Biology subjects

Emery, N.

Publications and source records attributed to Emery, N..

6 recordsLinked to original sources

bioRxiv2026

Flowable Grafts Made from Granular Extracellular Matrix (gECM) Hydrogels Promote Integrative Repair of Articular Cartilage in a Large-Animal Model

Focal injuries to articular cartilage in load-bearing joints fail to heal and often progress to degeneration, underscoring the need for repair strategies that result in restored cartilage structure and function rather than fibrocartilage formation. Granular extracellular matrix (gECM) hydrogels, flowable grafts composed of densely-packed matrix particles, offer a promising approach but lack long-term functional validation in large-animal models. Here, we developed a flowable gECM hydrogel composed of decellularized cartilage microparticles incorporated within a thiol-functionalized hyaluronan matrix. Proteomic analysis confirmed enrichment of cartilage-specific gECM matrisome components. When implanted into critical-sized femoral condyle defects in a goat model and evaluated 12 months post-implantation, both gECM hydrogel and microdrilling (surgical controls) achieved >80% defect filling. However, in contrast to microdrilling, gECM repair tissue exhibited surface tribological (friction, adhesion) and compressive mechanical properties comparable to native cartilage, with a similar proteoglycan-to-collagen ratio, enrichment of type II collagen, minimal type I collagen (typical of a fibrous scar), improved quantitative MRI metrics, and evidence of lateral cartilage integration and subchondral bone remodeling. Together, these findings demonstrate that a flowable gECM hydrogel supports integrative, cartilage-like repair in a load-bearing joint, supporting advancement of this approach toward clinical translation. One Sentence SummaryA granular ECM hydrogel implanted in a goat condyle provided a robust repair, filling the defect tissue with integrated, hyaline-like cartilage at 12 months.

bioengineering↗

bioRxiv2021

Epigenetic remodeling during monolayer cell expansion reduces therapeutic potential

Understanding how cells remember previous mechanical environments to influence their fate, or mechanical memory, informs the design of biomaterials and therapies in medicine. Current regeneration therapies require two-dimensional (2D) cell expansion processes to achieve large cell populations critical for the repair of damaged (e.g. connective and musculoskeletal) tissues. However, the influence of mechanical memory on cell fate following expansion is unknown, and mechanisms defining how physical environments influence the therapeutic potential of cells remain poorly understood. Here, we show that the organization of histone H3 trimethylated at lysine 9 (H3K9me3) and expression of tissue-identifying genes in primary cartilage cells (chondrocytes) transferred to three-dimensional (3D) hydrogels depends on the number of previous population doublings on tissue culture plastic during 2D cell expansion. Decreased levels of H3K9me3 occupying promoters of dedifferentiation genes after the 2D culture were also retained in 3D culture. Suppression of H3K9me3 during expansion of cells isolated from a murine model similarly resulted in the loss of the chondrocyte phenotype and global remodeling of nuclear architecture. In contrast, increasing levels of H3K9me3 through inhibiting H3K9 demethylases partially rescued the chondrogenic nuclear architecture and gene expression, which has important implications for tissue repair therapies, where expansion of large numbers of phenotypically-suitable cells is required. Overall, our findings indicate mechanical memory in primary cells is encoded in the chromatin architecture, which impacts cell fate and the phenotype of expanded cells. SIGNIFICANCE STATEMENTTissue regeneration procedures, such as cartilage defect repair (e.g. Matrix-induced Autologous Chondrocyte Implantation) often require cell expansion processes to achieve sufficient cells to transplant into an in vivo environment. However, the chondrocyte cell expansion on 2D stiff substrates induces epigenetic changes that persist even when the chondrocytes are transferred to a different (e.g. 3D) or in vivo environment. Treatments to alter epigenetic gene regulation may be a viable strategy to improve existing cartilage defect repair procedures and other tissue engineering procedures that involve cell expansion.

bioengineering↗

bioRxiv2021

Short-interval fires and vegetation change in southern California

QuestionsIn southern California, shortened fire return intervals may contribute to a decrease in native chaparral shrub presence and an increase in non-native annual grass presence. To test the hypothesis that short-fire return intervals promote a loss in shrub cover, we examined the contribution of single short-interval fires and abiotic conditions on the change of shrub cover within Ventura and Los Angeles counties. Through evaluating pre- and post-fire historical aerial images, we answered the following questions, 1) How has vegetation type cover changed after repeat fires? and 2) What landscape variables contribute the most to the observed change? LocationVentura County and Los Angeles County, California, USA. MethodsWe assessed the impact of a single short-interval fire by comparing vegetation recovery in adjacent once- and twice-burned fire burn polygons (long- and short-interval respectively). Pixel plots were examined within each polygon and vegetation cover was classified to vegetation type. We determined the best predictor of vegetation type cover with a linear mixed effects model comparison using Akaike Information Criterion. ResultsPre-fire and post-fire community type cover was highly correlated. Burn interval was the best predictor of tree cover change (lower cover in twice-burned pixel plots). Aspect was the best predictor of sage scrub cover change (greater cover on north-facing aspects). Years since fire was the best predictor of chaparral cover change (positive correlation) and sage scrub cover change (negative correlation). Conversion of chaparral to sage scrub cover was more likely to occur than conversion of chaparral to annual grass cover. ConclusionsOur study did not find extensive evidence of a decrease in chaparral shrub cover due to a single short-interval fire. Instead, post-fire cover was highly correlated with pre-fire cover. Chaparral recovery, however, was dynamic suggesting that stand recovery may be strongly influenced by local scale conditions and processes.

ecology↗

bioRxiv2020

The soybean (Glycine max L.) cytokinin oxidase/dehydrogenase multigene family; identification of natural variations for altered cytokinin content and seed yield

Cytokinins (CKs) play a fundamental role in regulating dynamics of organ source/sink relationships during plant development, including flowering and seed formation stages. As a result, CKs are key drivers of seed yield. The cytokinin oxidase/dehydrogenase (CKX) is one of the critical enzymes responsible for regulating plant CK levels by causing their irreversible degradation. Variation of CKX gene activity is significantly correlated with seed yield in many crop species while in soybean (Glycine max L.), the possible associations between CKX gene family members (GFMs) and yield parameters have not yet been assessed. In this study, seventeen GmCKX GFMs were identified, and natural variations among GmCKX genes were probed among soybean cultivars with varying yield characteristics. The key CKX genes responsible for regulating CK content during seed filling stages of reproductive development were highlighted using comparative phylogenetics, gene expression analysis and CK metabolite profiling. Five of the seventeen identified GmCKX GFMs, showed natural variations in the form of single nucleotide polymorphisms (SNPs). The gene GmCKX14, with high expression during critical seed filling stages, was found to have a non-synonymous mutation (H105Q), on one of the active site residues, Histidine 105, previously reported to be essential for co-factor binding to maintain structural integrity of the enzyme. Soybean lines with this mutation had higher CK content and desired yield characteristics. The potential for marker-assisted selection based on the identified natural variation within GmCKX14, is discussed in the context of hormonal control that can result in higher soybean yield. Key MessageNatural variations in soybean cytokinin oxidase/dehydrogenase gene, GmCKX14, with high expression during seed development, were linked to increased sink strength via altered cytokinin profiles in high yielding cultivars.

plant biology↗

bioRxiv2020

Environmental influences and individual characteristics that affect learner-centered teaching practices

Research-based teaching practices can improve student learning outcomes in a variety of complex educational environments. The implementation of learner-centered teaching practices in STEM can both benefit or be constrained by different factors related to individual instructors and the teaching environment. However, we know little of how the instructional climate varies across institutions and how this climate affects teaching practices. Our study sought to describe the relative importance of environmental influences and individual characteristics on learner- centered teaching practices across institutions. We also assessed departmental climate for 35 US higher education institutions. We found that self-efficacy in teaching and professional development exert a strong influence on faculty teaching practices. While departmental climate did not emerge as a significant predictor of teaching practices, there was consistently low support for teaching, and institution size was negatively correlated with leadership and evaluation of effective teaching. We also found that professional development may prepare instructors to teach learner-centered courses in different collegial teaching climates. Our results suggest that through cultivating self-efficacy and participating in iterative professional development, instructors can implement effective teaching practices across institutional environments.

scientific communication and education↗

bioRxiv2017

Fog and live fuel moisture in coastal California shrublands

Across most Mediterranean-type climate regions, seasonal drought desiccates plants, facilitating ignition and the spread of wildfires. Along the California coast, summertime fog has the potential to ameliorate drought conditions and thus reduce plant flammability during a critical time of elevated fire risk. This study investigated the uptake of dry season fog and how it affects live fuel moisture in six dominant shrub species from chaparral and sage scrub plant associations. Fog water uptake was evaluated using stable isotopes of hydrogen and oxygen at several field sites in Santa Barbara County, California. Clear evidence of fog water uptake was identified only in Baccharis pilularis, from the sage scrub association. To determine the effects of fog on live fuel moisture, meteorological variables and indices including fog deposition were combined into principal components and the scores regressed against the live fuel moisture loss rate during the summer drought. Fog deposition slowed rates of live fuel moisture loss for all three sage scrub species tested, but it did not affect the chaparral species. Fog is a more regular occurrence in the sage scrub association and thus it is likely that fog ameliorates drought for species that experience consistent fog during the summer months. In coastal California, summer fog can be essential to plant water relations and reduce live fuel moisture loss rates during the summer drought. Understanding these effects is important in the context of changing climate in southern California and Mediterranean-type climate regions around the world.

ecology↗