An Exploration of the Relationship Between Active Learning and Student Motivation in STEM: A Mixed Methods Study.

Much of the research about STEM students' motivation measures the relationship between student motivation and academic outcomes, focusing on the student's mindset. This study takes a different approach, considering student motivation and instructional practices. Teaching practices and student motivation were analyzed simultaneously in undergraduate Biology classes using a self-determination theory-based survey and the Classroom Observation Protocol for Undergraduate STEM, and observation notes were collected to document instructor and student behaviors. Quantitative data was used to differentiate students' motivational levels and qualitative data was collected to describe how instructors use specific teaching practices. The results provide a lens into how students' intrinsic motivation varies alongside the instructional practices and interactions in these classes. We found a correlation between higher levels of student motivation in interactive lecture and student-centered teaching profiles. This study highlights how the same practice can be implemented by multiple instructors with varying student motivation scores, pointing out the importance of fidelity to evidence-based instructional practice methods. The results of this study are discussed in the context of published empirical studies examining evidence-based instructional practices that are conceptually supportive of autonomy, competence, and relatedness. Active learning practices observed in this study correlated to positive learning outcomes are discussed and may serve as a guide for instructors interested in implementing specific active learning practices. Recommendations for instructors and departments that are interested in flexible methods to monitor progress toward active learning practices in biology and other STEM disciplines by combining the COPUS and self-determination survey results are presented.

Genomic Surveillance of SARS-CoV-2 Sequence Variants at Universities in Southwest Idaho.

Although the impact of the SARS-CoV-2 pandemic on major metropolitan areas is broadly reported and readily available, regions with lower populations and more remote areas in the United States are understudied. The objective of this study is to determine the progression of SARS-CoV-2 sequence variants in a frontier and remote intermountain west state among university-associated communities. This study was conducted at two intermountain west universities from 2020 to 2022. Positive SARS-CoV-2 samples were confirmed by quantitative real-time reverse transcription-polymerase chain reaction and variants were identified by the next-generation sequencing of viral genomes. Positive results were obtained for 5355 samples, representing a positivity rate of 3.5% overall. The median age was 22 years. Viral genomic sequence data were analyzed for 1717 samples and phylogeny was presented. Associations between viral variants, age, sex, and reported symptoms among 1522 samples indicated a significant association between age and the Delta variant (B 1.167.2), consistent with the findings for other regions. An outbreak event of AY122 was detected August-October 2021. A 2-month delay was observed with respect to the timing of the first documented viral infection within this region compared to major metropolitan regions of the US.

Proteomic dataset for decellularization of porcine auricular cartilage.

OBJECTIVES: Osteoarthritis (OA) is a major concern in the United States and worldwide. Development and validation of robust decellularization techniques is critical in generating suitable bioscaffolds for future OA treatment options. DATA DESCRIPTIONS: In the present study, proteins from porcine auricular cartilage before and after decellularization were extracted, digested, and identified using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The data represents protein profiles of both non-decellularized and decellularized porcine auricular cartilage. This data is intended to be useful to scientists who are interesting in generating biomaterials for potential relevant clinical applications using decellularized cartilage tissue.

Effects of Doxorubicin on Extracellular Matrix Regulation in Primary Cardiac Fibroblasts from Mice.

OBJECTIVE: Doxorubicin (DOX) is a highly effective chemotherapeutic used to treat many adult and pediatric cancers. However, its use is limited due to a dose-dependent cardiotoxicity, which can lead to lethal cardiomyopathy. In contrast to the extensive research efforts on toxic effects of DOX in cardiomyocytes, its effects and mechanisms on cardiac extracellular matrix (ECM) homeostasis and remodeling are poorly understood. In this study, we examined the potential effects of DOX on cardiac ECM to further our mechanistic understanding of DOX-induced cardiotoxicity. RESULTS: DOX-induced significant down-regulation of several ECM related genes in primary cardiac fibroblasts, including Adamts1, Adamts5, Col4a1, Col4a2, Col5a1, Fbln1, Lama2, Mmp11, Mmp14, Postn, and TGFß. Quantitative proteomics analysis revealed significant global changes in the fibroblast proteome following DOX treatment. A pathway analysis using iPathwayGuide of the differentially expressed proteins revealed changes in a list of biological pathways that involve cell adhesion, cytotoxicity, and inflammation. An apparent increase in Picrosirius red staining indicated that DOX-induced an increase in collagen production in cardiac primary fibroblasts after 3-day treatment. No significant changes in collagen organization nor glycoprotein production were observed.

Doxorubicin-induced modulation of TGF-ß signaling cascade in mouse fibroblasts: insights into cardiotoxicity mechanisms.

Doxorubicin (DOX)-induced cardiotoxicity has been widely observed, yet the specific impact on cardiac fibroblasts is not fully understood. Additionally, the modulation of the transforming growth factor beta (TGF-ß) signaling pathway by DOX remains to be fully elucidated. This study investigated DOX's ability to modulate the expression of genes and proteins involved in the TGF-ß signaling cascade in mouse fibroblasts from two sources by assessing the impact of DOX treatment on TGF-ß inducible expression of pivotal genes and proteins within fibroblasts. Mouse embryonic fibroblasts (NIH3T3) and mouse primary cardiac fibroblasts (CFs) were treated with DOX in the presence of TGF-ß1 to assess changes in protein levels by western blot and changes in mRNA levels by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). Our results revealed a dose-dependent reduction in cellular communication network factor 2 (CCN2) protein levels upon DOX treatment in both NIH3T3 and CFs, suggesting an antifibrotic activity by DOX in these fibroblasts. However, DOX only inhibited the TGF-ß1 induced expression of COL1 in NIH3T3 cells but not in CFs. In addition, we observed that DOX treatment reduced the expression of BMP1 in NIH3T3 but not primary cardiac fibroblasts. No significant changes in SMAD2 protein expression and phosphorylation in either cells were observed after DOX treatment. Finally, DOX inhibited the expression of Atf4 gene and increased the expression of Cdkn1a, Id1, Id2, Runx1, Tgfb1, Inhba, Thbs1, Bmp1, and Stat1 genes in NIH3T3 cells but not CFs, indicating the potential for cell-specific responses to DOX and its modulation of the TGF-ß signaling pathway.

Doxorubicin-Induced Modulation of TGF-ß Signaling Cascade in Mouse Fibroblasts: Insights into Cardiotoxicity Mechanisms.

Doxorubicin (DOX)-induced cardiotoxicity has been widely observed, yet the specific impact on cardiac fibroblasts is not fully understood. Additionally, the modulation of the transforming growth factor beta (TGF-ß) signaling pathway by DOX remains to be fully elucidated. This study investigated DOX's ability to modulate the expression of genes and proteins involved in the TGF-ß signaling cascade in mouse fibroblasts from two sources by assessing the impact of DOX treatment on TGF-ß inducible expression of pivotal genes and proteins within fibroblasts. Mouse embryonic fibroblasts (NIH3T3) and mouse primary cardiac fibroblasts (CFs) were treated with DOX in the presence of TGF-ß1 to assess changes in protein levels by western blot and changes in mRNA levels by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). Our results revealed a dose-dependent reduction in cellular communication network factor 2 (CCN2) protein levels upon DOX treatment in both NIH3T3 and CFs. Moreover, we observed that DOX inhibited the TGF-ß1 induced expression of BMP1 in NIH3T3 cells, while BMP1 levels remained high in CFs, and that TGF-ß1 induces the phosphorylation of SMAD2 in both NIH3T3 cells and CFs. While DOX treatment diminished the extent of phosphorylation, the reduction did not reach statistical significance. DOX also inhibited the TGF-ß1 induced expression of COL1 in NIH3T3 cells and CFs. Finally, DOX inhibited the TGF-ß1 induced expression of Atf4 and increased the expression of Cdkn1a, Id1, Id2, Runx1, Tgfb1, Inhba, Thbs1, Bmp1, and Stat1 in NIH3T3 cells but not CFs, indicating the potential for cell-specific responses to DOX and its modulation of the TGF-ß signaling pathway. Understanding the underlying mechanisms of the ability of DOX to modulate gene expression and signaling pathways in fibroblasts holds promise for future development of targeted therapeutic strategies to mitigate DOX-induced cardiotoxicity specifically affecting CFs.

Shared Core Facilities Serve as Hubs for Biomedical Research Network at Institutions of Emerging Excellence.

We analyzed co-authorship patterns within the National Institutes of Health Center of Biomedical Research Excellence in Matrix Biology program from 2014 to 2022. In this study, we analyzed junior investigators, senior researchers, and research scientists within a shared core facility. Social network analysis techniques were applied to evaluate the co-authorship network based on journal publications from members of the center. The results indicated that co-authorship network visualization and analysis is a useful tool for understanding the relationship between a shared core facility and young investigators within a research center. Young investigators collaborated with and relied upon the individual research scientists of the shared core facility to serve as contributing members of their extended research team. This reliance on the shared core facility effectively increases the size and productivity of the research team led by the young investigator. Our results indicate that shared core facility staff may serve as hubs within the network of biomedical researchers, particularly at institutions with a growing research emphasis. Listen to this article.

Advances in Cartilage Tissue Engineering Using Bioinks with Decellularized Cartilage and Three-Dimensional Printing.

Osteoarthritis, a chronic, debilitating, and painful disease, is one of the leading causes of disability and socioeconomic burden, with an estimated 250 million people affected worldwide. Currently, there is no cure for osteoarthritis and treatments for joint disease require improvements. To address the challenge of improving cartilage repair and regeneration, three-dimensional (3D) printing for tissue engineering purposes has been developed. In this review, emerging technologies are presented with an overview of bioprinting, cartilage structure, current treatment options, decellularization, bioinks, and recent progress in the field of decellularized extracellular matrix (dECM)-bioink composites is discussed. The optimization of tissue engineering approaches using 3D-bioprinted biological scaffolds with dECM incorporated to create novel bioinks is an innovative strategy to promote cartilage repair and regeneration. Challenges and future directions that may lead to innovative improvements to currently available treatments for cartilage regeneration are presented.

How to Develop a Grant Writing Course for Undergraduate Students.

Grant writing is an important skill to develop, allowing students to envision solutions to issues that impact their local, regional, and global communities. Additionally, grant writing, like other research-associated activities, can improve student success in and out of the classroom. Grant writing can help students understand the alignment between research activities and a "big picture" understanding of the common good and societal impact of the research. Grant writing can improve students' ability to articulate the significance and broader impacts of research. Faculty mentors can play a major role in grant writing activities by helping to guide undergraduate students through the process. A course-based approach can help instructors who mentor students in research by providing scaffolding and scheduling tools. This article provides an overview of a grant writing course used as an efficient and effective way for undergraduate students to be guided through the grant proposal writing process with a greater potential for positive outcomes. We discuss why undergraduate students should learn how to write grant proposals, the advantages of teaching grant writing in a course-based format, time management, learning outcomes, and ways to assess student learning. © 2023 Wiley Periodicals LLC.

Purification and Isolation of Proteins from Hyaline Cartilage.

Proteins from hyaline or articular cartilage can be isolated and purified using a series of chemical extraction steps and various identification techniques including mass spectrometry and immunoblotting. The isolation and purification of proteins from cartilage will facilitate the study of specific proteins and multimeric complexes of cartilage proteins to better understand their functions in normal healthy cartilage as well as pathological conditions of cartilage. Cartilage tissue engineering efforts rely on the comprehensive understanding of the composition of cartilage and the function of each of the protein constituents.

The Shape of the Jaw-Zebrafish Col11a1a Regulates Meckel's Cartilage Morphogenesis and Mineralization.

The expression of the col11a1a gene is essential for normal skeletal development, affecting both cartilage and bone. Loss of function mutations have been shown to cause abnormalities in the growth plate of long bones, as well as in craniofacial development. However, the specific effects on Meckel's cartilage have not been well studied. To further understand the effect of col11a1a gene function, we analyzed the developing jaw in zebrafish using gene knockdown by the injection of an antisense morpholino oligonucleotide using transgenic Tg(sp7:EGFP) and Tg(Fli1a:EGFP) EGFP reporter fish, as well as wildtype AB zebrafish. Our results demonstrate that zebrafish col11a1a knockdown impairs the cellular organization of Meckel's cartilage in the developing jaw and alters the bone formation that occurs adjacent to the Meckel's cartilage. These results suggest roles for Col11a1a protein in cartilage intermediates of bone development, the subsequent mineralization of the bony collar of long bones, and that which occurs adjacent to Meckel's cartilage in the developing jaw.

Overview on Grant Writing for Graduate Student Research.

Grant writing is an important skill to develop during graduate school. This article provides an overview of grant writing for graduate students. Specific topics covered include understanding your funding needs, identifying appropriate grant opportunities, analyzing the guidelines for the proposal, planning and time management, understanding the priorities of the funding agency or organization, proposal organization and writing strategies, additional forms and letters of support that may be required, the editing and revising process, and submission of your grant proposal. Courses and workshops are an efficient and effective way to be guided through the grant proposal writing process with a greater potential for positive outcomes. © 2022 Wiley Periodicals LLC.

Collagen a1(XI) structure prediction by Alphafold 2.

Collagen α1(XI) is a minor fibrillar collagen involved in the critical regulation of collagen fibrils such as nucleation, assembly, and regulation of fibril diameter. The amino propeptide domain of the collagen α1(XI) is retained on the surface of the collagen fibril for an extended period of time and may play a crucial role in the interaction with extracellular matrix glycosaminoglycans and other proteins during the process of fibrillogenesis. Understanding the mechanism of action of this protein will ultimately help us understand the organization and assembly of the extracellular matrix that underlies the structural integrity of connective tissues.

Gateway Scholars Program - reducing barriers to STEM for undergraduate students through scholarship and supportive programs.

This report presents the Gateway Scholars Program, an NSF-S-STEM supported program that recruited academically talented undergraduate students with demonstrated financial need. The objectives of our program included establishing a mentored cohort program, implementing enhanced risk-based advising, integrating evidence-based instructional practices in the curriculum, engaging students in co-curricular experiences, and generating new knowledge about the effect of activities on retention, student success, and degree attainment. Knowledge about broadening participation and effectiveness of evidence-based practices in STEM curricular and co-curricular activities and systems developed through this program have the potential to impact all STEM departments.

Social network analysis of biomedical research growth at a primarily undergraduate institution.

The National Institutes of Health Institutional Development Award Programs support the establishment and growth of biomedical research infrastructure in states that receive a low level of federal funding for biomedical research. The purpose of this investigation was to analyze the growth in research productivity over time. This program fostered an environment in which a biomedical research program could be developed and allowed to grow at Boise State University, a primarily undergraduate institution. The growth of the biomedical research community can be visualized through social network analysis.

Authentication of a novel antibody to zebrafish collagen type XI alpha 1 chain (Col11a1a).

OBJECTIVE: Extracellular matrix proteins play important roles in embryonic development and antibodies that specifically detect these proteins are essential to understanding their function. The zebrafish embryo is a popular model for vertebrate development but suffers from a dearth of authenticated antibody reagents for research. Here, we describe a novel antibody designed to detect the minor fibrillar collagen chain Col11a1a in zebrafish (AB strain). RESULTS: The Col11a1a antibody was raised in rabbit against a peptide comprising a unique sequence within the zebrafish Col11a1a gene product. The antibody was affinity-purified and characterized by ELISA. The antibody is effective for immunoblot and immunohistochemistry applications. Protein bands identified by immunoblot were confirmed by mass spectrometry and sensitivity to collagenase. Col11a1a knockout zebrafish were used to confirm specificity of the antibody. The Col11a1a antibody labeled cartilaginous structures within the developing jaw, consistent with previously characterized Col11a1 antibodies in other species. Col11a1a within formalin-fixed paraffin-embedded zebrafish were recognized by the antibody. The antibodies and the approaches described here will help to address the lack of well-defined antibody reagents in zebrafish research.

Emerging Perspectives on Leukemia Inhibitory Factor and its Receptor in Cancer.

Tumorigenesis and metastasis have deep connections to inflammation and inflammatory cytokines, but the mechanisms underlying these relationships are poorly understood. Leukemia Inhibitory Factor (LIF) and its receptor (LIFR), part of the interleukin-6 (IL-6) cytokine family, make up one such ill-defined piece of the puzzle connecting inflammation to cancer. Although other members of the IL-6 family have been shown to be involved in the metastasis of multiple types of cancer, the role of LIF and LIFR has been challenging to determine. Described by others in the past as enigmatic and paradoxical, LIF and LIFR are expressed in a diverse array of cells in the body, and the narrative surrounding them in cancer-related processes has been vague, and at times even contradictory. Despite this, recent insights into their functional roles in cancer have highlighted interesting patterns that may allude to a broader understanding of LIF and LIFR within tumor growth and metastasis. This review will discuss in depth the signaling pathways activated by LIF and LIFR specifically in the context of cancer-the purpose being to summarize recent literature concerning the downstream effects of LIF/LIFR signaling in a variety of cancer-related circumstances in an effort to begin teasing out the intricate web of contradictions that have made this pair so challenging to define.

Decellularized Porcine Cartilage Scaffold; Validation of Decellularization and Evaluation of Biomarkers of Chondrogenesis.

Osteoarthritis is a major concern in the United States and worldwide. Current non-surgical and surgical approaches alleviate pain but show little evidence of cartilage restoration. Cell-based treatments may hold promise for the regeneration of hyaline cartilage-like tissue at the site of injury or wear. Cell-cell and cell-matrix interactions have been shown to drive cell differentiation pathways. Biomaterials for clinically relevant applications can be generated from decellularized porcine auricular cartilage. This material may represent a suitable scaffold on which to seed and grow chondrocytes to create new cartilage. In this study, we used decellularization techniques to create an extracellular matrix scaffold that supports chondrocyte cell attachment and growth in tissue culture conditions. Results presented here evaluate the decellularization process histologically and molecularly. We identified new and novel biomarker profiles that may aid future cartilage decellularization efforts. Additionally, the resulting scaffold was characterized using scanning electron microscopy, fluorescence microscopy, and proteomics. Cellular response to the decellularized scaffold was evaluated by quantitative real-time PCR for gene expression analysis.

Data Management Tools to Measure the Impact of Core Facilities.

The Biomolecular Research Center at Boise State University is a research core facility that supports the study of biomolecules with an emphasis on protein structure and function, molecular interactions, and imaging. The mission of the core is to facilitate access to instrumentation that might otherwise be unavailable because of the cost, training for new users, and scientific staff with specialized skills to support early-stage investigators, as well as more established senior investigators. Data collection and management of users and their research output is essential to understand the impact of the center on the research environment and research productivity. However, challenges are often encountered when trying to fully quantify the impact of a core facility on the institution, as well as on the career success of individual investigators. This challenge can be exacerbated under the conditions of unprecedented growth in biomedical research and shared core facility use that has been experienced at Boise State University, an institution of emerging research excellence. Responding to these challenges required new approaches to information management, reporting, assessment, and evaluation. Our specific data management, evaluation, and assessment challenges included 1) collection and management of annual reporting information from investigators, staff, and students in a streamlined manner that did not lead to reporting fatigue; 2) application of software for analyzing synergy among programs' management strategy and investigator success; and 3) consolidation of core facility management, billing, and reporting capabilities into 1 cohesive system. The data management tools adopted had a beneficial effect by saving time, reducing administrative burden, and streamlining reporting. Practices implemented for data management have facilitated effective evaluation and future program planning. The substantial burden of assessment requirements necessitates early consideration of a strategy for data management to allow assessment of impact.

A repeated triple lysine motif anchors complexes containing bone sialoprotein and the type XI collagen A1 chain involved in bone mineralization.

While details remain unclear, initiation of woven bone mineralization is believed to be mediated by collagen and potentially nucleated by bone sialoprotein (BSP). Interestingly, our recent publication showed that BSP and type XI collagen form complexes in mineralizing osteoblastic cultures. To learn more, we examined the protein composition of extracellular sites of de novo hydroxyapatite deposition which were enriched in BSP and Col11a1 containing an alternatively spliced "6b" exonal sequence. An alternate splice variant "6a" sequence was not similarly co-localized. BSP and Col11a1 co-purify upon ion-exchange chromatography or immunoprecipitation. Binding of the Col11a1 "6b" exonal sequence to bone sialoprotein was demonstrated with overlapping peptides. Peptide 3, containing three unique lysine-triplet sequences, displayed the greatest binding to osteoblastic cultures; peptides containing fewer lysine triplet motifs or derived from the "6a" exon yielded dramatically lower binding. Similar results were obtained with 6-carboxyfluorescein (FAM)-conjugated peptides and western blots containing extracts from osteoblastic cultures. Mass spectroscopic mapping demonstrated that FAM-peptide 3 bound to 90 kDa BSP and its 18 to 60 kDa fragments, as well as to 110 kDa nucleolin. In osteoblastic cultures, FAM-peptide 3 localized to biomineralization foci (site of BSP) and to nucleoli (site of nucleolin). In bone sections, biotin-labeled peptide 3 bound to sites of new bone formation which were co-labeled with anti-BSP antibodies. These results establish the fluorescent peptide 3 conjugate as the first nonantibody-based method to identify BSP on western blots and in/on cells. Further examination of the "6b" splice variant interactions will likely reveal new insights into bone mineralization during development.