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Harris FR, Sikes ML, Bergman M, Goller CC, Hasley AO, Sjogren CA, Ramirez MV, Gordy CL. Hands-on immunology: Engaging learners of all ages through tactile teaching tools. Front Microbiol 2022; 13:966282. [PMID: 36090062 PMCID: PMC9453673 DOI: 10.3389/fmicb.2022.966282] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Ensuring the public has a fundamental understanding of human–microbe interactions, immune responses, and vaccines is a critical challenge in the midst of a pandemic. These topics are commonly taught in undergraduate- and graduate-level microbiology and immunology courses; however, creating engaging methods of teaching these complex concepts to students of all ages is necessary to keep younger students interested when science seems hard. Building on the Tactile Teaching Tools with Guided Inquiry Learning (TTT-GIL) method we used to create an interactive lac operon molecular puzzle, we report here two TTT-GIL activities designed to engage diverse learners from middle schoolers to masters students in exploring molecular interactions within the immune system. By pairing physical models with structured activities built on the constructivist framework of Process-Oriented Guided Inquiry Learning (POGIL), TTT-GIL activities guide learners through their interaction with the model, using the Learning Cycle to facilitate construction of new concepts. Moreover, TTT-GIL activities are designed utilizing Universal Design for Learning (UDL) principles to include all learners through multiple means of engagement, representation, and action. The TTT-GIL activities reported here include a web-enhanced activity designed to teach concepts related to antibody–epitope binding and specificity to deaf and hard-of-hearing middle and high school students in a remote setting and a team-based activity that simulates the evolution of the Major Histocompatibility Complex (MHC) haplotype of a population exposed to pathogens. These activities incorporate TTT-GIL to engage learners in the exploration of fundamental immunology concepts and can be adapted for use with learners of different levels and educational backgrounds.
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Affiliation(s)
- Felix R. Harris
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - Michael L. Sikes
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - Michael Bergman
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States
| | - Carlos C. Goller
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
- Biotechnology Program, North Carolina State University, Raleigh, NC, United States
| | - Andrew O. Hasley
- Biotechnology Program, North Carolina State University, Raleigh, NC, United States
| | - Caroline A. Sjogren
- Biotechnology Program, North Carolina State University, Raleigh, NC, United States
| | - Melissa V. Ramirez
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - Claire L. Gordy
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
- *Correspondence: Claire L. Gordy,
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Gordy CL, Ramirez MV, Vandegrift M, Goller CC. Editorial: Research Topic Tools, Techniques, and Strategies for Teaching in a Real-World Context With Microbiology. Front Microbiol 2021; 12:755500. [PMID: 34721362 PMCID: PMC8548768 DOI: 10.3389/fmicb.2021.755500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/16/2021] [Indexed: 11/23/2022] Open
Affiliation(s)
- Claire L Gordy
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - Melissa V Ramirez
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - Micah Vandegrift
- NC State University Libraries, North Carolina State University, Raleigh, NC, United States
| | - Carlos C Goller
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States.,Biotechnology Program (BIT), North Carolina State University, Raleigh, NC, United States
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Ramirez MV, Gordy CL. STEM BUILD: An Online Community To Decrease Barriers to Implementation of Inclusive Tactile Teaching Tools. J Microbiol Biol Educ 2020; 21:21.1.12. [PMID: 32313589 PMCID: PMC7148141 DOI: 10.1128/jmbe.v21i1.1963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/07/2020] [Indexed: 05/24/2023]
Abstract
Access to 3D printing and other "maker" technologies has opened new doors for the creation of classroom activities using physical models. Multiple strategies for implementing 3D-printed models exist, and work to define best practices is ongoing. We outline the strengths and weaknesses of common strategies for employing physical models in undergraduate biology courses and describe a novel strategy that we have developed to pair 3D-printed models with guided inquiry learning to create inclusive and interactive learning experiences. We further introduce the STEM BUILD website, a resource that we have developed to facilitate collaboration among instructors, makers, researchers, and Universal Design for Learning experts and reduce barriers to broad implementation of inclusive kinesthetic learning activities.
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Affiliation(s)
- Melissa V. Ramirez
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695
| | - Claire L. Gordy
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695
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Gordy CL, Sandefur CI, Lacara T, Harris FR, Ramirez MV. Building the lac Operon: A Guided-Inquiry Activity Using 3D-Printed Models. J Microbiol Biol Educ 2020; 21:21.1.28. [PMID: 32341727 PMCID: PMC7173627 DOI: 10.1128/jmbe.v21i1.2091] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/06/2020] [Indexed: 05/09/2023]
Abstract
Undergraduate biology courses rely heavily on visual representation of information. Students view images of plants, animals, and microbes, interpret data presented in graphs, and use drawings to understand how cells and molecules interact in three dimensions. Traditional teaching approaches exclude students with visual impairments and disadvantage students with disabilities that affect their interpretation and processing of visual and spatial information, and also students who simply do not identify as "visual learners." By using new technologies to develop tactile teaching tools (TTTs) that can be employed in classrooms, we aim to create inclusive learning environments and more effectively instruct diverse learners. The advent of affordable and accessible 3D printing technology makes it possible to create tactile models that represent molecules, cells, and entire organisms more accurately than traditional visual representations. We describe the assessment of a 3D gene expression puzzle as a guided inquiry learning activity in which students must correctly assemble a series of components in order to achieve an output. Upon completion of the puzzle, the TTT provides tactile feedback through vibration to signal transcriptional activation. Analysis of pre- and postassessment performance demonstrated statistically significant increases in individual students' paired assessment scores in two different classroom implementations, with a greater effect size at a rural minority-serving institution than an urban R1 university. These encouraging preliminary data suggest that TTTs with guided-inquiry learning disproportionately benefit disadvantaged student populations and could serve as a tool in leveling the playing field when teaching abstract biological concepts in diverse educational settings.
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Affiliation(s)
- Claire L. Gordy
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695
| | - Conner I. Sandefur
- Department of Biology, University of North Carolina at Pembroke, Pembroke, NC 28372
| | - Tessa Lacara
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695
| | - Felix R. Harris
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695
| | - Melissa V. Ramirez
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695
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Ramirez MV, Dawson CC, Crew R, England K, Slayden RA. MazF6 toxin of Mycobacterium tuberculosis demonstrates antitoxin specificity and is coupled to regulation of cell growth by a Soj-like protein. BMC Microbiol 2013; 13:240. [PMID: 24172039 PMCID: PMC3834876 DOI: 10.1186/1471-2180-13-240] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 10/24/2013] [Indexed: 09/03/2023] Open
Abstract
Background Molecular programs employed by Mycobacterium tuberculosis (Mtb) for the establishment of non-replicating persistence (NRP) are poorly understood. In order to investigate mechanisms regulating entry into NRP, we asked how cell cycle regulation is linked to downstream adaptations that ultimately result in NRP. Based on previous reports and our recent studies, we reason that, in order to establish NRP, cells are halted in the cell cycle at the point of septum formation by coupled regulatory mechanisms. Results Using bioinformatic consensus modeling, we identified an alternative cell cycle regulatory element, SojMtb encoded by rv1708. SojMtb coordinates a regulatory mechanism involving cell cycle control at the point of septum formation and elicits the induction of the MazF6 toxin. MazF6 functions as an mRNA interferase leading to bacteriostasis that can be prevented by interaction with its cognate antitoxin, MazE6. Further, MazEF6 acts independently of other Maz family toxin:antitoxin pairs. Notably, sojMtb and mazEF6 transcripts where identified at 20, 40 and 100 days post-infection in increasing abundance indicating a role in adaption during chronic infection. Conclusions Here we present the first evidence of a coupled regulatory system in which cell cycle regulation via SojMtb is linked to downstream adaptations that are facilitated through the activity of the MazEF6 TA pair.
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Affiliation(s)
| | | | | | | | - Richard A Slayden
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
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Nandakumar S, Kannanganat S, Dobos KM, Lucas M, Spencer JS, Fang S, McDonald MA, Pohl J, Birkness K, Chamcha V, Ramirez MV, Plikaytis BB, Posey JE, Amara RR, Sable SB. O-mannosylation of the Mycobacterium tuberculosis adhesin Apa is crucial for T cell antigenicity during infection but is expendable for protection. PLoS Pathog 2013; 9:e1003705. [PMID: 24130497 PMCID: PMC3795050 DOI: 10.1371/journal.ppat.1003705] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [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: 04/24/2013] [Accepted: 08/28/2013] [Indexed: 01/24/2023] Open
Abstract
Glycosylation is the most abundant post-translational polypeptide chain modification in nature. Although carbohydrate modification of protein antigens from many microbial pathogens constitutes important components of B cell epitopes, the role in T cell immunity is not completely understood. Here, using ELISPOT and polychromatic flow cytometry, we show that O-mannosylation of the adhesin, Apa, of Mycobacterium tuberculosis (Mtb) is crucial for its T cell antigenicity in humans and mice after infection. However, subunit vaccination with both mannosylated and non-mannosylated Apa induced a comparable magnitude and quality of T cell response and imparted similar levels of protection against Mtb challenge in mice. Both forms equally improved waning BCG vaccine-induced protection in elderly mice after subunit boosting. Thus, O-mannosylation of Apa is required for antigenicity but appears to be dispensable for its immunogenicity and protective efficacy in mice. These results have implications for the development of subunit vaccines using post-translationally modified proteins such as glycoproteins against infectious diseases like tuberculosis.
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Affiliation(s)
- Subhadra Nandakumar
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Sunil Kannanganat
- Department of Microbiology and Immunology, Yerkes National Primate Research Center and Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Karen M. Dobos
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Megan Lucas
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - John S. Spencer
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Sunan Fang
- Biotechnology Core Facility Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Melissa A. McDonald
- Biotechnology Core Facility Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jan Pohl
- Biotechnology Core Facility Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Kristin Birkness
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Venkateswarlu Chamcha
- Department of Microbiology and Immunology, Yerkes National Primate Research Center and Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Melissa V. Ramirez
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Bonnie B. Plikaytis
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - James E. Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Rama Rao Amara
- Department of Microbiology and Immunology, Yerkes National Primate Research Center and Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Suraj B. Sable
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
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Slayden RA, Jackson M, Zucker J, Ramirez MV, Dawson CC, Crew R, Sampson NS, Thomas ST, Jamshidi N, Sisk P, Caspi R, Crick DC, McNeil MR, Pavelka MS, Niederweis M, Siroy A, Dona V, McFadden J, Boshoff H, Lew JM. Updating and curating metabolic pathways of TB. Tuberculosis (Edinb) 2013; 93:47-59. [PMID: 23375378 DOI: 10.1016/j.tube.2012.11.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 11/25/2012] [Indexed: 01/08/2023]
Abstract
The sequencing of complete genomes has accelerated biomedical research by providing information about the overall coding capacity of bacterial chromosomes. The original TB annotation resulted in putative functional assignment of ∼60% of the genes to specific metabolic functions, however, the other 40% of the encoded ORFs where annotated as conserved hypothetical proteins, hypothetical proteins or encoding proteins of unknown function. The TB research community is now at the beginning of the next phases of post-genomics; namely reannotation and functional characterization by targeted experimentation. Arguably, this is the most significant time for basic microbiology in recent history. To foster basic TB research, the Tuberculosis Community Annotation Project (TBCAP) jamboree exercise began the reannotation effort by providing additional information for previous annotations, and refining and substantiating the functional assignment of ORFs and genes within metabolic pathways. The overall goal of the TBCAP 2012 exercise was to gather and compile various data types and use this information with oversight from the scientific community to provide additional information to support the functional annotations of encoding genes. Another objective of this effort was to standardize the publicly accessible Mycobacterium tuberculosis reference sequence and its annotation. The greatest benefit of functional annotation information of genome sequence is that it fuels TB research for drug discovery, diagnostics, vaccine development and epidemiology.
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Bowerman PA, Ramirez MV, Price MB, Helm RF, Winkel BSJ. Analysis of T-DNA alleles of flavonoid biosynthesis genes in Arabidopsis ecotype Columbia. BMC Res Notes 2012; 5:485. [PMID: 22947320 PMCID: PMC3526476 DOI: 10.1186/1756-0500-5-485] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 08/23/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The flavonoid pathway is a long-standing and important tool for plant genetics, biochemistry, and molecular biology. Numerous flavonoid mutants have been identified in Arabidopsis over the past several decades in a variety of ecotypes. Here we present an analysis of Arabidopsis lines of ecotype Columbia carrying T-DNA insertions in genes encoding enzymes of the central flavonoid pathway. We also provide a comprehensive summary of various mutant alleles for these structural genes that have been described in the literature to date in a wide variety of ecotypes. FINDINGS The confirmed knockout lines present easily-scorable phenotypes due to altered pigmentation of the seed coat (or testa). Knockouts for seven alleles for six flavonoid biosynthetic genes were confirmed by PCR and characterized by UPLC for altered flavonol content. CONCLUSION Seven mutant lines for six genes of the central flavonoid pathway were characterized in ecotype, Columbia. These lines represent a useful resource for integrating biochemical and physiological studies with genomic, transcriptomic, and proteomic data, much of which has been, and continues to be, generated in the Columbia background.
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Lewis DR, Ramirez MV, Miller ND, Vallabhaneni P, Ray WK, Helm RF, Winkel BS, Muday GK. Auxin and ethylene induce flavonol accumulation through distinct transcriptional networks. Plant Physiol 2011; 156:144-64. [PMID: 21427279 PMCID: PMC3091047 DOI: 10.1104/pp.111.172502] [Citation(s) in RCA: 187] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 03/19/2011] [Indexed: 05/18/2023]
Abstract
Auxin and ethylene are key regulators of plant growth and development, and thus the transcriptional networks that mediate responses to these hormones have been the subject of intense research. This study dissected the hormonal cross talk regulating the synthesis of flavonols and examined their impact on root growth and development. We analyzed the effects of auxin and an ethylene precursor on roots of wild-type and hormone-insensitive Arabidopsis (Arabidopsis thaliana) mutants at the transcript, protein, and metabolite levels at high spatial and temporal resolution. Indole-3-acetic acid (IAA) and 1-aminocyclopropane-1-carboxylic acid (ACC) differentially increased flavonol pathway transcripts and flavonol accumulation, altering the relative abundance of quercetin and kaempferol. The IAA, but not ACC, response is lost in the transport inhibitor response1 (tir1) auxin receptor mutant, while ACC responses, but not IAA responses, are lost in ethylene insensitive2 (ein2) and ethylene resistant1 (etr1) ethylene signaling mutants. A kinetic analysis identified increases in transcripts encoding the transcriptional regulators MYB12, Transparent Testa Glabra1, and Production of Anthocyanin Pigment after hormone treatments, which preceded increases in transcripts encoding flavonoid biosynthetic enzymes. In addition, myb12 mutants were insensitive to the effects of auxin and ethylene on flavonol metabolism. The equivalent phenotypes for transparent testa4 (tt4), which makes no flavonols, and tt7, which makes kaempferol but not quercetin, showed that quercetin derivatives are the inhibitors of basipetal root auxin transport, gravitropism, and elongation growth. Collectively, these experiments demonstrate that auxin and ethylene regulate flavonol biosynthesis through distinct signaling networks involving TIR1 and EIN2/ETR1, respectively, both of which converge on MYB12. This study also provides new evidence that quercetin is the flavonol that modulates basipetal auxin transport.
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Frazzon APG, Ramirez MV, Warek U, Balk J, Frazzon J, Dean DR, Winkel BSJ. Functional analysis of Arabidopsis genes involved in mitochondrial iron-sulfur cluster assembly. Plant Mol Biol 2007; 64:225-40. [PMID: 17417719 DOI: 10.1007/s11103-007-9147-x] [Citation(s) in RCA: 27] [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] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Accepted: 02/01/2007] [Indexed: 05/14/2023]
Abstract
Machinery for the assembly of the iron-sulfur ([Fe-S]) clusters that function as cofactors in a wide variety of proteins has been identified in microbes, insects, and animals. Homologs of the genes involved in [Fe-S] cluster biogenesis have recently been found in plants, as well, and point to the existence of two distinct systems in these organisms, one located in plastids and one in mitochondria. Here we present the first biochemical confirmation of the activity of two components of the mitochondrial machinery in Arabidopsis, AtNFS1 and AtISU1. Analysis of the expression patterns of the corresponding genes, as well as AtISU2 and AtISU3, and the phenotypes of plants in which these genes are up or down-regulated are consistent with a role for the mitochondrial [Fe-S] assembly system in the maturation of proteins required for normal plant development.
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