results in a flawed and inequitable system given that not all faculty equally share this conviction.
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Affiliation(s)
- Emma C Goodwin
- Research for Inclusive STEM Education Center, School of Life Sciences, Arizona State University, Tempe, Arizona, 85281
| | - Danielle Pais
- Research for Inclusive STEM Education Center, School of Life Sciences, Arizona State University, Tempe, Arizona, 85281
| | - Jingyi He
- Research for Inclusive STEM Education Center, School of Life Sciences, Arizona State University, Tempe, Arizona, 85281
| | - Logan E Gin
- Research for Inclusive STEM Education Center, School of Life Sciences, Arizona State University, Tempe, Arizona, 85281
- Sheridan Center for Teaching and Learning, Brown University, Providence, Rhode Island 02912
| | - Sara E Brownell
- Research for Inclusive STEM Education Center, School of Life Sciences, Arizona State University, Tempe, Arizona, 85281
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2
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Shortlidge EE, Kern AM, Goodwin EC, Olimpo JT. Preparing Teaching Assistants to Facilitate Course-based Undergraduate Research Experiences (CUREs) in the Biological Sciences: A Call to Action. CBE Life Sci Educ 2023; 22:es4. [PMID: 37816213 PMCID: PMC10756030 DOI: 10.1187/cbe.22-09-0183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 06/22/2023] [Accepted: 07/31/2023] [Indexed: 10/12/2023]
Abstract
Course-based undergraduate research experiences (CUREs) offer an expanding avenue to engage students in real-world scientific practices. Increasingly, CUREs are instructed by graduate teaching assistants (TAs), yet TAs may be underprepared to facilitate and face unique barriers when teaching CUREs. Consequently, unless TAs are provided professional development (PD) and resources to teach CUREs effectively, they and their students may not reap the assumed benefits of CURE instruction. Here, we describe three perspectives - that of the CURE TA, the CURE designer/facilitator, and the CURE student - that are collectively intended to inform the development of tentative components of CURE TA PD. We compare these perspectives to previous studies in the literature in an effort to identify commonalities across all sources and offer potential insights for advancing CURE TA PD efforts across a diversity of institutional environments. We propose that the most effective CURE TA PD programs will promote the use of CURE-specific instructional strategies as benchmarks for guiding change in teaching practices and should focus on three major elements: 1) enhancement of research and teaching acumen, 2) development of effective and inclusive mentoring practices, and 3) identification and understanding of the factors that make CUREs a unique learning experience.
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Affiliation(s)
| | - Amie M. Kern
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968
| | - Emma C. Goodwin
- Department of Biology, Portland State University, Portland, OR 97201
- School of Life Sciences, Arizona State University, Tempe, AZ 85281
| | - Jeffrey T. Olimpo
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968
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3
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Busch CA, Wiesenthal NJ, Mohammed TF, Anderson S, Barstow M, Custalow C, Gajewski J, Garcia K, Gilabert CK, Hughes J, Jenkins A, Johnson M, Kasper C, Perez I, Robnett B, Tillett K, Tsefrekas L, Goodwin EC, Cooper KM. The Disproportionate Impact of Fear of Negative Evaluation on First-Generation College Students, LGBTQ+ Students, and Students with Disabilities in College Science Courses. CBE Life Sci Educ 2023; 22:ar31. [PMID: 37347813 PMCID: PMC10424224 DOI: 10.1187/cbe.22-10-0195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 05/05/2023] [Accepted: 05/19/2023] [Indexed: 06/24/2023]
Abstract
Fear of negative evaluation (FNE), defined as a sense of dread associated with being negatively judged in a social situation, has been identified as the primary factor underlying undergraduate anxiety in active-learning science courses. However, no quantitative studies have examined the extent to which science undergraduates experience FNE and how they are impacted by FNE in college science courses. To address this gap, we surveyed 566 undergraduates from one university in the U.S. Southwest who were enrolled in life sciences courses where they had opportunities to speak in front of the whole class. Participants were asked a suite of questions regarding their experiences with FNE in large-enrollment college science courses. We found that first-generation college students, LGBTQ+ students, and students with disabilities reported disproportionately high levels of FNE compared with their counterparts. Additionally, students reported that FNE can cause them to overthink their responses and participate less in class. Participants rated being cold called and presenting alone as forms of whole-class participation that elicit the highest levels of FNE. This research highlights the impact of FNE on undergraduates and provides student-generated recommendations to reduce FNE in active-learning science courses.
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Affiliation(s)
- Carly A. Busch
- Research for Inclusive STEM Education Center, Arizona State University, Tempe, AZ 85287
| | | | - Tasneem F. Mohammed
- Research for Inclusive STEM Education Center, Arizona State University, Tempe, AZ 85287
| | - Shauna Anderson
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Margaret Barstow
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Cydney Custalow
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Jas Gajewski
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Kristin Garcia
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Cynthia K. Gilabert
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Joseph Hughes
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Aliyah Jenkins
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Miajah Johnson
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Cait Kasper
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Israel Perez
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Brieana Robnett
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Kaytlin Tillett
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Lauren Tsefrekas
- Biology Education Research Course, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Emma C. Goodwin
- Research for Inclusive STEM Education Center, Arizona State University, Tempe, AZ 85287
| | - Katelyn M. Cooper
- Research for Inclusive STEM Education Center, Arizona State University, Tempe, AZ 85287
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4
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Goodwin EC, Shapiro C, Freise AC, Toven-Lindsey B, Moberg Parker J. Synthesizing Research Narratives to Reveal the Big Picture: a CREATE(S) Intervention Modified for Journal Club Improves Undergraduate Science Literacy. J Microbiol Biol Educ 2023; 24:e00055-23. [PMID: 37614891 PMCID: PMC10443313 DOI: 10.1128/jmbe.00055-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/27/2023] [Indexed: 08/25/2023]
Abstract
Communicating science effectively is an essential part of the development of science literacy. Research has shown that introducing primary scientific literature through journal clubs can improve student learning outcomes, including increased scientific knowledge. However, without scaffolding, students can miss more complex aspects of science literacy, including how to analyze and present scientific data. In this study, we apply a modified CREATE(S) process (Concept map the introduction, Read methods and results, Elucidate hypotheses, Analyze data, Think of the next Experiment, and Synthesis map) to improve students' science literacy skills, specifically their understanding of the process of science and their ability to use narrative synthesis to communicate science. We tested this hypothesis using a retrospective quasi-experimental study design in upper-division undergraduate courses. We compared learning outcomes for CREATES intervention students to those for students who took the same courses before CREATES was introduced. Rubric-guided, direct evidence assessments were used to measure student gains in learning outcomes. Analyses revealed that CREATES intervention students versus the comparison group demonstrated improved ability to interpret and communicate primary literature, especially in the methods, hypotheses, and narrative synthesis learning outcome categories. Through a mixed-methods analysis of a reflection assignment completed by the CREATES intervention group, students reported the synthesis map as the most frequently used step in the process and highly valuable to their learning. Taken together, the study demonstrates how this modified CREATES process can foster scientific literacy development and how it could be applied in science, technology, engineering, and math journal clubs.
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Affiliation(s)
- Emma C. Goodwin
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Casey Shapiro
- Center for Educational Assessment, Center for the Advancement of Teaching, Division of Undergraduate Education, University of California Los Angeles, Los Angeles, California, USA
| | - Amanda C. Freise
- Department of Microbiology, Immunology & Molecular Genetics, University of California Los Angeles, Los Angeles, California, USA
| | - Brit Toven-Lindsey
- Center for Educational Assessment, Center for the Advancement of Teaching, Division of Undergraduate Education, University of California Los Angeles, Los Angeles, California, USA
| | - Jordan Moberg Parker
- Department of Microbiology, Immunology & Molecular Genetics, University of California Los Angeles, Los Angeles, California, USA
- Department of Biomedical Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, California, USA
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5
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Goodwin EC, Cary JR, Shortlidge EE. Not the same CURE: Student experiences in course-based undergraduate research experiences vary by graduate teaching assistant. PLoS One 2022; 17:e0275313. [PMID: 36166457 PMCID: PMC9514618 DOI: 10.1371/journal.pone.0275313] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/13/2022] [Indexed: 11/19/2022] Open
Abstract
To expose all undergraduate science students to the benefits of participating in research, many universities are integrating course-based undergraduate research experiences (CUREs) into their introductory biology laboratory curriculum. At large institutions, the bulk of introductory labs are instructed by graduate teaching assistants (GTAs). Graduate students, who are often teachers and researchers in training, may vary in their capacity to effectively teach undergraduates via the CURE model. To explore variation in GTA teaching and the subsequent outcomes for students, we used a case study research design at one institution where introductory biology students participate in GTA-taught CURE lab sections. We used multiple data sources, including in-class focus groups, worksheets, and surveys to explore student perceptions of the GTA-led CURE. Students perceived variation both in the ability of their GTAs to create a supportive and comfortable learning environment, and in the instructional priorities of their GTAs. We also compared student and GTA perspectives of student engagement with research elements in the CURE. While GTAs were divided in their perceptions of whether the CURE provided students with the opportunity to experience the element of relevant discovery, most students—regardless of their GTA—did not perceive that relevant discovery was emphasized in the CURE. Finally, individual GTAs seemed to influence how students perceived why they were participating in the CURE. These data imply that students in CUREs may have vastly different and potentially inequitable research experiences depending on their instructor.
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Affiliation(s)
- Emma C. Goodwin
- Department of Biology, Portland State University, Portland, Oregon, United States of America
| | - Jessica R. Cary
- Department of Biology, Portland State University, Portland, Oregon, United States of America
| | - Erin E. Shortlidge
- Department of Biology, Portland State University, Portland, Oregon, United States of America
- * E-mail:
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6
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Goodwin EC, Cary JR, Shortlidge EE. Enthusiastic but Inconsistent: Graduate Teaching Assistants' Perceptions of Their Role in the CURE Classroom. CBE Life Sci Educ 2021; 20:ar66. [PMID: 34714689 PMCID: PMC8715784 DOI: 10.1187/cbe.21-04-0106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/30/2021] [Accepted: 09/29/2021] [Indexed: 05/09/2023]
Abstract
Despite growing evidence of positive student outcomes from course-based undergraduate research experiences (CUREs), little consideration has been given to employing graduate teaching assistants (GTAs) as CURE instructors. GTAs may be novice researchers and/or teachers and likely vary in their interest in teaching a CURE. Guided by expectancy-value theory, we explored how GTAs' self-efficacy and values regarding teaching a CURE impact motivation and perceptions of their roles as CURE instructors. Using a multiple case study design, we interviewed nine GTAs who taught a network CURE at one research institution. Though most GTAs held a relatively high value for teaching a CURE for a range of reasons, some GTAs additionally perceived high costs associated with teaching the CURE. Through the interview data, we established three profiles to describe GTA perceptions of their role as CURE instructors: "Student Supporters," "Research Mentors," and "Content Deliverers." Those implementing GTA-led CUREs should consider that GTAs likely have different perceptions of both their role in the classroom and the associated costs of teaching a CURE. The variability in GTA perceptions of CUREs implies that undergraduate students of different GTAs are unlikely to experience the CURE equivalently.
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Affiliation(s)
- Emma C. Goodwin
- Biology Department, Portland State University, Portland, OR 97201
| | - Jessica R. Cary
- Biology Department, Portland State University, Portland, OR 97201
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7
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Goodwin EC, Anokhin V, Gray MJ, Zajic DE, Podrabsky JE, Shortlidge EE. Is This Science? Students' Experiences of Failure Make a Research-Based Course Feel Authentic. CBE Life Sci Educ 2021; 20:ar10. [PMID: 33600220 PMCID: PMC8108493 DOI: 10.1187/cbe.20-07-0149] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Course-based undergraduate research experiences (CUREs) and inquiry-based curricula both expose students to the scientific process. CUREs additionally engage students in novel and scientifically relevant research, with the intention of providing an "authentic" research experience. However, we have little understanding of which course design elements impact students' beliefs that they are experiencing "authentic" research. We designed a study to explore introductory biology students' perceptions of research authenticity in CURE and inquiry classes. Using the Laboratory Course Assessment Survey, we found that students in CURE sections perceived higher levels of authentic research elements than students in inquiry-based sections. To identify specific factors that impact perceptions of research authenticity, we administered weekly reflection questions to CURE students. Coding of reflection responses revealed that experiences of failure, iteration, using scientific practices, and the relevant discoveries in their projects enhanced students' perceived authenticity of their research experiences. Although failure and iteration can occur in both CUREs and inquiry-based curricula, our findings indicate these experiences-in conjunction with the Relevant Discovery element of a CURE-may be particularly powerful in enhancing student perceptions of research authenticity in a CURE.
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Affiliation(s)
- Emma C. Goodwin
- Biology Department, Portland State University, Portland, OR 97201
| | - Vladimir Anokhin
- Biology Department, Portland State University, Portland, OR 97201
| | | | - Daniel E. Zajic
- Biology Department, Portland State University, Portland, OR 97201
| | | | - Erin E. Shortlidge
- Biology Department, Portland State University, Portland, OR 97201
- *Address correspondence to: Erin E. Shortlidge ()
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8
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Dolan EL, Borrero M, Callis-Duehl K, Musgrove MMC, de Lima J, Ero-Tolliver I, Gerhart LM, Goodwin EC, Hamilton LR, Henry MA, Herrera J, Huot B, Kiser S, Ko ME, Kravec ME, Lee M, Limeri LB, Peffer ME, Pires D, Lugo JSR, Sharp SM, Suarez NA. Undergraduate Biology Education Research Gordon Research Conference: A Meeting Report. CBE Life Sci Educ 2020; 19:mr1. [PMID: 32357093 PMCID: PMC8697667 DOI: 10.1187/cbe.19-09-0188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/31/2020] [Accepted: 02/27/2020] [Indexed: 06/11/2023]
Abstract
The 2019 Undergraduate Biology Education Research Gordon Research Conference (UBER GRC), titled "Achieving Widespread Improvement in Undergraduate Education," brought together a diverse group of researchers and practitioners working to identify, promote, and understand widespread adoption of evidence-based teaching, learning, and success strategies in undergraduate biology. Graduate students and postdocs had the additional opportunity to present and discuss research during a Gordon Research Seminar (GRS) that preceded the GRC. This report provides a broad overview of the UBER GRC and GRS and highlights major themes that cut across invited talks, poster presentations, and informal discussions. Such themes include the importance of working in teams at multiple levels to achieve instructional improvement, the potential to use big data and analytics to inform instructional change, the need to customize change initiatives, and the importance of psychosocial supports in improving undergraduate student well-being and academic success. The report also discusses the future of the UBER GRC as an established meeting and describes aspects of the conference that make it unique, both in terms of facilitating dissemination of research and providing a welcoming environment for conferees.
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Affiliation(s)
- Erin L. Dolan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602
| | - Michelle Borrero
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, PR 00931
| | - Kristine Callis-Duehl
- Education Research and Outreach, Donald Danforth Plant Science Center, St. Louis, MO 63123
| | | | - Joelyn de Lima
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824
| | - Isi Ero-Tolliver
- Department of Biological Sciences, Hampton University, Hampton, VA 23666
| | - Laci M. Gerhart
- Department of Evolution and Ecology, University of California, Davis, Davis, CA 95616
| | - Emma C. Goodwin
- Department of Biology, Portland State University, Portland, OR 97201
| | | | | | - Jose Herrera
- Office of the Provost, Mercy College, Dobbs Ferry, NY 10522
| | - Bethany Huot
- Biological Sciences Program, Michigan State University, East Lansing, MI 48824
| | - Stacey Kiser
- Science Division, Lane Community College, Eugene, OR 97405
| | - Melissa E. Ko
- Thinking Matters Program, Stanford University, Stanford, CA 94305
| | - Marcy E. Kravec
- Department of Biological Sciences, Florida International University, Miami, FL 33199
| | - Mark Lee
- Department of Biology, Spelman College, Atlanta, GA 30314
| | - Lisa B. Limeri
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602
| | - Melanie E. Peffer
- Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309
| | - Debra Pires
- Department of Life Sciences Core Education, University of California, Los Angeles, Los Angeles, CA 90095
| | - Juan S. Ramirez Lugo
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, PR 00931
| | - Starlette M. Sharp
- Department of Curriculum and Instruction–Science Education, Pennsylvania State University, University Park, PA 16802
| | - Nicole A. Suarez
- Center for Research in Mathematics and Science Education, University of California, San Diego, and San Diego State University, San Diego, CA 92120
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Gaballa JM, Dabrian K, Desai R, Ngo R, Park D, Sakaji E, Sun Y, Tan B, Brinck M, Brobst O, Fernando R, Kim H, McCarthy S, Murphy M, Sarkis A, Sevier P, Singh A, Wu D, Wu MY, Ennis HA, Luhar R, Miller JE, Orchanian SB, Salbato AN, Alam S, Brenner L, Kailani Z, Laskow J, Ma X, Miikeda A, Nol-Bernardino P, Sukhina A, Walas N, Wei W, Do NP, Fournier CT, Kim CJ, Mosier SF, Pierson C, Romero IG, Sanchez M, Sawyerr O, Wang J, Watanabe R, Wu S, Chen A, Kazane K, Kettoola Y, Goodwin EC, Lund AJ, Villella W, Williams D, Freise A, Moberg Parker J. Genome Sequences of Cluster K Mycobacteriophages Deby, LaterM, LilPharaoh, Paola, SgtBeansprout, and Sulley. Microbiol Resour Announc 2019; 8:e01481-18. [PMID: 30643892 PMCID: PMC6328665 DOI: 10.1128/mra.01481-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 11/27/2018] [Indexed: 12/03/2022] Open
Abstract
Mycobacteriophages Deby, LaterM, LilPharaoh, Paola, SgtBeansprout, and Sulley were isolated from soil using Mycobacterium smegmatis mc2155. Genomic analysis indicated that they belong to subclusters K1 and K5. Their genomic architectures are typical of cluster K mycobacteriophages, with most variability occurring on the right end of the genome sequence.
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Affiliation(s)
- Joseph M. Gaballa
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Keeyon Dabrian
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Rachel Desai
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Ryan Ngo
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Diane Park
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Erin Sakaji
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Yiwei Sun
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Boon Tan
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Marcia Brinck
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Olivia Brobst
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Rebecca Fernando
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Hannah Kim
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, USA
| | - Siobhan McCarthy
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Michael Murphy
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Alexandra Sarkis
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Parker Sevier
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Amitoj Singh
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Darwin Wu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Min-Ying Wu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Hayley A. Ennis
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Rohan Luhar
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Justin E. Miller
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Stephanie B. Orchanian
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Alysha N. Salbato
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Sai Alam
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Lauren Brenner
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Zilla Kailani
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Joel Laskow
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Xinyu Ma
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Aika Miikeda
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Paola Nol-Bernardino
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Alisa Sukhina
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Nikolina Walas
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Wenyuan Wei
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Nam Phuong Do
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Christina T. Fournier
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Christy J. Kim
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Samantha F. Mosier
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Carly Pierson
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Ivonne G. Romero
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Mikael Sanchez
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Oyinlola Sawyerr
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Joyce Wang
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Rina Watanabe
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Samuel Wu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Annie Chen
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Katelynn Kazane
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Yousif Kettoola
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Emma C. Goodwin
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Andrew J. Lund
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, USA
| | - William Villella
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Drake Williams
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Amanda Freise
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
| | - Jordan Moberg Parker
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
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10
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Goodwin EC, Cao JN, Fletcher M, Flaiban JL, Shortlidge EE. Catching the Wave: Are Biology Graduate Students on Board with Evidence-Based Teaching? CBE Life Sci Educ 2018; 17:ar43. [PMID: 30142051 PMCID: PMC6234819 DOI: 10.1187/cbe.17-12-0281] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 04/11/2018] [Accepted: 04/18/2018] [Indexed: 05/24/2023]
Abstract
Graduate students hold a critical role in responding to national calls for increased adoption of evidence-based teaching (EBT) in undergraduate classrooms, as they not only serve as teaching assistants, but also represent the pool from which future faculty will emerge. Through interviews with 32 biology graduate students from 25 institutions nationwide, we sought to understand the progress these graduate students are making in adopting EBT through qualitative exploration of their perceptions of and experiences with both EBT and instructional professional development. Initial inductive content analysis of interview transcripts guided the holistic placement of participants within stages of Rogers's diffusions of innovations model, which we use as a theoretical framework to describe the progress of EBT adoption. We found that most graduate students in our sample are aware of and value EBT, but only 37.5% have implemented EBT. Many who were progressing toward EBT adoption had sought out supplementary instructional experiences beyond the requirements of their programs, and 72% perceived an institutional lack of support for teaching-related professional development opportunities. These data indicate that, while many graduate students are already engaged with the movement to adopt EBT, graduate training programs should emphasize increasing access to quality training in EBT strategies.
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Affiliation(s)
- Emma C. Goodwin
- Biology Department, Portland State University, Portland, OR 97201
| | - Jane N. Cao
- Biology Department, Portland State University, Portland, OR 97201
| | - Miles Fletcher
- Biology Department, Portland State University, Portland, OR 97201
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11
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Fournier MV, Chen J, Obenauer J, Goodwin EC, Tannenbaum SH, Brufsky AM. Abstract P2-10-08: A predictive test for neoadjuvant chemotherapy in breast cancer identifies a subset of triple negative patients with resistant disease and the poorest prognosis. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p2-10-08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Prediction of pathological complete response (pCR) for neoadjuvant treatment is an area of unmet clinical need, especially for triple negative breast cancer (TNBC) as pCR is correlated with better outcomes. Predicting which patients will have residual disease (RD) provides an opportunity to improve treatment planning. We developed a test to predict which patients are likely to achieve pCR or RD to the standard of care (taxane-based) neoadjuvant chemotherapy using gene expression profiling of 325 previously identified novel biomarkers.
Three microarray datasets were used (GSE22226, GSE25055, and GSE25065) including a total of 594 stage II-III breast cancer patients of which 125 (21%) achieved pCR, and 469 (79%) RD. ER+ tumors were present in 57% of the patients and 52% were PGR+. Almost 90% of the patients were Her2-. Of 231 TNBC, 78 (33.8%) achieved pCR, while 153 (66.2%) RD. Of 303 ER+Her- patients 26 (8.6%) achieved pCR while 277 (91.4%) RD. The cohort was divided into balanced populations with 476 patients used for training (80%) and test (20%) rounds of model development, while 118 patients were reserved as a validation set. Combining a “winnowing” process to remove genes with least predictive power, and hundreds of thousands of step-wise runs, followed by ranking genes based on conditional probabilities, we developed a 17-gene cassette (BA100) which was locked-down in the validation set with ROC (AUC) = 0.818. With a cut-off of 83% sensitivity and 68% specificity (PPV 0.4; NPV 0.94), BA100 achieved a 16% true positive rate (true pCR) and 55% true negative rate (true RD) identifying 76% of the patients who achieved pCR, and 69% of the patients with RD. In TNBC, BA100 classified 29% as true positives (TP), 36% as false positive (FP), 30% true negative (TN), and 4.8% false negative (FN). Kaplan Meier (KM) curves showed a significant difference in 5-year disease-free survival (5Y DFS) between TP and TN (p=0.00453) or FP (p=2.09E-06). However, FP had even worse outcomes than TN patients. To improve the TP rate, additional genes expressed in TNBC plus the original 325 genes were subjected to a second round of gene selection to discriminate between TP and FP, resulting in a 16-gene cassette (BA100.1). With a cut-off of 95% sensitivity and 73% specificity (PPV 0.7; NPV 0.95), applying BA100.1 reduced the FP rates from 24% to 9%, while correctly identifying 88% of RD in the validation set. KM curves showed no significant difference in 5Y DFS between 124 TNBC (53.7%) classified as TN versus 29 TNBC (12.6%) classified as FP, while a significant difference in survival rate was found between TNBC classified as TN vs TP (Cox Proportional Harzard p=8.42e-05).
Taken together, we developed a predictive test consisting of two gene cassettes that accurately identified 71% (88/104) of pCR, and 88% (417/469) of RD patients. Gene cassettes include several transcriptional repressors, PI3K signal transduction, components of telomerase, DNA repair genes, fatty acid metabolism and estrogen-independent proliferation. The test stratified TNBC with differential response to chemotherapy and survival rates so that novel approaches can be used without delay. Further validation will confirm the test utility.
Citation Format: Fournier MV, Chen J, Obenauer J, Goodwin EC, Tannenbaum SH, Brufsky AM. A predictive test for neoadjuvant chemotherapy in breast cancer identifies a subset of triple negative patients with resistant disease and the poorest prognosis [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-10-08.
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Affiliation(s)
- MV Fournier
- Bioarray Genetics Inc., Farmington, CT; Rancho Biosciences LLC, San Diego, CA; University of Connecticut Health Center, Farmington, CT; University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - J Chen
- Bioarray Genetics Inc., Farmington, CT; Rancho Biosciences LLC, San Diego, CA; University of Connecticut Health Center, Farmington, CT; University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - J Obenauer
- Bioarray Genetics Inc., Farmington, CT; Rancho Biosciences LLC, San Diego, CA; University of Connecticut Health Center, Farmington, CT; University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - EC Goodwin
- Bioarray Genetics Inc., Farmington, CT; Rancho Biosciences LLC, San Diego, CA; University of Connecticut Health Center, Farmington, CT; University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - SH Tannenbaum
- Bioarray Genetics Inc., Farmington, CT; Rancho Biosciences LLC, San Diego, CA; University of Connecticut Health Center, Farmington, CT; University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - AM Brufsky
- Bioarray Genetics Inc., Farmington, CT; Rancho Biosciences LLC, San Diego, CA; University of Connecticut Health Center, Farmington, CT; University of Pittsburgh School of Medicine, Pittsburgh, PA
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12
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Goodwin EC, DiMaio D. Induced senescence in HeLa cervical carcinoma cells containing elevated telomerase activity and extended telomeres. Cell Growth Differ 2001; 12:525-34. [PMID: 11714633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Proliferation of normal somatic human cells in culture is limited by replicative senescence, a growth-arrested state that appears to be triggered by the erosion of telomeres. Tumor cells such as HeLa cervical carcinoma cells, which contain short telomeres, can be induced to undergo senescence by various manipulations including oncogene withdrawal. Repression of the human papillomavirus (HPV) type 18 E6/E7 genes in HeLa cells by the bovine papillomavirus E2 transcriptional regulatory protein results in reactivation of the dormant p53 and p105(Rb) tumor suppressor pathways in these cells, repression of telomerase, and profound growth arrest. Strikingly, the growth-arrested cells rapidly and synchronously acquired numerous characteristics of primary cells undergoing replicative senescence. To explore the role of telomerase and telomere length in induced senescence, we expressed an exogenous hTERT gene, which encodes the catalytic subunit of telomerase, to generate stable HeLa cell clones with elevated telomerase activity and extended telomeres. Expression of the E2 protein in these cells repressed HPV E6/E7 expression, activated tumor suppressor pathways, and induced senescence as assessed by growth arrest, morphological changes, senescence-associated beta-galactosidase expression, and increased autofluorescence. Cells carrying the hTERT gene and control cells displayed identical responses to E2 expression. Therefore, HeLa cell senescence induced by HPV repression is not triggered by short telomeres or low levels of telomerase activity.
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Affiliation(s)
- E C Goodwin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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13
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Goodwin EC, DiMaio D. Repression of human papillomavirus oncogenes in HeLa cervical carcinoma cells causes the orderly reactivation of dormant tumor suppressor pathways. Proc Natl Acad Sci U S A 2000; 97:12513-8. [PMID: 11070078 PMCID: PMC18795 DOI: 10.1073/pnas.97.23.12513] [Citation(s) in RCA: 336] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Most cervical carcinomas express high-risk human papillomaviruses (HPVs) E6 and E7 proteins, which neutralize cellular tumor suppressor function. To determine the consequences of removing the E6 and E7 proteins from cervical cancer cells, we infected HeLa cells, a cervical carcinoma cell line that contains HPV18 DNA, with a recombinant virus that expresses the bovine papillomavirus E2 protein. Expression of the E2 protein resulted in rapid repression of HPV E6 and E7 expression, followed approximately 12 h later by profound inhibition of cellular DNA synthesis. Shortly after E6/E7 repression, there was dramatic posttranscriptional induction of p53. Two p53-responsive genes, mdm2 and p21, were induced with slightly slower kinetics than p53 and appeared to be functional, as assessed by inhibition of cyclin-dependent kinase activity and p53 destabilization. There was also dramatic posttranscriptional induction of p105(Rb) and p107 after E6/E7 repression, followed shortly thereafter by induction of p130. By 24 h after infection, only hypophosphorylated p105(Rb) was detectable and transcription of several Rb/E2F-regulated genes was dramatically repressed. Constitutive expression of the HPV16 E6/E7 genes alleviated E2-induced growth inhibition and impaired activation of the Rb pathway and repression of E2F-responsive genes. This dynamic response strongly suggests that the p53 and Rb tumor suppressor pathways are intact in HeLa cells and that repression of HPV E6 and E7 mobilizes these pathways in an orderly fashion to deliver growth inhibitory signals to the cells. Strikingly, the major alterations in the cell cycle machinery underlying cervical carcinogenesis can be reversed by repression of the endogenous HPV oncogenes.
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Affiliation(s)
- E C Goodwin
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
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14
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Wu L, Goodwin EC, Naeger LK, Vigo E, Galaktionov K, Helin K, DiMaio D. E2F-Rb complexes assemble and inhibit cdc25A transcription in cervical carcinoma cells following repression of human papillomavirus oncogene expression. Mol Cell Biol 2000; 20:7059-67. [PMID: 10982822 PMCID: PMC86242 DOI: 10.1128/mcb.20.19.7059-7067.2000] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2000] [Accepted: 07/05/2000] [Indexed: 11/20/2022] Open
Abstract
Expression of the bovine papillomavirus E2 protein in cervical carcinoma cells represses expression of integrated human papillomavirus (HPV) E6/E7 oncogenes, followed by repression of the cdc25A gene and other cellular genes required for cell cycle progression, resulting in dramatic growth arrest. To explore the mechanism of repression of cell cycle genes in cervical carcinoma cells following E6/E7 repression, we analyzed regulation of the cdc25A promoter, which contains two consensus E2F binding sites and a consensus E2 binding site. The wild-type E2 protein inhibited expression of a luciferase gene linked to the cdc25A promoter in HT-3 cervical carcinoma cells. Mutation of the distal E2F binding site in the cdc25A promoter abolished E2-induced repression, whereas mutation of the proximal E2F site or the E2 site had no effect. None of these mutations affected the activity of the promoter in the absence of E2 expression. Expression of the E2 protein also led to posttranscriptional increase in the level of E2F4, p105(Rb), and p130 and induced the formation of nuclear E2F4-p130 and E2F4-p105(Rb) complexes. This resulted in marked rearrangement of the protein complexes that formed at the distal E2F site in the cdc25A promoter, including the replacement of free E2F complexes with E2F4-p105(Rb) complexes. These experiments indicated that repression of E2F-responsive promoters following HPV E6/E7 repression was mediated by activation of the Rb tumor suppressor pathway and the assembly of repressing E2F4-Rb DNA binding complexes. Importantly, these experiments revealed that HPV-induced alterations in E2F transcription complexes that occur during cervical carcinogenesis are reversed by repression of HPV E6/E7 expression.
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MESH Headings
- Binding Sites
- Bovine papillomavirus 1/genetics
- Bovine papillomavirus 1/physiology
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Carcinoma, Squamous Cell/virology
- Carrier Proteins
- Cell Cycle/genetics
- Cell Cycle/physiology
- Cell Cycle Proteins
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Viral/genetics
- Consensus Sequence
- Cysteine Endopeptidases/metabolism
- DNA, Neoplasm/genetics
- DNA, Neoplasm/metabolism
- DNA-Binding Proteins/biosynthesis
- DNA-Binding Proteins/genetics
- E2F Transcription Factors
- E2F4 Transcription Factor
- Female
- Gene Expression Regulation, Neoplastic
- Gene Expression Regulation, Viral
- Genes, Retinoblastoma
- Humans
- Macromolecular Substances
- Multienzyme Complexes/metabolism
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Papillomaviridae/genetics
- Papillomaviridae/physiology
- Papillomavirus Infections/genetics
- Papillomavirus Infections/metabolism
- Papillomavirus Infections/pathology
- Papillomavirus Infections/virology
- Phosphoproteins/biosynthesis
- Phosphoproteins/genetics
- Promoter Regions, Genetic
- Proteasome Endopeptidase Complex
- Protein Binding
- Proteins
- Recombinant Fusion Proteins/biosynthesis
- Recombinant Fusion Proteins/genetics
- Retinoblastoma Protein/biosynthesis
- Retinoblastoma Protein/genetics
- Retinoblastoma Protein/metabolism
- Retinoblastoma-Binding Protein 1
- Retinoblastoma-Like Protein p130
- Transcription Factor DP1
- Transcription Factors/biosynthesis
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transfection
- Tumor Cells, Cultured/metabolism
- Tumor Virus Infections/genetics
- Tumor Virus Infections/metabolism
- Tumor Virus Infections/pathology
- Tumor Virus Infections/virology
- Uterine Cervical Neoplasms/genetics
- Uterine Cervical Neoplasms/metabolism
- Uterine Cervical Neoplasms/pathology
- Uterine Cervical Neoplasms/virology
- Viral Proteins/biosynthesis
- Viral Proteins/genetics
- Viral Proteins/physiology
- cdc25 Phosphatases/biosynthesis
- cdc25 Phosphatases/genetics
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Affiliation(s)
- L Wu
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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15
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Abstract
Expression of the bovine papillomavirus E2 regulatory protein in human cervical carcinoma cell lines repressed expression of the resident human papillomavirus E6 and E7 oncogenes and within a few days caused essentially all of the cells to synchronously display numerous phenotypic markers characteristic of cells undergoing replicative senescence. This process was accompanied by marked but in some cases transient alterations in the expression of cell cycle regulatory proteins and by decreased telomerase activity. We propose that the human papillomavirus E6 and E7 proteins actively prevent senescence from occurring in cervical carcinoma cells, and that once viral oncogene expression is extinguished, the senescence program is rapidly executed. Activation of endogenous senescence pathways in cancer cells may represent an alternative approach to treat human cancers.
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Affiliation(s)
- E C Goodwin
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
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16
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Naeger LK, Goodwin EC, Hwang ES, DeFilippis RA, Zhang H, DiMaio D. Bovine papillomavirus E2 protein activates a complex growth-inhibitory program in p53-negative HT-3 cervical carcinoma cells that includes repression of cyclin A and cdc25A phosphatase genes and accumulation of hypophosphorylated retinoblastoma protein. Cell Growth Differ 1999; 10:413-22. [PMID: 10392903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
The bovine papillomavirus E2 protein can inhibit the proliferation of HT-3 cells, a p53-negative cervical carcinoma cell line containing integrated human papillomavirus type 30 DNA. Here, we analyzed HT-3 cells to explore the mechanism of p53-independent E2-mediated growth inhibition. Expression of the E2 protein repressed expression of the endogenous human papillomavirus type 30 E6/E7 genes. This was accompanied by hypophosphorylation and increased accumulation of p105Rb and repression of E2F1 expression. The E2 protein also caused reduced cyclin-dependent kinase (cdk) 2 activity, but this did not appear to be due to increased expression of cdk inhibitors. Rather, expression of cyclin A, which regulates cdk2 activity, and the cdc25A and cdc25B phosphatases, which are thought to activate cdk2, was significantly reduced at both the RNA and protein levels in response to E2 expression. The E2 protein reduced expression of cdc25A and cdc25B in both HT-3 and HeLa cells, but not in cells that were not growth-inhibited by the E2 protein. E2 point mutants unable to inhibit cell growth did not repress cdc25A and cdc25B expression, nor did the cell cycle inhibitors hydroxyurea and mimosine. Based on these results and the known properties of cell cycle components, we propose a model to account for E2-induced growth inhibition of cervical carcinoma cell lines.
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Affiliation(s)
- L K Naeger
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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17
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Goodwin EC, Naeger LK, Breiding DE, Androphy EJ, DiMaio D. Transactivation-competent bovine papillomavirus E2 protein is specifically required for efficient repression of human papillomavirus oncogene expression and for acute growth inhibition of cervical carcinoma cell lines. J Virol 1998; 72:3925-34. [PMID: 9557678 PMCID: PMC109618 DOI: 10.1128/jvi.72.5.3925-3934.1998] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/1997] [Accepted: 02/10/1998] [Indexed: 02/07/2023] Open
Abstract
The papillomavirus E2 proteins can function as sequence-specific transactivators or transrepressors of transcription and as cofactors in viral DNA replication. We previously demonstrated that acute expression of the bovine papillomavirus type 1 (BPV1) E2 protein in HeLa and HT-3 cervical carcinoma cell lines greatly reduced cellular proliferation by imposing a specific G1/S phase growth arrest. In this report, we analyzed the effects of a panel of point mutations in the BPV1 E2 protein to identify the functional requirements for acute growth inhibition. Disruption of E2-specific transactivation by mutations within either the transactivation domain or the DNA binding domain severely impaired E2-mediated growth inhibition in HeLa and HT-3 cells, even though these mutants retain various other E2 activities. This result indicates that functional transactivation activity is required for acute E2-mediated growth inhibition. HeLa cells, which contain a wild-type p53 gene, and HT-3 cells, which contain a transactivation-defective p53 gene, exhibited similar responses to the E2 mutants, suggesting that identical functions of the E2 protein were required for growth arrest regardless of p53 status. Replacement of the E2 transactivation domain with that of the herpes simplex virus VP16 generated a chimeric transactivator that efficiently stimulated expression of an E2-responsive reporter plasmid yet was completely defective for growth inhibition, suggesting that an E2-specific transactivation function is required for growth arrest. Surprisingly, the transactivation-defective E2 mutants were also markedly defective in their ability to repress transcription of the native human papillomavirus type 18 (HPV18) E6/E7 oncogenes in HeLa cells and of the HPV18 promoter present in a transfected reporter plasmid. These mutants were also defective in their ability to increase p53 levels. Therefore, efficient repression of the HPV18 promoter in HeLa cells is not merely a consequence of the binding of an E2 protein to appropriately situated binding sites in the promoter.
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Affiliation(s)
- E C Goodwin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520-8005, USA
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18
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Abstract
The methylation of internal adenosine residues in mRNA only occurs within GAC or AAC sequences. Although both of these sequence motifs are utilized, a general preference has been noted for the extended sequence RGACU. Not all RGACU sequences in an mRNA are methylated and the mechanisms that govern the selection of methylation sites in mRNA remain unclear. To address this problem we have examined the methylation of transcripts containing sequences of a natural mRNA, namely, bovine prolactin mRNA. In this mRNA, a specific AGACU sequence in the 3' untranslated region is the predominant site of methylation both in vivo and in vitro. The degree to which N6-adenosine methyltransferase recognizes the sequence context of the consensus methylation site was explored by mutational analysis of the nucleotides adjacent to the core sequence as well as the extended regions in which the core element was found. Our results indicate that efficient methylation depends on the extended five nucleotide consensus sequence but is strongly influenced by the context in which the consensus sequence occurs within the overall mRNA molecule. Furthermore, consensus methylation sites present in an RNA duplex are not recognized by the methyltransferase.
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Affiliation(s)
- P Narayan
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 44106
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19
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Goodwin EC, Rottman FM. The 3'-flanking sequence of the bovine growth hormone gene contains novel elements required for efficient and accurate polyadenylation. J Biol Chem 1992; 267:16330-4. [PMID: 1644817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In addition to the conserved AAUAAA hexanucleotide, GU- and U-rich sequences in the 3'-flanking region are thought to be critical for efficient polyadenylation. The 3'-flanking sequence requirements for efficient and accurate polyadenylation of the bovine growth hormone (bGH) gene were determined by quantitative S1 nuclease analysis of transcripts derived from various bGH 3' deletions and block mutations transiently transfected into COS-1 cells. Though the bGH 3'-flanking sequence contains a portion of the putative GU efficiency element, we find that mutation of this element leads to a marginal decrease in efficiency similar to that from mutation of other sequences that do not contain recognizable GU- or U-rich motifs. The data are consistent with a diffuse efficiency element in the bGH polyadenylation signal rather than a discrete element as is thought to exist in other mammalian signals. We have also determined that a region from 18 to 27 nucleotides downstream of the cleavage site contains sequences required for correctly positioning the cleavage site.
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Affiliation(s)
- E C Goodwin
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
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20
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Goodwin EC, Rottman FM. The use of RNase H and poly(A) junction oligonucleotides in the analysis of in vitro polyadenylation reaction products. Nucleic Acids Res 1992; 20:916. [PMID: 1311834 PMCID: PMC312043 DOI: 10.1093/nar/20.4.916] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- E C Goodwin
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 44106
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21
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Woychik RP, Camper SA, Lyons RH, Horowitz S, Goodwin EC, Rottman FM. Cloning and nucleotide sequencing of the bovine growth hormone gene. Nucleic Acids Res 1982; 10:7197-210. [PMID: 6296767 PMCID: PMC326998 DOI: 10.1093/nar/10.22.7197] [Citation(s) in RCA: 154] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A gene coding for bovine growth hormone was isolated from a bovine genomic library. The nucleotide sequence of the coding regions of the gene was found to be identical with that of a nearly full-length growth hormone cDNA clone. The gene sequence is approximately 1800 bp in length and contains four intervening sequences. The second intervening sequence of 227 nucleotides does not contain a repetitive element similar to that observed in the rat growth hormone gene. A comparison of the 5' and 3' flanking and untranslated regions of the bovine, human and rat growth hormone genes revealed many areas of highly conserved sequence. Especially noteworthy was the observation that all three genes had a 38 nucleotide homologous sequence within their 5' flanking regions located about 100 bp upstream from their transcription initiation sites.
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