@article{ramirez_2023, title={Mapping An Epidemiology Origin Story}, url={https://doi.org/10.52750/670791}, DOI={10.52750/670791}, abstractNote={A decade before John Snow was investigating cholera in London, James Ormiston McWilliam was across the world studying yellow fever in Cape Verde.McWilliam undertook a massive effort to interview all of the people on the island.His interviews were extraordinarily valuable and unique in that they were so extensive and were done without regard to race or social status.He conducted hundreds of interviews of mostly people of color -native, colonized and enslaved peoples.The first-hand accounts and observations of those working close to the illness proved fundamental to understanding disease transmission.This approach of utilizing interviews would become an integral part of the field of epidemiology.}, author={Ramirez, Melissa}, year={2023}, month={Aug} }
 @article{harris_sikes_bergman_goller_hasley_sjogren_ramirez_gordy_2022, title={Hands-on immunology: Engaging learners of all ages through tactile teaching tools}, volume={13}, ISSN={["1664-302X"]}, url={http://dx.doi.org/10.3389/fmicb.2022.966282}, DOI={10.3389/fmicb.2022.966282}, abstractNote={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.}, journal={FRONTIERS IN MICROBIOLOGY}, publisher={Frontiers Media SA}, author={Harris, Felix R. and Sikes, Michael L. and Bergman, Michael and Goller, Carlos C. and Hasley, Andrew O. and Sjogren, Caroline A. and Ramirez, Melissa V. and Gordy, Claire L.}, year={2022}, month={Aug} }
 @article{ramirez_flores_2022, title={Preview: Adapting to Global Change: What Can You Do?}, volume={1}, url={https://doi.org/10.52750/611416}, DOI={10.52750/611416}, publisher={North Carolina State University}, author={Ramirez, Melissa and Flores, Jason}, year={2022}, month={Jan} }
 @article{ramirez_flores_2022, title={Preview: Global Change: Why We Need to Act Now}, url={https://doi.org/10.52750/125810}, DOI={10.52750/125810}, author={Ramirez, Melissa and Flores, Jason}, year={2022}, month={Jan} }
 @article{ramirez_2022, title={Preview: Pandemics: Anticipating the Future}, url={https://doi.org/10.52750/854088}, DOI={10.52750/854088}, author={Ramirez, Melissa}, year={2022}, month={Jun} }
 @article{ramirez_2022, title={Preview: Pandemics: How We See the Disease}, url={https://doi.org/10.52750/448400}, DOI={10.52750/448400}, author={Ramirez, Melissa}, year={2022}, month={Jun} }
 @article{ramirez_2022, title={Preview: Pandemics: Setting the Stage}, url={https://doi.org/10.52750/147000}, DOI={10.52750/147000}, author={Ramirez, Melissa}, year={2022}, month={Jun} }
 @article{ramirez_2022, title={Preview: Pandemics: Solutions}, url={https://doi.org/10.52750/539967}, DOI={10.52750/539967}, author={Ramirez, Melissa}, year={2022}, month={Jun} }
 @article{ramirez_2022, title={Preview: Pandemics: The Current Crisis}, url={https://doi.org/10.52750/189737}, DOI={10.52750/189737}, author={Ramirez, Melissa}, year={2022}, month={Jun} }
 @article{ramirez_flores_2022, title={Preview: Radical Change: Achieving Hopeful Scenarios}, volume={1}, url={https://doi.org/10.52750/861177}, DOI={10.52750/861177}, publisher={North Carolina State University}, author={Ramirez, Melissa and Flores, Jason}, year={2022}, month={Jan} }
 @article{ramirez_flores_2022, title={Preview: The Science of Global Change}, url={https://doi.org/10.52750/880328}, DOI={10.52750/880328}, author={Ramirez, Melissa and Flores, Jason}, year={2022}, month={Jan} }
 @article{ramirez_flores_2022, title={Preview: The Unequal Burden of Global Change}, volume={1}, url={https://doi.org/10.52750/311273}, DOI={10.52750/311273}, publisher={North Carolina State University}, author={Ramirez, Melissa and Flores, Jason}, year={2022}, month={Jan} }
 @article{gordy_ramirez_vandegrift_goller_2021, title={Editorial: Research Topic Tools, Techniques, and Strategies for Teaching in a Real-World Context With Microbiology}, volume={12}, ISSN={["1664-302X"]}, url={http://dx.doi.org/10.3389/fmicb.2021.755500}, DOI={10.3389/fmicb.2021.755500}, abstractNote={EDITORIAL article Front. Microbiol., 13 October 2021 | https://doi.org/10.3389/fmicb.2021.755500}, journal={FRONTIERS IN MICROBIOLOGY}, publisher={Frontiers Media SA}, author={Gordy, Claire L. and Ramirez, Melissa V. and Vandegrift, Micah and Goller, Carlos C.}, year={2021}, month={Oct} }
 @article{gordy_sandefur_lacara_harris_ramirez_2020, title={Building the lac Operon: A Guided-Inquiry Activity Using 3D-Printed Models}, volume={21}, ISSN={["1935-7885"]}, url={http://europepmc.org/abstract/med/32341727}, DOI={10.1128/jmbe.v21i1.2091}, abstractNote={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.}, number={1}, journal={JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION}, author={Gordy, Claire L. and Sandefur, Conner I and Lacara, Tessa and Harris, Felix R. and Ramirez, Melissa V}, year={2020}, month={Feb} }
 @article{gordy_sandefur_lacara_harris_ramirez_2020, title={Building the lac operon: A guided-inquiry activity using 3D-printed models}, volume={1}, url={https://doi.org/10.1101/2020.01.14.904847}, DOI={10.1101/2020.01.14.904847}, abstractNote={Abstract}, number={1}, journal={Journal of Microbiology & Biology Education}, publisher={Cold Spring Harbor Laboratory}, author={Gordy, Claire L. and Sandefur, Conner I. and Lacara, Tessa and Harris, Felix R. and Ramirez, Melissa V.}, year={2020}, month={Jan}, pages={60} }
 @article{ramirez_gordy_2020, title={STEM BUILD: An Online Community To Decrease Barriers to Implementation of Inclusive Tactile Teaching Tools}, volume={21}, ISSN={["1935-7885"]}, url={http://dx.doi.org/10.1128/jmbe.v21i1.1963}, DOI={10.1128/jmbe.v21i1.1963}, abstractNote={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.}, number={1}, journal={JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION}, publisher={American Society for Microbiology}, author={Ramirez, Melissa V and Gordy, Claire L.}, year={2020}, month={Feb} }
 @article{ramirez_lee_hamm_taveirne_lee_2018, title={A Cross-Platform Comparison of Student’s Perceptions of the Learning Environment in an Introductory Microbiology Course}, volume={3}, url={http://dx.doi.org/10.1101/274571}, DOI={10.1101/274571}, abstractNote={AbstractStudents’ positive perceptions of the learning environment increase retention and persistence in STEM disciplines. This study presents results from a Learning Environment Questionnaire administered at the beginning and end of the semester in a redesigned general/introductory microbiology course offered in traditional lecture, flipped and online sections. Split-sample t-tests and chi-squared tests were used for cross-section and within section analyses, respectively. The findings support the study hypothesis that student perceptions of the learning environment will vary as a function of platform. This work demonstrates the additional effect of the time in the semester when students complete the questionnaire and this effect on students’ perceptions over the course of the semester relative to their initial perceptions. The results of this study offer insight on student perceptions of the learning environment as universities embrace online education in introductory and gateway courses as a response to rising student enrollments and diminishing resources.}, journal={[]}, publisher={Cold Spring Harbor Laboratory}, author={Ramirez, Melissa V. and Lee, Virginia S. and Hamm, Lindsay and Taveirne, Michael E. and Lee, Alice M.}, year={2018}, month={Mar} }
 @article{crew_ramirez_england_slayden_2015, title={MadR1, a Mycobacterium tuberculosis cell cycle stress response protein that is a member of a widely conserved protein class of prokaryotic, eukaryotic and archeal origin}, volume={95}, url={http://dx.doi.org/10.1016/j.tube.2015.03.005}, DOI={10.1016/j.tube.2015.03.005}, abstractNote={Stress-induced molecular programs designed to stall division progression are nearly ubiquitous in bacteria, with one well-known example being the participation of the SulA septum inhibiting protein in the SOS DNA damage repair response. Mycobacteria similarly demonstrate stress-altered growth kinetics, however no such regulators have been found in these organisms. We therefore set out to identify SulA-like regulatory proteins in Mycobacterium tuberculosis. A bioinformatics modeling-based approach led to the identification of rv2216 as encoding for a protein with weak similarity to SulA, further analysis distinguished this protein as belonging to a group of uncharacterized growth promoting proteins. We have named the mycobacterial protein encoded by rv2216 morphology altering division regulator protein 1, MadR1. Overexpression of madR1 modulated cell length while maintaining growth kinetics similar to wild-type, and increased the proportion of bent or V-form cells in the population. The presence of MadR1-GFP at regions of cellular elongation (poles) and morphological differentiation (V-form) suggests MadR1 involvement in phenotypic heterogeneity and longitudinal cellular growth. Global transcriptional analysis indicated that MadR1 functionality is linked to lipid editing programs required for growth and persistence. This is the first report to differentiate the larger class of these conserved proteins from SulA proteins and characterizes MadR1 effects on the mycobacterial cell.}, number={3}, journal={Tuberculosis}, publisher={Elsevier BV}, author={Crew, Rebecca and Ramirez, Melissa V. and England, Kathleen and Slayden, Richard A.}, year={2015}, month={May}, pages={251–258} }
 @article{ramirez_dawson_crew_england_slayden_2013, title={MazF6 toxin of Mycobacterium tuberculosis demonstrates antitoxin specificity and is coupled to regulation of cell growth by a Soj-like protein}, volume={13}, url={http://dx.doi.org/10.1186/1471-2180-13-240}, DOI={10.1186/1471-2180-13-240}, abstractNote={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. 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, soj Mtb and mazEF6 transcripts where identified at 20, 40 and 100 days post-infection in increasing abundance indicating a role in adaption during chronic infection. 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.}, number={1}, journal={BMC Microbiology}, publisher={Springer Science and Business Media LLC}, author={Ramirez, Melissa V and Dawson, Clinton C and Crew, Rebecca and England, Kathleen and Slayden, Richard A}, year={2013}, month={Dec} }
 @article{nandakumar_kannanganat_dobos_lucas_spencer_fang_mcdonald_pohl_birkness_chamcha_et al._2013, title={O-mannosylation of the Mycobacterium tuberculosis Adhesin Apa Is Crucial for T Cell Antigenicity during Infection but Is Expendable for Protection}, volume={9}, url={http://dx.doi.org/10.1371/journal.ppat.1003705}, DOI={10.1371/journal.ppat.1003705}, abstractNote={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.}, number={10}, journal={PLoS Pathogens}, publisher={Public Library of Science (PLoS)}, author={Nandakumar, Subhadra and Kannanganat, Sunil and Dobos, Karen M. and Lucas, Megan and Spencer, John S. and Fang, Sunan and McDonald, Melissa A. and Pohl, Jan and Birkness, Kristin and Chamcha, Venkateswarlu and et al.}, editor={Salgame, PadminiEditor}, year={2013}, month={Oct}, pages={e1003705} }
 @article{slayden_jackson_zucker_ramirez_dawson_crew_sampson_thomas_jamshidi_sisk_et al._2013, title={Updating and curating metabolic pathways of TB}, volume={93}, url={http://dx.doi.org/10.1016/j.tube.2012.11.001}, DOI={10.1016/j.tube.2012.11.001}, abstractNote={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.}, number={1}, journal={Tuberculosis}, publisher={Elsevier BV}, author={Slayden, Richard A. and Jackson, Mary and Zucker, Jeremy and Ramirez, Melissa V. and Dawson, Clinton C. and Crew, Rebecca and Sampson, Nicole S. and Thomas, Suzanne T. and Jamshidi, Neema and Sisk, Peter and et al.}, year={2013}, month={Jan}, pages={47–59} }
 @article{bowerman_ramirez_price_helm_winkel_2012, title={Analysis of T-DNA alleles of flavonoid biosynthesis genes in Arabidopsis ecotype Columbia}, volume={5}, url={http://dx.doi.org/10.1186/1756-0500-5-485}, DOI={10.1186/1756-0500-5-485}, abstractNote={Abstract}, number={1}, journal={BMC Research Notes}, publisher={Springer Science and Business Media LLC}, author={Bowerman, Peter A and Ramirez, Melissa V and Price, Michelle B and Helm, Richard F and Winkel, Brenda SJ}, year={2012}, month={Dec} }
 @article{lewis_ramirez_miller_vallabhaneni_ray_helm_winkel_muday_2011, title={Auxin and Ethylene Induce Flavonol Accumulation through Distinct Transcriptional Networks
 
 
 }, volume={156}, url={http://dx.doi.org/10.1104/pp.111.172502}, DOI={10.1104/pp.111.172502}, abstractNote={Abstract}, number={1}, journal={Plant Physiology}, publisher={Oxford University Press (OUP)}, author={Lewis, Daniel R. and Ramirez, Melissa V. and Miller, Nathan D. and Vallabhaneni, Prashanthi and Ray, W. Keith and Helm, Richard F. and Winkel, Brenda S.J. and Muday, Gloria K.}, year={2011}, month={May}, pages={144–164} }
 @article{ramirez_cowart_campbell_morlock_sikes_winchell_posey_2010, title={Rapid Detection of Multidrug-Resistant Mycobacterium tuberculosis by Use of Real-Time PCR and High-Resolution Melt Analysis}, volume={48}, url={http://dx.doi.org/10.1128/jcm.00812-10}, DOI={10.1128/jcm.00812-10}, abstractNote={ABSTRACT}, number={11}, journal={Journal of Clinical Microbiology}, publisher={American Society for Microbiology}, author={Ramirez, Melissa V. and Cowart, Kelley C. and Campbell, Patricia J. and Morlock, Glenn P. and Sikes, David and Winchell, Jonas M. and Posey, James E.}, year={2010}, month={Nov}, pages={4003–4009} }
 @article{frazzon_ramirez_warek_balk_frazzon_dean_winkel_2007, title={Functional analysis of Arabidopsis genes involved in mitochondrial iron-sulfur cluster assembly}, volume={64}, url={http://dx.doi.org/10.1007/s11103-007-9147-x}, DOI={10.1007/s11103-007-9147-x}, abstractNote={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.}, number={3}, journal={Plant Molecular Biology}, publisher={Springer Science and Business Media LLC}, author={Frazzon, Ana Paula Guedes and Ramirez, Melissa V. and Warek, Ujwala and Balk, Janneke and Frazzon, Jeverson and Dean, Dennis R. and Winkel, Brenda S. J.}, year={2007}, month={Apr}, pages={225–240} }