Pete and the Missing Scissors: a primary literature-focused case study that highlights the impact of SARS-CoV-2 on splicing.

This case study was designed to help students explore the molecular mechanisms of the spliceosome and how SARS-CoV-2 impacts host cell spliceosomal function while interpreting figures from primary literature (A. K. Banjeree, et al., Cell 183:1325-1339, e1-e10, 2020, https://doi.org/10.1016/j.cell.2020.10.004). "Pete and the Missing Scissors" was designed and implemented in the spring of 2022 and fall of 2022 in two large-enrollment (150+) introductory molecular biology courses at a large, public research institution. The case study was formatted in alignment with the National Center for Case Study Teaching in Science (NCCSTS) framework, which has been shown to be an effective, student-centered approach to teaching complex biological concepts at the undergraduate level. The case study had four student learning objectives (SLOs) that aligned with Bloom's Revised Taxonomy and required students to develop an understanding of the molecular mechanisms of splicing and analyze and interpret a figure from primary literature. Both formative and summative assessment questions are included in this activity, with each question mapping to one of the case study SLOs. Summative assessment questions were given in a pre-/post-manner, and a paired t-test was used to evaluate differences between students' pre- and post-assessment scores. Assessment results demonstrated that students in both courses mastered each of the SLOs of this case study, given the significant increase in post-assessment scores compared to the pre-assessment. These findings indicate that the "Pete and the Missing Scissors" case study is an effective approach to develop students' understanding of the spliceosome, as well as ability to interpret figures from primary literature.

A gut microbiome tactile teaching tool and guided-inquiry activity promotes student learning.

The gut microbiome and its physiological impacts on human and animal health is an area of research emphasis. Microbes themselves are invisible and may therefore be abstract and challenging to understand. It is therefore important to infuse this topic into undergraduate curricula, including Anatomy and Physiology courses, ideally through an active learning approach. To accomplish this, we developed a novel tactile teaching tool with guided-inquiry (TTT-GI) activity where students explored how the gut microbiome ferments carbohydrates to produce short chain fatty acids (SCFAs). This activity was implemented in two sections of a large-enrollment Human Anatomy and Physiology course at a research intensive (R1) university in the Spring of 2022 that was taught using a hyflex format. Students who attended class in person used commonly available building toys to assemble representative carbohydrates of varying structural complexity, whereas students who attended class virtually made these carbohydrate structures using a digital learning tool. Students then predicted how microbes within the gut would ferment different carbohydrates into SCFAs, as well as the physiological implications of the SCFAs. We assessed this activity to address three research questions, with 182 students comprising our sample. First, we evaluated if the activity learning objectives were achieved through implementation of a pre-and post-assessment schema. Our results revealed that all three learning objectives of this activity were attained. Next, we evaluated if the format in which this TTT-GI activity was implemented impacted student learning. While we found minimal and nonsignificant differences in student learning between those who attended in-person and those who attended remotely, we did find significant differences between the two course sections, which differed in length and spacing of the activity. Finally, we evaluated if this TTT-GI approach was impactful for diverse students. We observed modest and nonsignificant positive learning gains for some populations of students traditionally underrepresented in STEM (first-generation students and students with one or more disabilities). That said, we found that the greatest learning gains associated with this TTT-GI activity were observed in students who had taken previous upper-level biology coursework.

Introduction to Research: A Scalable, Online Badge Implemented in Conjunction with a Classroom-Based Undergraduate Research Experience (CURE) that Promotes Students Matriculation into Mentored Undergraduate Research.

The benefits of mentored undergraduate research to student success, retention, and persistence in science, technology, engineering, and mathematics (STEM) have long been identified. However, many students miss out on the opportunity to engage in research often due to unfamiliarity of various research opportunities or how to approach potential research mentors. To address this, we developed a scalable online badge, Introduction to Research, that draws on aspects of the Entering Research curriculum (Branchaw, Pfund, & Rediske, 2010) to help students explore and prepare for undergraduate research in the biomedical and behavioral sciences. Students in the BUILD Training Program, part of the larger STEM BUILD at UMBC Initiative, completed the badge in conjunction with a 3-week classroom-based undergraduate research experience (CURE) before the start of their second year of undergraduate study at the University of Maryland, Baltimore County (UMBC). We were interested in investigating how this intervention, online badge plus CURE, correlated to students engaging in undergraduate research before the end of their second year at UMBC. We did this through student self-report, comparing students who had participated in the online badge plus CURE (BTP) to those who participated in neither (Control). Our data demonstrate that students who participated in the Introduction to Research Badge and CURE entered into mentored research at a significantly higher rate than students who were exposed to neither. Further, previously validated instruments of students 'research self-efficacy and science identity were used to compare how the Introduction to Research Badge and CURE may impact these two psycho-social variables. Students who participated in the Introduction to Research Badge and CURE had significantly higher gains in research self-efficacy compared to the control group. However, no change was observed in science identity for either group. Collectively, our results suggest that students who engage in the Introduction to Research Badge in combination with a CURE engage in mentored research within a year of completion at higher levels than students who engage in neither.

Supporting Deaf Students in Undergraduate Research Experiences: Perspectives of American Sign Language Interpreters.

Deaf undergraduates are eager to engage in research but often feel marginalized due to lack of appropriate accommodations to allow for effective communication within heterogeneous research teams consisting of hearing peers and/or mentors. In this case study, we interviewed four American Sign Language (ASL) interpreters who provided full-time accommodations to teams consisting of one deaf student and two hearing peers during a six-week internship. We queried the interpreters on their role and experiences in supporting the research teams. Our findings indicate that the interpreters can be a valuable asset to heterogeneous teams by supporting both deaf and hearing individuals and advocating for the deaf student. That said, interpreters also had to overcome challenges unique to interpreting in the research environment, such as deciding when and how to interpret. The insights provided by the interpreters interviewed here are valuable as undergraduate research programs evaluate how to provide appropriate accommodations to deaf students engaged in research. In addition, they also highlight the need for research experience coordinators and mentors to consider supporting diverse teams in developing effective communication strategies and applying universal design for learning to the research environment.

Evolution of an 8-week upper-division metagenomics course: Diagramming a learning path from observational to quantitative microbiome analysis.

Metagenomics is a tool that enables researchers to study genetic material recovered directly from microbial communities or microbiomes. Fueled by advances in sequencing technologies, bioinformatics tools, and sample processing, metagenomics studies promise to expand our understanding of human health and the use of microorganisms for agriculture and industry. Therefore, teaching students about metagenomics is crucial to prepare them for modern careers in the life sciences. However, the increasing number of different approaches makes teaching metagenomics to students a challenge. This 8-week metagenomics laboratory course has the objective of introducing upper-level undergraduate and graduate students to strategies for designing, executing, and analyzing microbiome investigations. The laboratory component begins with sample processing, library preparation, and submission for high-throughput sequencing before transitioning to computer-based activities, which include an introduction to several fundamental computational metagenomics tools. Students analyze their sequencing results and deposit findings in sequence databases. The laboratory component is complemented by a weekly lecture, where active learning sessions promote retrieval practice and allow students to reflect on and diagram processes performed in the laboratory. Attainment of student learning outcomes was assessed through the completion of various course assignments: laboratory reports, presentations, and a cumulative final exam. Further, students' perceptions of their gains relevant to the learning outcomes were evaluated using pre- and postcourse surveys. Collectively, these data demonstrate that this course results in the attainment of the learning outcomes and that this approach provides an adaptable way to expose students to the cutting-edge field of metagenomics.

Students' Understanding and Perceptions of Assigned Team Roles in a Classroom Laboratory Environment.

Using a cooperative learning framework in a quantitative reasoning laboratory course, students were assigned to static teams of four in which they adopted roles that rotated regularly. The roles included: team leader, protocol manager, data recorder, and researcher. Using a mixed-methods approach, we investigated students' perceptions of the team roles and specifically addressed students' understanding of the roles, students' beliefs in their ability to enact the roles, and whether working with assigned team roles supported the teams to work effectively and cohesively. Although students expressed confidence in their understanding of the team roles, their understanding differed from the initial descriptions. This suggests that students' understanding of team roles may be influenced by a variety of factors, including their experiences within their teams. Students also reported that some roles appeared to lack a purpose, implying that for roles to be successful, they must have a clear purpose. Finally, the fact that many students reported ignoring the team roles suggests that students do not perceive roles as a requirement for team productivity and cohesion. On the basis of these findings, we provide recommendations for instructors wishing to establish a classroom group laboratory environment.

Unique Down to Our Microbes-Assessment of an Inquiry-Based Metagenomics Activity.

Metagenomics is an important method for studying microbial life. However, undergraduate exposure to metagenomics is hindered by associated software, computing demands, and dataset access. In this inquiry-based activity designed for introductory life science majors and nonmajors, students perform an investigation of the bacterial communities inhabiting the human belly button and associated metagenomics data collected through a citizen science project and visualized using an open-access bioinformatics tool. The activity is designed for attainment of the following student learning outcomes: defining terms associated with metagenomics analyses, describing the biological impact of the microbiota on human health, formulating a hypothesis, analyzing and interpreting metagenomics data to compare microbiota, evaluating a specific hypothesis, and synthesizing a conceptual model as to why bacterial populations vary. This activity was implemented in six introductory biology and biotechnology courses across five institutions. Attainment of student learning outcomes was assessed through completion of a quiz and students' presentations of their findings. In presentations, students demonstrated their ability to develop novel hypotheses and analyze and interpret metagenomic data to evaluate their hypothesis. In quizzes, students demonstrated their ability to define key terms and describe the biological impact of the microbiota on human health. Student learning gains assessment also revealed that students perceived gains for all student learning outcomes. Collectively, our assessment demonstrates achievement of the learning outcomes and supports the utility of this inquiry-based activity to engage undergraduates in the scientific process via analyses of metagenomics datasets and associated exploration of a microbial community that lives on the human body.

Think 500, not 50! A scalable approach to student success in STEM.

BACKGROUND: UMBC, a diverse public research university, "builds" upon its reputation in producing highly capable undergraduate scholars to create a comprehensive new model, STEM BUILD at UMBC. This program is designed to help more students develop the skills, experience and motivation to excel in science, technology, engineering, and mathematics (STEM). This article provides an in-depth description of STEM BUILD at UMBC and provides the context of this initiative within UMBC's vision and mission. KEY HIGHLIGHTS: The STEM BUILD model targets promising STEM students who enter as freshmen or transfer students and do not qualify for significant university or other scholarship support. Of primary importance to this initiative are capacity, scalability, and institutional sustainability, as we distill the advantages and opportunities of UMBC's successful scholars programs and expand their application to more students. The general approach is to infuse the mentoring and training process into the fabric of the undergraduate experience while fostering community, scientific identity, and resilience. At the heart of STEM BUILD at UMBC is the development of BUILD Group Research (BGR), a sequence of experiences designed to overcome the challenges that undergraduates without programmatic support often encounter (e.g., limited internship opportunities, mentorships, and research positions for which top STEM students are favored). BUILD Training Program (BTP) Trainees serve as pioneers in this initiative, which is potentially a national model for universities as they address the call to retain and graduate more students in STEM disciplines - especially those from underrepresented groups. As such, BTP is a research study using random assignment trial methodology that focuses on the scalability and eventual incorporation of successful measures into the traditional format of the academy. IMPLICATIONS: Critical measures to transform institutional culture include establishing an extensive STEM Living and Learning Community to increase undergraduate retention, expanding the adoption of "active learning" pedagogies to increase the efficiency of learning, and developing programs to train researchers to effectively mentor a greater portion of the student population. The overarching goal of STEM BUILD at UMBC is to retain students in STEM majors and better prepare them for post baccalaureate, graduate, or professional programs as well as careers in biomedical and behavioral research.

Who Scared the Cat? A Molecular Crime Scene Investigation Laboratory Exercise.

This introductory laboratory exercise gives first-year life science majors or nonmajors an opportunity to gain knowledge and experience in basic bioinformatics and molecular biology laboratory techniques and analysis in the context of a mock crime scene investigation. In this laboratory, students determine if a human (Lady) or dog (Kona) committed the fictional crime of scaring a cat. Students begin by performing in silico PCR using provided dog- and human-specific PCR primers to determine the sequences to be amplified and predict PCR amplicon sizes. They then BLAST (Basic Local Alignment Search Tool) the in silico PCR results to confirm that the PCR primers are designed to amplify genomic fragments of the cardiac actin gene in both dogs and humans. Finally, they use DNA quantification techniques, PCR, and agarose gel electrophoresis to identify the culprit and they confirm results by analyzing Sanger sequencing. Student learning gains were demonstrated by successful execution of the lab and by analysis and interpretation of data in the completion of laboratory reports. The student learning gains were also demonstrated by increased performance on a post-laboratory assessment compared to the pre-assessment. A post-activity assessment also revealed that students perceived gains in the skills and conceptual knowledge associated with the student learning outcomes. Finally, assessment of this introductory molecular biology and bio-informatics activity reveals that it allows first-year students to develop higher-order data analysis and interpretation skills.

Immunological tools: engaging students in the use and analysis of flow cytometry and enzyme-linked immunosorbent assay (ELISA).

Flow cytometry and enzyme-linked immunosorbent assay (ELISA) are commonly used techniques associated with clinical and research applications within the immunology and medical fields. The use of these techniques is becoming increasingly valuable in many life science and engineering disciplines as well. Herein, we report the development and evaluation of a novel half-semester course that focused on introducing undergraduate and graduate students to advance conceptual and technical skills associated with flow cytometry and ELISA, with emphasis on applications, experimental design, and data analysis. This course was offered in the North Carolina State University Biotechnology Program over three semesters and consisted of weekly lectures and laboratories. Students performed and/or analyzed flow cytometry and ELISA in three separate laboratory exercises: (1) identification of transgenic zebrafish hematopoietic cells, (2) analysis of transfection efficiency, and (3) analysis of cytokine production upon lipopolysaccharide stimulation. Student learning outcomes were achieved as demonstrated by multiple means of assessment, including three laboratory reports, a data analysis laboratory practicum, and a cumulative final exam. Further, anonymous student self-assessment revealed increased student confidence in the knowledge and skill sets defined in the learning outcomes.

Fibroblast Migration Is Regulated by Myristoylated Alanine-Rich C-Kinase Substrate (MARCKS) Protein.

Myristoylated alanine-rich C-kinase substrate (MARCKS) is a ubiquitously expressed substrate of protein kinase C (PKC) that is involved in reorganization of the actin cytoskeleton. We hypothesized that MARCKS is involved in regulation of fibroblast migration and addressed this hypothesis by utilizing a unique reagent developed in this laboratory, the MANS peptide. The MANS peptide is a myristoylated cell permeable peptide corresponding to the first 24-amino acids of MARCKS that inhibits MARCKS function. Treatment of NIH-3T3 fibroblasts with the MANS peptide attenuated cell migration in scratch wounding assays, while a myristoylated, missense control peptide (RNS) had no effect. Neither MANS nor RNS peptide treatment altered NIH-3T3 cell proliferation within the parameters of the scratch assay. MANS peptide treatment also resulted in inhibited NIH-3T3 chemotaxis towards the chemoattractant platelet-derived growth factor-BB (PDGF-BB), with no effect observed with RNS treatment. Live cell imaging of PDGF-BB induced chemotaxis demonstrated that MANS peptide treatment resulted in weak chemotactic fidelity compared to RNS treated cells. MANS and RNS peptides did not affect PDGF-BB induced phosphorylation of MARCKS or phosphoinositide 3-kinase (PI3K) signaling, as measured by Akt phosphorylation. Further, no difference in cell migration was observed in NIH-3T3 fibroblasts that were transfected with MARCKS siRNAs with or without MANS peptide treatment. Genetic structure-function analysis revealed that MANS peptide-mediated attenuation of NIH-3T3 cell migration does not require the presence of the myristic acid moiety on the amino-terminus. Expression of either MANS or unmyristoylated MANS (UMANS) C-terminal EGFP fusion proteins resulted in similar levels of attenuated cell migration as observed with MANS peptide treatment. These data demonstrate that MARCKS regulates cell migration and suggests that MARCKS-mediated regulation of fibroblast migration involves the MARCKS amino-terminus. Further, this data demonstrates that MANS peptide treatment inhibits MARCKS function during fibroblast migration and that MANS mediated inhibition occurs independent of myristoylation.

Attenuation of acute graft-versus-host disease in the absence of the transcription factor RORγt.

Graft-versus-host disease (GVHD) remains the most significant complication after allogeneic stem cell transplantation. Previously, acute GVHD had been considered to be mediated predominantly by Th1-polarized T cells. Recently, investigators have identified a second proinflammatory lineage of T cells termed Th17 that is critically dependent on the transcription factor retinoic acid-related orphan receptor (ROR)γt. In this study, we have evaluated the role of Th17 cells in murine acute GVHD by infusing donor T cells lacking RORC and as a consequence the isoform RORγt. Recipients given donor CD4(+) and CD8(+) T cells lacking RORC had significantly attenuated acute GVHD and markedly decreased tissue pathology in the colon, liver, and lung. Using a clinically relevant haploidentical murine transplantation model, we showed that RORC(-/-) CD4(+) T cells alone diminished the severity and lethality of acute GVHD. This was not found when CD4(+) T cells from RORC(-/-) mice were given to completely mismatched BALB/c mice, and it was correlated with absolute differences in the generation of TNF in the colon after transplant. Thus, CD4(+) T cell expression of RORC is important in the pathogenesis of acute GVHD.

Two myristoylated alanine-rich C-kinase substrate (MARCKS) paralogs are required for normal development in zebrafish.

Myristoylated alanine-rich C-kinase substrate (MARCKS) is an actin binding protein substrate of protein kinase C (PKC) and critical for mouse and Xenopus development. Herein two MARCKS paralogs, marcksa and marcksb, are identified in zebrafish and the role of these genes in zebrafish development is evaluated. Morpholino-based targeting of either MARCKS protein resulted in increased mortality and a range of gross phenotypic abnormalities. Phenotypic abnormalities were classified as mild, moderate or severe, which is characterized by a slight curve of a full-length tail, a severe curve or twist of a full-length tail and a truncated tail, respectively. All three phenotypes displayed abnormal neural architecture. Histopathology of Marcks targeted embryos revealed abnormalities in retinal layering, gill formation and skeletal muscle morphology. These results demonstrate that Marcksa and Marcksb are required for normal zebrafish development and suggest that zebrafish are a suitable model to further study MARCKS function.