bluuebunny/crossref_metadata_2025_split huggingface dataset:
Teaching Cell Signaling Through Research: The Freshman Research Initiative at The University of Texas at Austin
Authors: Clark Greg , Rodenbusch Stacia , Roux Stanley 
Published: November 2023

At large research institutions, undergraduate students typically first encounter faculty research as upper‐division students. The Freshman Research Initiative (FRI) at UT‐Austin is a faculty‐initiated reinvention of our undergraduate research paradigm, recruiting over 800 freshmen each year into an integrated three‐semester research‐based course sequence that increases the number and diversity of students engaged in research, and significantly impacts student success and engagement in science. Each year, freshmen are recruited into an eighteen‐month set of courses that promote critical thinking, interaction with faculty, hands‐on experimentation, data interpretation, student presentation, publication, and peer mentoring. One of the 28 different research areas offered to students in the FRI program is the Cell Signaling Lab. Student involvement in the execution and design of original research is the cornerstone of this lab class. The objectives of this lab for freshman students are: to carry out novel experiments and discover new findings on a question of significant current interest in plant biology; to learn methods of experimental design, data gathering, data interpretation, and data presentation; to develop skills of devising alternative hypotheses to interpret experimental results; to learn, through experimentation and data interpretation, basic principles of stimulus‐response coupling in plants. The Cell Signaling class is addressing the question of what signaling steps mediate the effects of extracellular ATP and ADP on the polarized growth of single‐celled root hairs. We will present details about the impact of the FRI program on the academic performance of participating students and discuss the feasibility of having students in a lab class work on a specific question important to the faculty members' research program.Support or Funding InformationThis work is funded by the Howard Hughes Medical Institute (HHMI) and the the Freshman Research Initiative (FRI).
Northwest Biosciences Consortium RCN‐UBE: Organization and Development of a Faculty Network Leadership Team
Authors: Kruchten Anne , Baumgartner Erin , Beadles‐Bohling Amy , Brown Jeffrey , Duncan Jason , Kayes Lori , Kiser Stacey , Seidel Shannon , Shriner Walter , Stavrianeas Stasinos , Tillberg Chad 
Published: November 2023

The Northwest Biosciences Consortium (NWBC) is a group of two‐year and four‐year college faculty at both public and private institutions in the State of Oregon. Funded by an NSF RCN‐UBE grant, this group is working towards creating modern, student‐centered, integrated, and investigative introductory biology experiences for all students aligned with the Vision and Change: A Call to Action mandate. The NWBC has held three successful faculty development workshops for faculty in biology education throughout the Pacific Northwest, with our most recent February 2017 workshop focusing on non‐majors biology education. In our fourth year of the grant we now report on the building of our leadership network of faculty at public four year colleges, public two year colleges, and private four year colleges. The network is primarily centered in the state of Oregon, but due to increasing interest among regional institutions and movement of faculty in both tenured and non‐tenured positions, we have learned to coordinate our network beyond the state and even the Pacific Northwest. We report here on the origination of the network, the development of the leadership team in the first two years, growing pains and challenges faced by the team, and recent self‐reflection of the leadership team using Theory of Change models and evaluative interviews conducted by external evaluators. We believe that the story of the leadership team can serve as a model for the development of other leadership teams interested in developing regional faculty networks to reform biology education.Support or Funding InformationSupported by the National Science Foundation RCN‐UBE grant (DBI‐1248121).
Computational Studies of the Nudix Hydrolase Superfamily and Nitrophenyl Phosphatase Subfamily of the Had Superfamily
Authors: O'Donovan Kevin , Nulsen Jacob , Craig Paul , O'Handley Suzanne 
Published: November 2023

The Protein Structure Initiative (PSI) was an effort by consortiums to solve as many unique protein structures as possible; the Protein Data Bank contains a number of enzymes whose structures have been solved, but for which no enzymatic activity has been determined. The Enzyme Function Initiative (EFI) is an effort to determine as many unique enzyme functions as possible. There are a number of putative NUDIX Hydrolase and Haloacid Dehalogenase (HAD) superfamily members whose structures have been solved, but for which no enzymatic activity has been determined. We have catalogued the structurally‐determined enzymes within the NUDIX Hydrolase superfamily and the nitrophenyl phosphatase subfamily of the HAD superfamily using BLAST, Dali, and SCOP. We are now beginning to characterize these enzymes in the biochemistry teaching laboratory.Computational programs, such as ProMOL, aid in annotating uncharacterized enzymes. ProMOL works by aligning the relative spatial arrangement of the catalytic residues of a reference enzyme with query searches. We have used ProMOL to design catalytic motifs for the NUDIX hydrolase superfamily and the nitrophenyl phosphatase subfamily of the HAD superfamily, which then can be used to uncover family members whose structures have been solved. Likewise, we have used the docking program PyRx to predict substrate specificity. Through this process, we have discovered the strengths and limitations of these programs. Bioinformatics tools, including databases and computational programs, are good starting points for determining protein function; however, the only way to definitively determine protein function is through experimentally determining activity.Support or Funding InformationNSF DUE‐IUSE 1503811
A Framework for Assessing Molecular Visualization Skills and Competencies
Authors: Dries Daniel R. , Craig Paul A. , Dean Diane , Jakubowski Henry V. , Novak Walter R. P. , Roca Alberto I. , Terrell Cassidy R. , Franzen Margaret A. 
Published: November 2023

Biochemistry education relies on visual representations to make the abstract concrete. Yet despite the heavy use of images in biochemistry and molecular biology (BMB) education, instructors have few resources that enable them to assess the impact of their instruction in visual literacy. Here we describe the recently‐published framework for three‐dimensional visual literacy to include learning goals and objectives at three levels of proficiency: novice (first year life science students), amateur (upper division undergraduates) and expert (graduate students or professionals in the field). We invite BMB educators to join our expanding group as we develop competencies and instruments for assessing students' visual literacy of biomolecules. These competencies and assessment instruments will be curated and catalogued within our online framework found at http://cbm.msoe.edu/crest/molviz/. We encourage the BMB community to use this framework for designing lessons, courses, and curriculum in accordance with Vision & Change and the ASBMB recommended curriculum.Support or Funding InformationThis material is based upon work supported by the National Science Foundation under award number DUE1323414. Any opinions, findings, and conclusions or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
Rheostat or Toggle: Examining the role of non‐conserved mutations to LURE students into research
Authors: Ayella Allan Klara , Moriah Beck R 
Published: November 2023

There is a growing movement to involve undergraduate students in authentic research experiences. A variety of studies have indicated the strength of this approach in developing scientific aptitude, confidence, critical thinking skills and likelihood to become career scientists. Course‐based undergraduate research experiences (CUREs) provide the opportunity to lure students into legitimate research at both primarily undergraduate and large research institutions. Here, we describe how to use a CURE‐based biochemistry lab course to explore the role of conserved and non‐conserved amino‐acid sites in structure and function of lactate dehydrogenase enzyme (LDH). Recent research suggests that substitutions at non‐conserved positions behave more like rheostats in modulating protein function, whereas substitutions at conserved positions result in “toggle switching.” In the first phase of this CURE, students used bioinformatics tools to carry out protein sequence alignments and 3D structural explorations to identify potential sites to mutate in the LDH gene. Site‐directed mutagenesis was then used to generate amino acid substitutions at non‐conserved sites in the LDH protein. Students confirmed mutations to the DNA sequence in protein expression vectors before carrying out protein purification of both wildtype and mutant LDH proteins. In the final phase, students assessed protein function using a variety of techniques. All students were required to determine LDH kinetic parameters (Km and Kcat). In addition, students were prompted to explore other enzyme structural or functional changes through alternative assays or broader biophysical and structural studies of their choice. For example, students initiated studies included the use of circular dichroism to determine structural changes and/or comparisons of thermal stability, examination of coenzyme binding effects and conformational changes via fluorescence spectroscopy. Formal assessments were carried out to determine gains in scientific aptitude, confidence and critical thinking. A culminating poster session allowed students to disseminate their research findings beyond the classroom and receive critical feedback from faculty and students from a broader realm. Attitudinal changes resulting from this experience were monitored by administering the CURE assessment tool developed by Lopata et. al before and after the course. Informal attitudinal assessments indicated that participating in this new curriculum increased student interest in attending graduate school and pursuing careers in biochemical research. Student confidence in their ability to conduct independent research also increased. We feel that because the outcome of each experiment was not known beforehand, students were able to primarily focus on the experimental design and data analysis hence increasing their scientific aptitude, confidence and critical thinking skills.Support or Funding InformationThis research was funded by Wichita State University and McPherson College.
Successes and Teachable Moments During a Partnership to Create a Research‐like Experience in a 2 Year College Organic Chemistry II Laboratory.
Authors: Jaco Nathan , Lutz Christopher , Grant Jennifer 
Published: November 2023

As part of the NSF ATE grant, MALDI‐based Research‐like Experiences in a 2YC/4YC Collaboration with a Renewable Fuels Industry Partner (DUE 1400885), the authors examined how best to combine state of the art training in research‐like experiences that included use of major research instrumentation embedded in an organic chemistry course. In this case a research‐like experience utilizing MALDI‐TOF mass spectrometery was conducted, an experience that also utilized Process Oriented‐Guided Inquiry Learning (POGIL) techniques to serve students at 2‐year colleges. This unique research experience fulminated into sharing of data, methods and feedback between the students and executives of a local biodiesel fuels company, Ever Cat Fuels of Anoka Minnesota.This presentation examines the structure and effectiveness of the artifacts used, as well as the outcomes generated as the research experience was implemented, and the feasibility of creating a modular curriculum that allows student to participate in research‐like experiences using a variety of different major research instruments. At the basis of the curriculum, we created a suite of materials that include a faculty training manual, a student manual, a paced set of Process Oriented Guided Inquiry Learning materials, and two videos. The first video has garnered an average of 1,500 view per month, representing a viewership from 59 countries.Materials used to deliver this research‐like experience will be delineated, and both the successes achieved and the lessons learned during implementation will be summarized. In particular we will highlight our efforts to make fatty acid identification more facile using triglyceride mass tables developed using Excel software. Triglyceride data used was based on the most highly abundant fatty acids present in similar materials shown with GC‐MS analysis. The tables have been constantly modified to benefit the user, by including possible cation adducts and a creating a search feature. Finally, several teaching scripts were developed introducing the biochemistry of Triglycerides and how to properly use the Excel tables in analyzing seed oils. Information from these scripts were then used create a student manual instructing the user on the process of setting up MALDI‐TOF analysis of triglycerides in natural oils.As this is the final year of this project, the authors are soliciting feedback on the quality and utility of these educational resources.Support or Funding InformationThis work was supported by the NSF Advanced Technology Education grant “MALDI‐based Research‐like Experiences in a 2YC/4YC Collaboration with a Renewable Fuels Industry Partner” (DUE 1400885).
Year‐long Research Experiences in Drug Discovery May Lead to Positive Outcomes for Transfer Students
Authors: Beckham Josh , Metola Pedro , Strong Lisa 
Published: November 2023

Conceptual understanding of biochemistry and success in science can be challenging for transfer students when transitioning into a degree plan from another institution. These goals may be more readily achieved through a curriculum tied to research. We have begun to test this hypothesis through establishing a pilot CURE (course based undergraduate research experience) called the Accelerated Research Initiative (ARI) built upon the successful framework of the Freshman Research Initiative (FRI) in the College of Natural Sciences at The University of Texas at Austin. The ARI caters to upper‐division undergraduates science majors (juniors and seniors). Several of the students in a starting class of 16 have transferred into the university from other 4 year institutions or from community colleges. The student‐researchers are guided by a non‐tenure track professor, several undergraduate TAs and peers who have prior research experience. For each project, the overall goal is to identify small molecule inhibitors of an enzyme from an infectious disease organism (bacterial or protozoan). Computational molecular docking software is used to make predictions about which compounds may bind. They then seek to test these in biochemical assays against the enzyme they have made through recombinant DNA cloning and protein expression. In order to gain insight into the students' perceptions of the experience so that the curriculum could be tailored in subsequent semesters, surveys and focus groups were used. The questions and discussion focused on gaining insight about the contexts, activities, and outcomes cited in other CUREs (Corwin et. al. 2015), such as: content and skills, self‐efficacy, persistence in science, ownership, communication, science identity, and mentoring. When compared to responses from transfer students who did not participate in a CURE, these perceptions of the course may help identify which aspects are most meaningful to achieving science success.Support or Funding InformationHoward Hughes Medical Institute (HHMI)
Stabilization of Dsg2 binding enhances GJ function and ameliorates arrhythmia caused by PG deficiency
Authors: Erber Bernd Markus , Schinner Camilla , Schlipp Angela , Waschke Jens 
Published: November 2023

Arrhythmogenic cardiomyopathy (AC) is a genetic disease of the cardiomyocyte intercalated disc which causes cardiac arrhythmia and sudden cardiac death. Mutations primarily affect desmosomal proteins including the cadherin‐type adhesion molecule desmoglein 2 (Dsg2) and the plaque protein plakoglobin (Pg), which are known to be required for mechanical cohesion of cardiomyocytes, and thereby impair gap junction (GJ)‐mediated propagation of excitation by unknown mechanisms. Therefore, therapy is symptomatic at present. We provide evidence that stabilization of Dsg2‐binding by a tandem peptide (TP) enhances GJ signal transduction in cardiomyocytes. TP was designed to cross‐link Dsg2 molecules separate from the hydrophobic binding pocket of the extracellular domain 1. TP stabilized Dsg2 interaction on the surface of living cardiomyocytes as revealed by atomic force microscopy (AFM) and rescued cardiomyocyte cohesion when either tryptophan was used to block the binding pocket or Dsg2 and Pg were depleted by siRNA. In parallel, disturbed localization of connexin 43 (Cx43) and impaired GJ‐mediated excitation propagation were also abolished by TP, partly via a mechanism involving PKC phosphorylation of Cx43. In hearts from a cardiomyocyte‐specific Pg‐deletion mouse model for AC, TP reduced arrhythmia immediately upon perfusion. These results indicate that stabilization of Dsg2 binding may represent a new approach to treat arrhythmia in AC.Support or Funding InformationFörderung für Forschung und Lehre (FöFoLe)
CD43 syalomucin contributes to cardiac inflammation and fibrosis in non‐ischemic heart failure
Authors: Velázquez Francisco , Salvador Ane , Nevers Tania , Ngwenyama Njabulo , Aronovitz Mark , Blanton Robert , Alcaide Pilar 
Published: November 2023

Left ventricular (LV) dysfunction and Heart Failure (HF), are one of the leading causes of hospitalizations and death in the developed world. HF is a very complex syndrome involving multiple factors that lead to LV remodeling and impairment of cardiac function. T cells have been found infiltrated in the LV of patients with ischemic and non‐ischemic HF and also increased in the systemic circulation, and this correlates with LV dysfunction. Moreover, studies in T cell deficient mice demonstrate a pathogenic role for T cells in non‐ischemic HF induced by LV pressure overload. We have previously demonstrated that intra‐myocardial E‐selectin and intracellular adhesion molecule‐1 (ICAM‐1) are upregulated in mice with HF, and suggested that these adhesion molecules may regulate T cell recruitment to the heart during pressure overload induced HF. Syalomucin CD43 is highly expressed on leukocytes, including T cells, and its highly glycosylated form expressed in activated T cells functions as an essential E‐selectin ligand that regulates specific T cell subset recruitment to sites of inflammation. However, the role of CD43 in cardiovascular disease is largely unexplored and its role in leukocyte recruitment in HF remains unknown. We hypothesized that CD43 regulates T cell recruitment to the LV during pressure overload induced HF. To test this, we used the mouse model of thoracic aortic constriction (TAC) in WT and CD43−/− mice and monitored them for 4 weeks. We observed that the expression of the highly glycosylated form of CD43 was induced in T cells isolated from cardiac lymph nodes from TAC WT mice as compared to Sham mice. CD43−/− mice had a higher survival rate and reduced interstitial and perivascular fibrosis as compared to WT mice. Echocardiography measurements determined that the ejection fraction and fractional shortening were both preserved in CD43−/− mice in response to TAC as compared to WT TAC mice, indicating preserved systolic function in CD43−/− mice. Immunohistochemistry showed that CD43−/− mice had decreased LV leukocyte infiltration, more specifically, decreased CD4+ T cells and CD11b+ monocytes as compared to WT mice in response to TAC. Our results demonstrate that CD43 plays a crucial role in leukocyte recruitment to the heart and in the pathology associated with non‐ischemic heart failure. Future studies will determine the molecular mechanisms by which CD43 functions in leukocyte trafficking and disease progression in non‐ischemic heart failure.Support or Funding InformationHL123658‐01S1
Resolvin D1 Programs Myocardial Infarction‐induced Cardiorenal Syndrome in Heart Failure Pathology
Authors: Halade Ganesh V. , Kain Vasundhara , Serhan Charles N. , Ingle Kevin A. 
Published: November 2023

Resolvins are innate immune responsive lipid mediators produced after myocardial infarction (MI) to resolve inflammation. MI‐induced bidirectional interaction between progressive left ventricle remodeling and kidney dysfunction is known to advance cardiorenal syndrome (CRS). Whether resolvins limits MI‐induced cardiorenal dysfunction is unclear. Thus, to define the role of resolvin D1 (RvD1) in post‐MI CRS, we tested the hypothesis using 8 to 12 weeks old male C57BL/6 mice that were subjected to coronary artery ligation surgery. RvD1 (3ug/kg/day) was injected 3 hour post‐MI for day (d)1 or continued till d5. No‐MI naïve and saline‐injected MI mice were used as controls. RvD1‐injected group promoted neutrophils (CD11b+/Ly6G+; 2.0±0.3%) egress from infarcted LV compared with MI‐control group (4.2±2.0%) at d5 post‐MI. Further, RvD1 injected mice showed higher reparative macrophages (F4/80+/Ly6Clow/CD206+; 20.0±1.0%) phenotype in the infarcted LV compared with MI‐control group (14.4±2.1%) at d5 post‐MI measured by flow cytometry. MI‐induced LV remote hypertrophy was limited in RvD1‐injected mice compared with MI‐control mice confirmed using wheat germ agglutinin staining. Post‐MI nephrin expression was diffused to glomerular membrane at d5 in MI‐control mice indicating renal injury impacting kidney glomerulus structure but to a lesser extent in RvD1‐injected mice validated using immunofluorescence staining. Administration of RvD1 attenuated MI‐induced renal inflammation decreasing neutrophil gelatinase‐associated lipocalin (2.0±0.1 fold p<0.05) gene and protein expression in the kidney at d1 post‐MI (2.2±0.1 fold; p<0.5) and d5 compared to MI‐control. In conclusion, RvD1 not only clears MI‐induced inflammation by increasing resolving leukocytes but also is renoprotective in nature in heart failure pathology.Support or Funding InformationHL132989 and AT006704 to GVH