1
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Hess RA, Erickson OA, Cole RB, Isaacs JM, Alvarez-Clare S, Arnold J, Augustus-Wallace A, Ayoob JC, Berkowitz A, Branchaw J, Burgio KR, Cannon CH, Ceballos RM, Cohen CS, Coller H, Disney J, Doze VA, Eggers MJ, Ferguson EL, Gray JJ, Greenberg JT, Hoffmann A, Jensen-Ryan D, Kao RM, Keene AC, Kowalko JE, Lopez SA, Mathis C, Minkara M, Murren CJ, Ondrechen MJ, Ordoñez P, Osano A, Padilla-Crespo E, Palchoudhury S, Qin H, Ramírez-Lugo J, Reithel J, Shaw CA, Smith A, Smith RJ, Tsien F, Dolan EL. Virtually the Same? Evaluating the Effectiveness of Remote Undergraduate Research Experiences. CBE Life Sci Educ 2023; 22:ar25. [PMID: 37058442 PMCID: PMC10228262 DOI: 10.1187/cbe.22-01-0001] [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: 01/04/2022] [Revised: 02/27/2023] [Accepted: 03/17/2023] [Indexed: 06/02/2023]
Abstract
In-person undergraduate research experiences (UREs) promote students' integration into careers in life science research. In 2020, the COVID-19 pandemic prompted institutions hosting summer URE programs to offer them remotely, raising questions about whether undergraduates who participate in remote research can experience scientific integration and whether they might perceive doing research less favorably (i.e., not beneficial or too costly). To address these questions, we examined indicators of scientific integration and perceptions of the benefits and costs of doing research among students who participated in remote life science URE programs in Summer 2020. We found that students experienced gains in scientific self-efficacy pre- to post-URE, similar to results reported for in-person UREs. We also found that students experienced gains in scientific identity, graduate and career intentions, and perceptions of the benefits of doing research only if they started their remote UREs at lower levels on these variables. Collectively, students did not change in their perceptions of the costs of doing research despite the challenges of working remotely. Yet students who started with low cost perceptions increased in these perceptions. These findings indicate that remote UREs can support students' self-efficacy development, but may otherwise be limited in their potential to promote scientific integration.
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Affiliation(s)
- Riley A. Hess
- Department of Psychology, University of Georgia, Athens, GA 30602
| | - Olivia A. Erickson
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602
| | - Rebecca B. Cole
- Department of Psychology, University of Georgia, Athens, GA 30602
| | - Jared M. Isaacs
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602
| | | | - Jonathan Arnold
- Department of Genetics, University of Georgia, Athens, GA 30602
| | | | - Joseph C. Ayoob
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260
| | - Alan Berkowitz
- Education Department, Cary Institute for Ecosystem Studies, Millbrook, NY 12545
| | - Janet Branchaw
- WISCIENCE and Department of Kinesiology, University of Wisconsin–Madison, Madison, WI 53706
| | - Kevin R. Burgio
- Education Department, Cary Institute for Ecosystem Studies, Millbrook, NY 12545
| | | | | | - C. Sarah Cohen
- Department of Biology, Estuary and Ocean Science Center, San Francisco State University, San Francisco, CA 94132
| | - Hilary Coller
- Department of Molecular, Cell and Developmental Biology and, University of California Los Angeles, Los Angeles, CA 90095
| | - Jane Disney
- Community Environmental Health Laboratory, Mt. Desert Island Biological Laboratory, Salisbury Cove, ME 04672
| | - Van A. Doze
- Department of Biomedical Sciences, University of North Dakota, Grand Forks, ND 58202
| | - Margaret J. Eggers
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717
| | - Edwin L. Ferguson
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 606307
| | - Jeffrey J. Gray
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Jean T. Greenberg
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 606307
| | - Alexander Hoffmann
- Department of Microbiology, Immunology, and Molecular Genetics and Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA 90095
| | - Danielle Jensen-Ryan
- Department of Math and Sciences, Laramie County Community College, Cheyenne, WY 82007
| | - Robert M. Kao
- Science Department, College of Arts and Sciences, Heritage University, Toppenish, WA 98948
| | - Alex C. Keene
- Department of Biology, Texas A&M University, College Station, TX 77840
| | - Johanna E. Kowalko
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015
| | - Steven A. Lopez
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115
| | | | - Mona Minkara
- Department of Bioengineering, Northeastern University, Boston, MA 02115
| | | | - Mary Jo Ondrechen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115
| | - Patricia Ordoñez
- Department of Computer Science, University of Puerto Rico–Río Piedras, San Juan, PR 00925
| | - Anne Osano
- Department of Natural Sciences, Bowie State University, Bowie, MD 20715
| | - Elizabeth Padilla-Crespo
- Department of Science and Technology, Inter American University of Puerto Rico–Aguadilla, Aguadilla, PR 00605
| | | | - Hong Qin
- Department of Computer Science and Engineering and Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, TN 37403
| | - Juan Ramírez-Lugo
- Department of Biology, University of Puerto Rico–Río Piedras, San Juan, PR 00925
| | - Jennifer Reithel
- Rocky Mountain Biological Laboratory, PO Box 519, Crested Butte, CO 81224
| | - Colin A. Shaw
- Undergraduate Scholars Program and Department of Earth Sciences, Montana State University, Bozeman, MT 59717
| | - Amber Smith
- Wisconsin Institute for Science Education and Community Engagement, University of Wisconsin–Madison, Madison, WI 53706
| | - Rosemary J. Smith
- Rocky Mountain Biological Laboratory, PO Box 519, Crested Butte, CO 81224
- Department of Biological Sciences, Idaho State University, Pocatello, ID 83209
| | - Fern Tsien
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA 70112
| | - Erin L. Dolan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602
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Ayoob JC, Ramírez-Lugo JS. Ten simple rules for running a summer research program. PLoS Comput Biol 2022; 18:e1010588. [PMID: 36327228 PMCID: PMC9632878 DOI: 10.1371/journal.pcbi.1010588] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To continue to advance the field of computational biology and fill the constantly growing need for new trainees who are well positioned for success, immersive summer research experiences have proven to be effective in preparing students to navigate the challenges that lay ahead in becoming future computational biologists. Here, we describe 10 simple rules for planning, offering, running, and improving a summer research program in computational biology that supports students in honing technical competencies for success in research and developing skills to become successful scientific professionals.
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Affiliation(s)
- Joseph C. Ayoob
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
| | - Juan S. Ramírez-Lugo
- Department of Biology, Universidad de Puerto Rico, Rio Piedras, San Juan, Puerto Rico, United States of America
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3
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Erickson OA, Cole RB, Isaacs JM, Alvarez-Clare S, Arnold J, Augustus-Wallace A, Ayoob JC, Berkowitz A, Branchaw J, Burgio KR, Cannon CH, Ceballos RM, Cohen CS, Coller H, Disney J, Doze VA, Eggers MJ, Farina S, Ferguson EL, Gray JJ, Greenberg JT, Hoffmann A, Jensen-Ryan D, Kao RM, Keene AC, Kowalko JE, Lopez SA, Mathis C, Minkara M, Murren CJ, Ondrechen MJ, Ordoñez P, Osano A, Padilla-Crespo E, Palchoudhury S, Qin H, Ramírez-Lugo J, Reithel J, Shaw CA, Smith A, Smith R, Summers AP, Tsien F, Dolan EL. "How Do We Do This at a Distance?!" A Descriptive Study of Remote Undergraduate Research Programs during COVID-19. CBE Life Sci Educ 2022; 21:ar1. [PMID: 34978923 PMCID: PMC9250374 DOI: 10.1187/cbe.21-05-0125] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The COVID-19 pandemic shut down undergraduate research programs across the United States. A group of 23 colleges, universities, and research institutes hosted remote undergraduate research programs in the life sciences during Summer 2020. Given the unprecedented offering of remote programs, we carried out a study to describe and evaluate them. Using structured templates, we documented how programs were designed and implemented, including who participated. Through focus groups and surveys, we identified programmatic strengths and shortcomings as well as recommendations for improvements from students' perspectives. Strengths included the quality of mentorship, opportunities for learning and professional development, and a feeling of connection with a larger community. Weaknesses included limited cohort building, challenges with insufficient structure, and issues with technology. Although all programs had one or more activities related to diversity, equity, inclusion, and justice, these topics were largely absent from student reports even though programs coincided with a peak in national consciousness about racial inequities and structural racism. Our results provide evidence for designing remote Research Experiences for Undergraduates (REUs) that are experienced favorably by students. Our results also indicate that remote REUs are sufficiently positive to further investigate their affordances and constraints, including the potential to scale up offerings, with minimal concern about disenfranchising students.
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Affiliation(s)
- Olivia A. Erickson
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602
| | - Rebecca B. Cole
- Department of Psychology, University of Georgia, Athens, GA 30602
| | - Jared M. Isaacs
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602
| | | | - Jonathan Arnold
- Department of Genetics, University of Georgia, Athens, GA 30602
| | - Allison Augustus-Wallace
- Department of Medicine & Office of Diversity & Community Engagement, Louisiana State University Health Sciences Center, New Orleans, LA 70112
| | - Joseph C. Ayoob
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260
| | - Alan Berkowitz
- Education Department, Cary Institute for Ecosystem Studies, Millbrook, NY 12545
| | - Janet Branchaw
- WISCIENCE and the Department of Kinesiology, University of Wisconsin–Madison, Madison, WI 53706
| | - Kevin R. Burgio
- Education Department, Cary Institute for Ecosystem Studies, Millbrook, NY 12545
- New York City Audubon Society, New York, NY 10010; and Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269
| | | | | | - C. Sarah Cohen
- Department of Biology, Estuary and Ocean Science Center, San Francisco State University, San Francisco, CA 94132
| | - Hilary Coller
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095
| | - Jane Disney
- Community Environmental Health Laboratory, Mt. Desert Island Biological Laboratory, Salisbury Cove, ME 04672
| | - Van A. Doze
- Department of Biomedical Sciences, University of North Dakota, Grand Forks, ND 58202
| | - Margaret J. Eggers
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717
| | - Stacy Farina
- Department of Biology, Howard University, Washington, DC 20059
| | - Edwin L. Ferguson
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | - Jeffrey J. Gray
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Jean T. Greenberg
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
| | - Alexander Hoffmann
- Department of Microbiology, Immunology, and Molecular Genetics, and Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, 90095
| | - Danielle Jensen-Ryan
- Department of Math and Sciences, Laramie County Community College, Cheyenne, WY 82007
| | - Robert M. Kao
- Science Department, College of Arts and Sciences, Heritage University, Toppenish, WA 98948
| | - Alex C. Keene
- Department of Biological Sciences, Florida Atlantic University, Jupiter, FL 33458
| | | | - Steven A. Lopez
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115
| | - Camille Mathis
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD 21218
| | - Mona Minkara
- Department of Bioengineering, Northeastern University, Boston, MA 02115
| | | | - Mary Jo Ondrechen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115
| | - Patricia Ordoñez
- Department of Computer Science, University of Puerto Rico Río Piedras, San Juan, PR 00925
| | - Anne Osano
- Department of Natural Sciences, Bowie State University, Bowie, MD 20715
| | - Elizabeth Padilla-Crespo
- Department of Science and Technology, Inter American University of Puerto Rico–Aguadilla, Aguadilla, PR 00605
| | - Soubantika Palchoudhury
- Civil and Chemical Engineering Department, University of Tennessee at Chattanooga, Chattanooga, TN 37403-2598
| | - Hong Qin
- Department of Computer Science and Engineering, Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, TN 37403
| | - Juan Ramírez-Lugo
- Department of Biology, University of Puerto Rico Río Piedras, San Juan, PR 00925
| | - Jennifer Reithel
- Rocky Mountain Biological Laboratory, PO Box 519, Crested Butte, CO 81224
| | - Colin A. Shaw
- Undergraduate Scholars Program and Department of Earth Sciences, Montana State University, Bozeman, MT 59717
| | - Amber Smith
- Wisconsin Institute for Science Education and Community Engagement, University of Wisconsin–Madison, Madison, WI 53706
| | - Rosemary Smith
- Rocky Mountain Biological Laboratory, PO Box 519, Crested Butte, CO 81224
- Department of Biological Sciences, Idaho State University, Pocatello, ID 83209
| | - Adam P. Summers
- Friday Harbor Laboratories, Bio/SAFS, University of Washington, Friday Harbor, WA 98250
| | - Fern Tsien
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA 70112
| | - Erin L. Dolan
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602
- *Address correspondence to: Erin L. Dolan, ()
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Ayoob JC, Boyce RD, Livshits S, Bruno TC, Delgoffe GM, Galson DL, Duncan AW, Atkinson JM, Oesterreich S, Evans S, Alikhani M, Baker TA, Pratt S, DeHaan KJ, Chen Y, Boone DN. Getting to YES: The Evolution of the University of Pittsburgh Medical Center Hillman Cancer Center Youth Enjoy Science (YES) Academy. J STEM Outreach 2022; 5:10.15695/jstem/v5i2.02. [PMID: 36910569 PMCID: PMC9997544 DOI: 10.15695/jstem/v5i2.02] [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] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The University of Pittsburgh Medical Center Hillman Cancer Center Academy (Hillman Academy) has the primary goal of reaching high school students from underrepresented and disadvantaged backgrounds and guiding them through a cutting-edge research and professional development experience that positions them for success in STEM. With this focus, the Hillman Academy has provided nearly 300 authentic mentored research internship opportunities to 239 students from diverse backgrounds over the past 13 years most of whom matriculated into STEM majors in higher education. These efforts have helped shape a more diverse generation of future scientists and clinicians, who will enrich these fields with their unique perspectives and lived experiences. In this paper, we describe our program and the strategies that led to its growth into a National Institutes of Health Youth Enjoy Science-funded program including our unique multi-site structure, tiered mentoring platform, multifaceted recruitment approach, professional and academic development activities, and a special highlight of a set of projects with Deaf and Hard of Hearing students. We also share student survey data from the past six years that indicate satisfaction with the program, self-perceived gains in key areas of scientific development, awareness of careers in STEM, and an increased desire to pursue advanced degrees in STEM.
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Affiliation(s)
- Joseph C Ayoob
- University of Pittsburgh School of Medicine, Department of Computational and Systems Biology
| | - Richard D Boyce
- University of Pittsburgh School of Medicine, Department of Biomedical Informatics
| | - Solomon Livshits
- University of Pittsburgh School of Medicine, Department of Biomedical Informatics
| | - Tullia C Bruno
- University of Pittsburgh School of Medicine, Department of Immunology (Tumor Microenvironment Center and Cancer Immunology and Immunotherapy Program).,UPMC Hillman Cancer Center
| | - Greg M Delgoffe
- University of Pittsburgh School of Medicine, Department of Immunology (Tumor Microenvironment Center and Cancer Immunology and Immunotherapy Program).,UPMC Hillman Cancer Center
| | - Deborah L Galson
- University of Pittsburgh School of Medicine, Department of Medicine (Division of Hematology/Oncology, McGowan Institute for Regenerative Medicine).,UPMC Hillman Cancer Center
| | - Andrew W Duncan
- University of Pittsburgh School of Medicine, Department of Pathology (McGowan Institute for Regenerative Medicine).,University of Pittsburgh School of Medicine, Department of Bioengineering.,UPMC Hillman Cancer Center
| | - Jennifer M Atkinson
- University of Pittsburgh School of Medicine, Department of Pharmacology and Chemical Biology.,Women's Cancer Research Center, Magee Women's Research Institute.,UPMC Hillman Cancer Center
| | - Steffi Oesterreich
- University of Pittsburgh School of Medicine, Department of Pharmacology and Chemical Biology.,Women's Cancer Research Center, Magee Women's Research Institute.,UPMC Hillman Cancer Center
| | - Steve Evans
- University of Pittsburgh School of Medicine, Department of Surgery
| | - Malihe Alikhani
- University of Pittsburgh, School of Computing and Information, Department of Computer Science
| | - Tobias A Baker
- University of Pittsburgh School of Medicine, Department of Biomedical Informatics
| | - Sheila Pratt
- University of Pittsburgh, School of Health and Rehabilitation Sciences, Department of Communication Science and Disorders
| | | | - Yuanyuan Chen
- University of Pittsburgh School of Medicine, Department of Ophthalmology
| | - David N Boone
- University of Pittsburgh School of Medicine, Department of Biomedical Informatics.,UPMC Hillman Cancer Center
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5
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Ayoob JC, Kangas JD. 10 simple rules for teaching wet-lab experimentation to computational biology students, i.e., turning computer mice into lab rats. PLoS Comput Biol 2020; 16:e1007911. [PMID: 32497035 PMCID: PMC7271982 DOI: 10.1371/journal.pcbi.1007911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Joseph C. Ayoob
- Joint Carnegie Mellon–University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, Pennsylvania, United States of America
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
| | - Joshua D. Kangas
- Joint Carnegie Mellon–University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, Pennsylvania, United States of America
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
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6
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Delubac D, Highley CB, Witzberger-Krajcovic M, Ayoob JC, Furbee EC, Minden JS, Zappe S. Microfluidic system with integrated microinjector for automated Drosophila embryo injection. Lab Chip 2012; 12:4911-4919. [PMID: 23042419 DOI: 10.1039/c2lc40104e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Drosophila is one of the most important model organisms in biology. Knowledge derived from the recently sequenced 12 genomes of various Drosophila species can today be combined with the results of more than 100 years of research to systematically investigate Drosophila biology at the molecular level. In order to enable automated, high-throughput manipulation of Drosophila embryos, we have developed a microfluidic system based on a Pyrex-silicon-Pyrex sandwich structure with integrated, surface-micromachined silicon nitride injector for automated injection of reagents. Our system automatically retrieves embryos from an external reservoir, separates potentially clustered embryos through a sheath flow mechanisms, passively aligns an embryo with the integrated injector through geometric constraints, and pushes the embryo onto the injector through flow drag forces. Automated detection of an embryo at injection position through an external camera triggers injection of reagents and subsequent ejection of the embryo to an external reservoir. Our technology can support automated screens based on Drosophila embryos as well as creation of transgenic Drosophila lines. Apart from Drosophila embryos, the layout of our system can be easily modified to accommodate injection of oocytes, embryos, larvae, or adults of other species and fills an important technological gap with regard to automated manipulation of multicellular organisms.
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Affiliation(s)
- Daniel Delubac
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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7
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Wu Z, Sweeney LB, Ayoob JC, Chak K, Andreone BJ, Ohyama T, Kerr R, Luo L, Zlatic M, Kolodkin AL. A combinatorial semaphorin code instructs the initial steps of sensory circuit assembly in the Drosophila CNS. Neuron 2011; 70:281-98. [PMID: 21521614 DOI: 10.1016/j.neuron.2011.02.050] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2011] [Indexed: 01/19/2023]
Abstract
Longitudinal axon fascicles within the Drosophila embryonic CNS provide connections between body segments and are required for coordinated neural signaling along the anterior-posterior axis. We show here that establishment of select CNS longitudinal tracts and formation of precise mechanosensory afferent innervation to the same CNS region are coordinately regulated by the secreted semaphorins Sema-2a and Sema-2b. Both Sema-2a and Sema-2b utilize the same neuronal receptor, plexin B (PlexB), but serve distinct guidance functions. Localized Sema-2b attraction promotes the initial assembly of a subset of CNS longitudinal projections and subsequent targeting of chordotonal sensory afferent axons to these same longitudinal connectives, whereas broader Sema-2a repulsion serves to prevent aberrant innervation. In the absence of Sema-2b or PlexB, chordotonal afferent connectivity within the CNS is severely disrupted, resulting in specific larval behavioral deficits. These results reveal that distinct semaphorin-mediated guidance functions converge at PlexB and are critical for functional neural circuit assembly.
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Affiliation(s)
- Zhuhao Wu
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Howard Hughes Medical Institute, Baltimore, MD 21205, USA
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8
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Abstract
Plexin receptors play a crucial role in the transduction of axonal guidance events elicited by semaphorin proteins. In Drosophila, Plexin A(PlexA) is a receptor for the transmembrane semaphorin semaphorin-1a (Sema-1a)and is required for motor and central nervous system (CNS) axon guidance in the developing embryonic nervous system. However, it remains unknown how PlexB functions during neural development and which ligands serve to activate this receptor. Here, we show that plexB, like plexA, is robustly expressed in the developing CNS and is required for motor and CNS axon pathfinding. PlexB and PlexA serve both distinct and shared neuronal guidance functions. We observe a physical association between these two plexin receptors in vivo and find that they can utilize common downstream signaling mechanisms. PlexB does not directly bind to the cytosolic semaphorin signaling component MICAL (molecule that interacts with CasL), but requires MICAL for certain axonal guidance functions. Ligand binding and genetic analyses demonstrate that PlexB is a receptor for the secreted semaphorin Sema-2a,suggesting that secreted and transmembrane semaphorins in Drosophilause PlexB and PlexA, respectively, for axon pathfinding during neural development. These results establish roles for PlexB in central and peripheral axon pathfinding, define a functional ligand for PlexB, and implicate common signaling events in plexin-mediated axonal guidance.
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Affiliation(s)
- Joseph C Ayoob
- Howard Hughes Medical Institute, Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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9
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Abstract
Cyclic nucleotide levels within extending growth cones influence how navigating axons respond to guidance cues. Pharmacological alteration of cAMP or cGMP signaling in vitro dramatically modulates how growth cones respond to attractants and repellents, although how these second messengers function in the context of guidance cue signaling cascades in vivo is poorly understood. We report here that the Drosophila receptor-type guanylyl cyclase Gyc76C is required for semaphorin-1a (Sema-1a)-plexin A repulsive axon guidance of motor axons in vivo. Our genetic analyses define a neuronal requirement for Gyc76C in axonal repulsion. Additionally, we find that the integrity of the Gyc76C catalytic cyclase domain is critical for Gyc76C function in Sema-1a axon repulsion. Our results support a model in which cGMP production by Gyc76C facilitates Sema-1a-plexin A-mediated defasciculation of motor axons, allowing for the generation of neuromuscular connectivity in the developing Drosophila embryo.
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Affiliation(s)
- Joseph C Ayoob
- Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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10
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Dabiri GA, Ayoob JC, Turnacioglu KK, Sanger JM, Sanger JW. Use of green fluorescent proteins linked to cytoskeletal proteins to analyze myofibrillogenesis in living cells. Methods Enzymol 2003; 302:171-86. [PMID: 12876770 DOI: 10.1016/s0076-6879(99)02017-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [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: 12/14/2022]
Abstract
Once the appropriate site has been selected for the attachment of GFP to the sarcomeric protein, it is quite remarkable that the large size of the GFP molecule does not appear to interfere with the localization of the fluorescent sarcomeric proteins into the sarcomeric regions of the myofibrils. A similar approach using truncated parts of sarcomeric proteins linked to GFP should allow studies of the targeting properties of other sarcomeric domains for localization and assembly studies.
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Affiliation(s)
- G A Dabiri
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6058, USA
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11
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Malish HR, Freeman NL, Zurawski DV, Chowrashi P, Ayoob JC, Sanger JW, Sanger JM. Potential role of the EPEC translocated intimin receptor (Tir) in host apoptotic events. Apoptosis 2003; 8:179-90. [PMID: 12766478 DOI: 10.1023/a:1022974710488] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [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: 11/12/2022]
Abstract
Apoptosis, or programmed cell death, is a well-ordered process that allows damaged or diseased cells to be removed from an organism without severe inflammatory reactions. Multiple factors, including microbial infection, can induce programmed death and trigger reactions in both host and microbial cellular pathways. Whereas an ultimate outcome is host cell death, these apoptotic triggering mechanisms may also facilitate microbial spread and prolong infection. To gain a better understanding of the complex events of host cell response to microbial infection, we investigated the molecular role of the microorganism Enteropathogenic Escherichia coli (EPEC) in programmed cell death. We report that wild type strain of EPEC, E2348/69, induced apoptosis in cultured PtK2 and Caco-2 cells, and in contrast, infections by the intracellularly localized Listeria monocytogenes did not. Fractionation and concentration of EPEC-secreted proteins demonstrated that soluble protein factors expressed by the bacteria were capable of inducing the apoptotic events in the absence of organism attachment, suggesting adherence is not required to induce host cell death. Among the known EPEC proteins secreted via the Type III secretion (TTS) system, we identified the translocated intimin receptor (Tir) in the apoptosis-inducing protein sample. In addition, host cell ectopic expression of an EPEC GFP-Tir showed mitochondrial localization of the protein and produced apoptotic effects in transfected cells. Taken together, these results suggest a potential EPEC Tir-mediated role in the apoptotic signaling cascade of infected host cells.
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Affiliation(s)
- H R Malish
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6058, USA
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12
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Affiliation(s)
- J C Ayoob
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, USA
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13
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Abstract
How do myofibrils assemble in cardiac muscle cells? When does titin first assemble into myofibrils? What is the role of titin in the formation of myofibrils in cardiac muscle cells? This chapter reviews when titin is first detected in cultured cardiomyocytes that have been freshly isolated from embryonic avian hearts. Our results support a model for myofibrillogenesis that involves three stages of assembly: premyofibrils, nascent myofibrils and mature myofibrils. Titin and muscle thick filaments were first detected associated with the nascent myofibrils. The Z-band targeting site for titin is localized in the N-terminus of titin. This region of titin binds alpha-actinin and less avidly vinculin. Thus the N-terminus of titin via its binding to alpha-actinin, and vinculin could also help mediate the costameric attachment of the Z-bands of mature myofibrils to the nearest cell surfaces.
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Affiliation(s)
- J W Sanger
- Department of Cell and Developmental Biology, University of Pennsylvania, School of Medicine, Philadelphia, USA
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14
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Ayoob JC, Shaner NC, Sanger JW, Sanger JM. Expression of green or red fluorescent protein (GFP or DsRed) linked proteins in nonmuscle and muscle cells. Mol Biotechnol 2001; 17:65-71. [PMID: 11280932 DOI: 10.1385/mb:17:1:65] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [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: 11/11/2022]
Abstract
The introduction of the green fluorescent protein (GFP) plasmids that allow proteins and peptides to be expressed with a fluorescent tag has had a major impact on the field of cell biology. It has enabled the dynamics of a wide variety of proteins to be analyzed that could not otherwise be detected in live cells. Transient transfections of muscle and nonmuscle cells with plasmids encoding various cytoskeletal proteins ligated to green fluorescent protein or Ds red protein allow changes in the cytoskeletal network to be studied in the same cell for time periods up to several days. With this approach, proteins that could not be purified and directly labeled with fluorescent dyes and microinjected into cells can now be expressed and visualized in a wide variety of cells. Procedures are presented for transfection of the nonmuscle cell, PtK2, and primary cultures of embryonic chick myocytes, and for studying the live transfected cells.
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Affiliation(s)
- J C Ayoob
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
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15
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Freeman NL, Zurawski DV, Chowrashi P, Ayoob JC, Huang L, Mittal B, Sanger JM, Sanger JW. Interaction of the enteropathogenic Escherichia coli protein, translocated intimin receptor (Tir), with focal adhesion proteins. Cell Motil Cytoskeleton 2000; 47:307-18. [PMID: 11093251 DOI: 10.1002/1097-0169(200012)47:4<307::aid-cm5>3.0.co;2-q] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
When enteropathogenic Escherichia coli (EPEC) attach and infect host cells, they induce a cytoskeletal rearrangement and the formation of cytoplasmic columns of actin filaments called pedestals. The attached EPEC and pedestals move over the surface of the host cell in an actin-dependent reaction [Sanger et al., 1996: Cell Motil Cytoskeleton 34:279-287]. The discovery that EPEC inserts the protein, translocated intimin receptor (Tir), into the membrane of host cells, where it binds the EPEC outer membrane protein, intimin [Kenny et al., 1997: Cell 91:511-520], suggests Tir serves two functions: tethering the bacteria to the host cell and providing a direct connection to the host's cytoskeleton. The sequence of Tir predicts a protein of 56.8 kD with three domains separated by two predicted trans-membrane spanning regions. A GST-fusion protein of the N-terminal 233 amino acids of Tir (Tir1) binds to alpha-actinin, talin, and vinculin from cell extracts. GST-Tir1 also coprecipitates purified forms of alpha-actinin, talin, and vinculin while GST alone does not bind these three focal adhesion proteins. Biotinylated probes of these three proteins also bound Tir1 cleaved from GST. Similar associations of alpha-actinin, talin, and vinculin were also detected with the C-terminus of Tir, i.e., Tir3, the last 217 amino acids. Antibody staining of EPEC-infected cultured cells reveals the presence of focal adhesion proteins beneath the attached bacteria. Our experiments support a model in which the cytoplasmic domains of Tir recruit a number of focal adhesion proteins that can bind actin filaments to form pedestals. Since pedestals also contain villin, tropomyosin and myosin II [Sanger et al., 1996: Cell Motil. Cytoskeleton 34:279-287], the pedestals appear to be a novel structure sharing properties of both focal adhesions and microvilli.
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Affiliation(s)
- N L Freeman
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia 19104-6058, USA
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16
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Ayoob JC, Turnacioglu KK, Mittal B, Sanger JM, Sanger JW. Targeting of cardiac muscle titin fragments to the Z-bands and dense bodies of living muscle and non-muscle cells. Cell Motil Cytoskeleton 2000; 45:67-82. [PMID: 10618168 DOI: 10.1002/(sici)1097-0169(200001)45:1<67::aid-cm7>3.0.co;2-t] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A 6.5-kb N-terminal region of embryonic chick cardiac titin, including the region previously reported as part of the protein zeugmatin, has been sequenced, further demonstrating that zeugmatin is part of the N-terminal region of titin, and not a separate Z-band protein. This Z-band region of cardiac titin, from both 7- and 19-day embryos as well as from adult animals, was found to contain six different small motifs, termed z-repeats [Gautel et al., 1996: J. Cell Sci. 109:2747-2754], of approximately 45 amino acids each sandwiched between flanking regions containing Ig domains. Fragments of Z-band titin, linked to GFP, were expressed in cultured cardiomyocytes to determine which regions were responsible for Z-band targeting. Transfections of primary cultures of embryonic chick cardiomyocytes demonstrated that the z-repeats play the major role in targeting titin fragments to the Z-band. Similar transfections of skeletal myotubes and non-muscle cells lead to the localization of these cardiac z-repeats in the Z-bands of the myofibrils and the dense bodies of the stress fibers. Over-expression of these z-repeat constructs in either muscle or non-muscle cells lead to the loss of the myofibrils or stress fibers, respectively. The transfection experiments also indicated that small domains of a protein, 40 to 50 amino acids, can be studied for their localization properties in living cells if a suitable linker is placed between these small domains and the much larger 28 kDa GFP protein.
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Affiliation(s)
- J C Ayoob
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia 19104-6804, USA
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17
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Dabiri GA, Turnacioglu KK, Ayoob JC, Sanger JM, Sanger JW. Transfections of primary muscle cell cultures with plasmids coding for GFP linked to full-length and truncated muscle proteins. Methods Cell Biol 1999; 58:239-60. [PMID: 9891385 DOI: 10.1016/s0091-679x(08)61959-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- G A Dabiri
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia 19104, USA
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