Biology subjects

Schaffer, S.

Publications and source records attributed to Schaffer, S..

6 recordsLinked to original sources

bioRxiv2026

ATF4 Coordinates Transcriptomic and Structural Adaptations in Aging Muscle

Aging is associated with a progressive loss of skeletal muscle function, known as sarcopenia; however, the molecular mechanisms coordinating cellular stress responses and structural adaptations permissive of sarcopenia remain incompletely understood. In our previous studies, we found aging differentially impacted mitochondrial networks by muscle, suggesting unique stress thresholds and response activation. Here, we investigate the role of activating transcription factor 4 (ATF4), a master regulator of the integrated stress response (ISR), in aged quadriceps muscle using complementary patient and aging mouse models. Older adults exhibited a marked decrease in aerobic capacity, muscle strength, and endurance when compared with young participants. These results paralleled findings in aged mice, with significant loss of muscle mass across multiple hindlimb muscles. Ultrastructural analysis revealed substantial age-related changes in mitochondrial morphology, including increased volume, surface area, and branching index, as well as a shift toward larger, more complex mitochondria. Our data indicate that ATF4 binds directly to the promoter region of the gene encoding TFAM, suggesting a transcriptional regulatory relationship to support DNA stability. These structural and transcriptional changes likely impair oxidative capacity and drive a feed-forward cycle of mitochondrial dysfunction and ISR activation. Our findings indicate that ATF4 coordinates transcriptomic and structural adaptations in aging muscle, identifying the ISR pathway as a potential therapeutic target for preserving muscle function in older adults.

cell biology↗

bioRxiv2024

Cytotoxicity and Characterization of 3D-Printable Resins Using a Low-Cost Printer for Muscle-based Biohybrid Devices

Biohybrid devices integrate biological and synthetic materials. The selection of an appropriate synthetic material to interface with living cells and tissues is crucial due to cellular chemical and mechanical sensitivities. As such, the stiffness of the material and its biocompatibility while in direct contact must be considered. In this study, the material properties and biocompatibility of six commercially available, 3D printable resins (three rigid and three elastomeric) were assessed for their suitability for biohybrid actuators. To characterize the material, uniaxial tension and compression tests with post-hoc Hookean and Yeoh model analyses were conducted for both nonsterile and sterilized (ethanol-soaking or autoclaved) samples. The mechanical properties of the elastomeric resins were minimally impacted by the different sterilization techniques. However, both Phrozen AquaGray 8K and Liqcreate Bio-Med Clear rigid resins were significantly softer in tensile tests after sterilization, and AquaGray became far more ductile. Asiga DentaGUIDE was much more stable in its mechanical properties than the other rigid resins. It was also shown that long-term exposure to saline solutions leads to a decrease in the Youngs moduli of these rigid resins before any sterilization has occurred. The print fidelity was also assessed for nonsterile and sterilized samples via manual scoring to determine the impacts of the sterilization processes on the part fidelity. Sterilization techniques had a minimal impact on print fidelity for both elastomeric and ridged resins with two exceptions. In both Formlabs Silicone 40A IPA/BuOAc post-treatment and Phrozen AquaGrey 8K groups, ethanol/UV-sterilization caused more degradation compared to autoclave-sterilization. In addition to the material analyses, cytotoxicity analyses using calcein AM and ethidium homodimer-1 fluorescence markers were conducted by directly culturing C2C12, a common myoblast cell line used in bioactuators, with sterilized resin samples. Of the elastomeric resins, only Formlabs Silicone 40A was shown to have minimal impacts on cell viability. For the rigid resins, Asiga DentaGUIDE, Liqcreate Bio-Med Clear, and ethanol-sterilized Phrozen AquaGray 8K demonstrated minimal impacts on cell viability. Based on these analyses, Asiga DentaGUIDE and Formlabs Silicone 40A demonstrate potential for applications in biohybrid muscle-based actuators when using low-cost 3D printers.

bioengineering↗

bioRxiv2021

Reconstitution of T cell immunity against EBV in the immunocompromised host by adoptive transfer of peptide-stimulated T cells after allogeneic stem cell transplantation

Reconstitution of T cell repertoire after allogeneic stem cell transplantation is a long and often incomplete process. As a result, reactivation of Epstein-Barr virus (EBV) is a frequent complication that may be treated by adoptive transfer of donor-derived EBV-specific T cells. We generated donor-derived EBV-specific T cells by peptide stimulation and adoptively transferred them to a patient with angioimmunoblastic T-cell lymphoma (AITL), who had developed persisting high titers of EBV concomitant to relapse after transplantation. T cell receptor beta (TCR{beta}) deep sequencing showed that the T cell repertoire of the patient early after transplantation (day 60) was strongly reduced and only very low numbers of EBV-specific T cells were detectable. Manufacturing and in vitro expansion of donor-derived EBV-specific T cells resulted in enrichment of EBV epitope-specific, HLA-restricted T cells. Monitoring after adoptive transfer revealed that the dominant TCR sequences from peptide-stimulated T cells persisted long-term and established an EBV-specific TCR clonotype repertoire in the host, with many of the EBV-specific TCRs present in the donor. This reconstituted repertoire was associated with immunological control of EBV and with lack of further AITL relapse. Author summaryA characteristic feature of all herpesviruses is their persistence in the hosts body after primary infection. Hence, the hosts immune system is confronted with the problem to control these viruses life-long. Well-known representative of the herpesvirus group are the classic Herpes-Simplex Virus (HSV-1) and Varicella Zoster Virus (VZV, causing chicken pox); a less known representative is Epstein Barr Virus (EBV, causing mononucleosis). When the immune system is severely compromised, for example after stem cell transplantation from a foreign (allogeneic) donor, these viruses can reappear, as they are already in the hosts body. Especially EBV cause life-threatening complications after stem cell transplantation and only reinforcement of the hosts immune system can reestablish viral control. Here we show that ex vivo manufactured EBV-specific T cells can reestablish long-term control of EBV and that these cells persist in the hosts body over months. These results give us a better understanding of viral immune reconstitution post-transplant and of clinically-relevant T cell populations against EBV.

immunology↗

bioRxiv2021

A parasite's paradise: Biotrophic species prevail oomycete community composition in tree canopies

Oomycetes (Stramenopiles, Protista) are among the most severe plant pathogens, comprising species with a high economic and ecologic impact on forest ecosystems. Their diversity and community structures are well studied in terrestrial habitats, but tree canopies as huge and diverse habitats have been widely neglected. A recent study highlighted distinct oomycete communities in the canopy region compared to forest soils when taking oomycete abundances into account, in contrast to the homogeneity at the incidence level. It remains however unknown if this homogeneity also leads to a functional homogenisation among microhabitats. In this study, we supplemented functional traits to oomycete canopy and ground communities, which were determined over a time period of two years with a metabarcoding approach. Our results showed that even though most oomycetes occurred in all habitats, a strong discrepancy between the strata and correspondingly the distribution of oomycete lifestyles could be observed, which was constant over time. Obligate biotrophic species, exclusively feeding on living host tissue, dominated the canopy region, implying tree canopies to be a hitherto neglected reservoir for parasitic protists. Parasites highly specialised on hosts that were not sampled could be determined in high abundances in the canopy and the surrounding air, challenging the strict host dependencies ruled for some oomycetes. Our findings further contribute to the understanding of oomycete ecosystem functioning in forest ecosystems.

microbiology↗

bioRxiv2021

On the phenology of protists: Recurrent patterns reveal seasonal variation of protistan (Rhizaria: Cercozoa, Endomyxa) communities in tree canopies

Tree canopies are colonized by billions of highly specialized microorganisms that are well adapted to the extreme microclimatic conditions, caused by diurnal fluctuations and seasonal changes. In this study we investigated seasonality patterns of protists in tree canopies of a temperate floodplain forest via high-throughput sequencing with group-specific primers for the phyla Cercozoa and Endomyxa. We observed consistent seasonality and identified divergent spring and autumn taxa. Tree crowns were characterized by a dominance of bacterivores and omnivores, while eukaryvores gained a distinctly larger share in litter and soil communities on the ground. Seasonality was largest among communities detected on the foliar surface. Higher variance within alpha diversity of foliar communities in spring indicated greater heterogeneity during community assembly. However, communities underwent distinct changes during the aging of leaves in autumn, reflecting recurring phenological changes during microbial colonization of leaves. Surprisingly, endomyxan root pathogens appeared to be exceptionally abundant across tree canopies during autumn season, demonstrating a potential role of the canopy surface as an important reservoir for wind-dispersed propagules. Overall, about 80% of detected OTUs could not be assigned to known species - representing only a fraction of dozens of microeukaryotic taxa whose canopy inhabitants are waiting to be discovered.

ecology↗

bioRxiv2020

To the canopy and beyond: Air samples reveal wind dispersal as a driver of ubiquitous protistan pathogen assembly in tree canopies

We analyzed air dispersal of the protistan phyla Cercozoa and Oomycota with an air sampler near the ground (~2 m) and in tree crowns (~25 m) of three tree species (oak, linden and ash) in a temperate floodplain forest in March (before leafing) and May (after leaf unfolding) with a cultivation-independent high throughput metabarcoding approach. Both, Cercozoa and Oomycota, contain important pathogens of forest trees and other vegetation. We found a high diversity of Cercozoa and Oomycota in air samples with 122 and 81 OTUs, respectively. Especially oomycetes showed a high temporal variation in beta diversity between both sampling dates. Differences in community composition between air samples in tree canopies and close to the ground were however negligible, and also tree species identity did not affect communities in air samples, indicating that the distribution of protistan propagules through the air was not spatially restricted in the forest ecosystem. OTUs of plant pathogens, whose host species that did not occur in the forest, demonstrate wind dispersal of propagules from outside the forest biome. Overall, our results lead to a better understanding of the stochastic processes of wind dispersal of protists and protistan pathogens, a prerequisite to understand the mechanisms of their community assembly in forest ecosystems. ImportanceWind dispersal has been shown to play a crucial role in protistan community assembly. The protistan taxa Cercozoa and Oomycota contain important plant parasites with a major ecologic and economic impact. However, comprehensive assessments of cercozoan and oomycete diversity in forest air samples were lacking. Using a cultivation-independent high throughput metabarcoding approach, we analyzed cercozoan and oomycete air dispersal in forest floors and the canopy region - a potential filter for microbial propagules. Our study provides insights into the diversity and community assembly of protists within the air, contributing to a better understanding which factors drive the distribution of plant pathogens within forest ecosystems.

ecology↗