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.

Age-dependent changes in collagen crosslinks reduce the mechanical toughness of human meniscus.

The mechanical resilience of the knee meniscus is provided by a group of structural proteins in the extracellular matrix. Aging can alter the quantity and molecular structure of these proteins making the meniscus more susceptible to debilitating tears. In this study, we determined the effect of aging on the quantity of structural proteins and collagen crosslinks in human lateral meniscus, and examined whether the quantity of these molecules was predictive of tensile toughness (area under the stress-strain curve). Two age groups were tested: a young group under 40 and an older group over 65 years old. Using mass spectrometry, we quantified the abundance of proteins and collagen crosslinks in meniscal tissue that was adjacent to the dumbbell-shaped specimens used to measure uniaxial tensile toughness parallel or perpendicular to the circumferential fiber orientation. We found that the enzymatic collagen crosslink deoxypyridinoline had a significant positive correlation with toughness, and reductions in the quantity of this crosslink with aging were associated with a loss of toughness in the ground substance and fibers. The non-enzymatic collagen crosslink carboxymethyl-lysine increased in quantity with aging, and these increases corresponded to reductions in ground substance toughness. For the collagenous (Types I, II, IV, VI, VIII) and non-collagenous structural proteins (elastin, decorin, biglycan, prolargin) analyzed in this study, only the quantity of collagen VIII was predictive of toughness. This study provides valuable insights on the structure-function relationships of the human meniscus, and how aging causes structural adaptations that weaken the tissue's mechanical integrity.

Effects of doxorubicin on autophagy in fibroblasts.

Objectives: Doxorubicin (DOX) is a highly effective chemotherapeutic used to treat many adult and pediatric cancers, such as solid tumors, leukemia, lymphomas and breast cancer. It can also cause injuries to multiple organs, including the heart, liver, and brain or kidney, although cardiotoxicity is the most prominent side effect of DOX. In this study, we examined the potential effects of DOX on autophagy activity in two different mouse fibroblasts.Methods: Mouse embryonic fibroblasts (NIH3T3) and mouse primary cardiac fibroblasts (CFs) were treated with DOX to assess changes in the expression of two commonly used autophagy protein markers, LC3II and p62. We also examined the effects of DOX the on expression of key genes that encode components of the molecular machinery and regulators modulating autophagy in response to both extracellular and intracellular signals.Results: We observed that LC3II levels increased and p62 levels decreased following the DOX treatment in NIH3T3 cells. However, similar effects were not observed in primary cardiac fibroblasts. In addition, DOX treatment induced the upregulation of a significant number of genes involved in autophagy in NIH3T3 cells, but not in primary cardiac fibroblasts.Conclusions: Taken together, these results indicate that DOX upregulates autophagy in fibroblasts in a cell-specific manner.

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.

Structure-Property-Processing Correlations of Graphene Bioscaffolds for Proliferation and Differentiation of C2C12 Cells.

Graphene - an atomically thin layer of carbon atoms arranged in a hexagonal lattice - has gained interest as a bioscaffold for tissue engineering due to its exceptional mechanical, electrical, and thermal properties. Graphene's structure and properties are tightly coupled to synthesis and processing conditions, yet their influence on biomolecular interactions at the graphene-cell interface remains unclear. In this study, C2C12 cells were grown on graphene bioscaffolds with specific structure-property- processing-performance (SP3) correlations. Bioscaffolds were prepared using three different methods - chemical vapor deposition (CVD), sublimation of silicon carbide (SiC), and printing of liquid phase exfoliated graphene. To investigate the biocompatibility of each scaffold, cellular morphology and gene expression patterns were investigated using the bipotential mouse C2C12 cell line. Using a combination of fluorescence microscopy and qRT-PCR, we demonstrate that graphene production methods determine the structural and mechanical properties of the resulting bioscaffold, which in turn determine cell morphology, gene expression patterns, and cell differentiation fate. Therefore, production methods and resultant structure and properties of graphene bioscaffolds must be chosen carefully when considering graphene as a bioscaffold for musculoskeletal tissue engineering.

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.

An amino-terminal fragment of apolipoprotein E4 leads to behavioral deficits, increased PHF-1 immunoreactivity, and mortality in zebrafish.

Although the increased risk of developing sporadic Alzheimer's disease (AD) associated with the inheritance of the apolipoprotein E4 (APOE4) allele is well characterized, the molecular underpinnings of how ApoE4 imparts risk remains unknown. Enhanced proteolysis of the ApoE4 protein with a toxic-gain of function has been suggested and a 17 kDa amino-terminal ApoE4 fragment (nApoE41-151) has been identified in post-mortem human AD frontal cortex sections. Recently, we demonstrated in vitro, exogenous treatment of nApoE41-151 in BV2 microglial cells leads to uptake, trafficking to the nucleus and increased expression of genes associated with cell toxicity and inflammation. In the present study, we extend these findings to zebrafish (Danio rerio), an in vivo model system to assess the toxicity of nApoE41-151. Exogenous treatment of nApoE41-151 to 24-hour post-fertilization for 24 hours resulted in significant mortality. In addition, developmental abnormalities were observed following treatment with nApoE41-151 including improper folding of the hindbrain, delay in ear development, deformed yolk sac, enlarged cardiac cavity, and significantly lower heart rates. A similar nApoE31-151 fragment that differs by a single amino acid change (C>R) at position 112 had no effects on these parameters under identical treatment conditions. Decreased presence of pigmentation was noted for both nApoE31-151- and nApoE41-151-treated larvae compared with controls. Behaviorally, touch-evoked responses to stimulus were negatively impacted by treatment with nApoE41-151 but did not reach statistical significance. Additionally, triple-labeling confocal microscopy not only confirmed the nuclear localization of the nApoE41-151 fragment within neuronal populations following exogenous treatment, but also identified the presence of tau pathology, one of the hallmark features of AD. Collectively, these in vivo data demonstrating toxicity as well as sublethal effects on organ and tissue development support a novel pathophysiological function of this AD associated-risk factor.

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.

Keratinocyte-derived S100A9 modulates neutrophil infiltration and affects psoriasis-like skin and joint disease.

OBJECTIVES: S100A9, an alarmin that can form calprotectin (CP) heterodimers with S100A8, is mainly produced by keratinocytes and innate immune cells. The contribution of keratinocyte-derived S100A9 to psoriasis (Ps) and psoriatic arthritis (PsA) was evaluated using mouse models, and the potential usefulness of S100A9 as a Ps/PsA biomarker was assessed in patient samples. METHODS: Conditional S100A9 mice were crossed with DKO* mice, an established psoriasis-like mouse model based on inducible epidermal deletion of c-Jun and JunB to achieve additional epidermal deletion of S100A9 (TKO* mice). Psoriatic skin and joint disease were evaluated in DKO* and TKO* by histology, microCT, RNA and proteomic analyses. Furthermore, S100A9 expression was analysed in skin, serum and synovial fluid samples of patients with Ps and PsA. RESULTS: Compared with DKO* littermates, TKO* mice displayed enhanced skin disease severity, PsA incidence and neutrophil infiltration. Altered epidermal expression of selective pro-inflammatory genes and pathways, increased epidermal phosphorylation of STAT3 and higher circulating TNFα were observed in TKO* mice. In humans, synovial S100A9 levels were higher than the respective serum levels. Importantly, patients with PsA had significantly higher serum concentrations of S100A9, CP, VEGF, IL-6 and TNFα compared with patients with only Ps, but only S100A9 and CP could efficiently discriminate healthy individuals, patients with Ps and patients with PsA. CONCLUSIONS: Keratinocyte-derived S100A9 plays a regulatory role in psoriatic skin and joint disease. In humans, S100A9/CP is a promising marker that could help in identifying patients with Ps at risk of developing PsA.

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.