Biology subjects

O'Dwyer, J.

Publications and source records attributed to O'Dwyer, J..

6 recordsLinked to original sources

bioRxiv2025

Functional assembly of the Qc-SNARE with Sec18 and Sec17 on membranes

Yeast vacuolar fusion is driven by Sec17, Sec18, SNAREs (R, Qa, Qb, Qc) and HOPS, a catalyst of SNARE assembly. Qc, the only vacuolar SNARE that is not membrane-anchored, has a unique path of assembly with other fusion catalysts. Qc is the only SNARE which binds Sec17 with high affinity. Sec18 confers a high affinity for Qc (but not Qb) on HOPS-dependent fusion, but it has been unclear how Sec18 acts. The membrane complex of Sec17 and Sec18 bind Qc to form a membrane:Sec18:Sec17:Qc complex. Sec18 ATP hydrolysis, though dispensable for fusion, provides a measure of the physical and functional interactions between Qc, Sec17, Sec18, and membranes. Each binary interface in this quaternary complex regulates Sec18 ATPase and fusion. Qc is better than other SNAREs, alone or in combination, for stimulating ATP hydrolysis. We propose a working model in which membrane-bound Qc:Sec17:Sec18 associates with the trans complex of HOPS:R:QaQb, displacing HOPS while providing both Qc for complete SNARE zippering and localized Sec17 apolar loops, the twin driving forces for fusion.

biochemistry↗

bioRxiv2025

Evaluation of adipose-derived stromal cell infused modified-hyaluronic acid scaffolds for post cancer breast reconstruction

IntroductionPrimary breast cancer surgery can compromise aesthetics and quality-of-life for breast cancer patients. While breast reconstruction improves these outcomes, current methods are limited by suboptimal aesthetic outcomes and potential complication risks. There is an urgent clinical need for improved approaches to post surgical reconstruction for breast cancer patients. Adipose-derived stromal cells (ADSCs) with biological scaffolds are being widely evaluated for tissue engineering applications in the field of reconstruction. AimsThis study aimed to assess the biomechanical properties, biocompatibility, adipogenic potential of ADSCs encapsulated in modified hyaluronic acid derivatives in vitro; and efficacy and tissue integration of this construct in vivo in a murine breast cancer and reconstruction model. MethodsADSCs were obtained, with informed consent, from female breast cancer patients undergoing autologous breast reconstruction or cosmetic procedures (n=8) aged 47{+/-}12 years. Modified hyaluronic acid solution was combined with 1x106 ADSCs/mL and crosslinked using hydrogen peroxide and horseradish peroxidase. Youngs modulus, cell viability and adipogenic potential of the cell-loaded hydrogels were assessed in vitro. In vivo, hydrogels combined with murine ADSCs were grafted into a murine breast cancer model and tissues were harvested for immunohistochemistry after 4 weeks. ResultsADSCs were characterised via morphology, Colony forming unit-fibroblast (CFU-F) assay, flow cytometry and multilineage differentiation. The cell-loaded hydrogels had a compressive Youngs modulus of 7.35{+/-}0.96 kPa after 21 days in culture, similar to human breast adipose tissue ([~]10 kPa). High ADSC viability was observed after 21 days in culture, and ADSCs differentiated into mature adipocytes. After 4 weeks in vivo, hydrogels exhibited adipocytes, vascular endothelium, and pericyte-like cells. ConclusionThis study demonstrates the potential suitability of modified hyaluronic acid hydrogels encapsulating ADSCs for adipose tissue engineering for post breast cancer reconstruction.

bioengineering↗

bioRxiv2025

Hyaluronic acid hydrogels: Establishing a sustained delivery system for extracellular vesicles

Extracellular vesicles (EVs) are versatile transporters of genetic cargo with enormous potential in the therapeutic setting. Scalable production of EVs, and routes to overcome rapid clearance are required. Biocompatible hydrogels may support precise, localized delivery of EVs to target sites. This study aimed to establish sustained production of EVs in a scalable 3D dynamic bioreactor and to fabricate hydrogels using tyramine-modified hyaluronic acid (HA-TA) to study EV integration and release patterns. MDA-MB-231 cells transduced with lentiviral GFP fused with CD63, were cultured in a 20kD dynamic hollow fiber bioreactor and GFP-EVs harvested over five weeks. GFP-EVs were characterized by Nanoparticle Tracking Analysis(NTA), Western Blot(WB) and Transmission Electron Microscopy(TEM). Tyramine modified hyaluronic acid(HA-TA) hydrogels were formulated via enzymatic crosslinking using hydrogen peroxide and horseradish peroxidase, to investigate EV release patterns in static and dynamic conditions. Hydrogel swelling was recorded at 1-72 hrs and hydrogels were loaded with GFP-EVs to assess distribution and release by Scanning Electron Microscopy(SEM) and NTA respectively. GFP-EV uptake was assessed by confocal microscopy. Longitudinal GFP expression was demonstrated in transduced cells and released EVs throughout bioreactor culture. TEM and NTA demonstrated successful isolation of EVs of 30-200 nm in size with intact lipid bilayers (average 4x109 EVs/harvest). Initial harvests exhibited subpopulations of larger EVs, which disappeared upon serum withdrawal. WB verified the presence of EV markers CD63, TSG101, and CD81. HA-TA hydrogels were successfully formed and swelling assays revealed the requirement for higher concentrations of HA-TA and crosslinkers for scaffold stability and continued swelling. GFP-EVs were successfully incorporated into the hydrogels with variable release patterns observed over time, depending on EV concentration and hydrogel formulation. EV clusters in hydrogels were visualized by SEM. Investigation of GFP-EV release patterns under static and dynamic conditions highlighted a significant increase in release under fluid flow conditions. Efficient transfer of released EVs to recipient cells was also demonstrated in vitro. The data demonstrate the potential for scalable production of engineered EVs in serum free conditions and subsequent incorporation into HA-TA hydrogels for sustained release. These biocompatible hydrogels hold promise for tuneable delivery of therapeutic EVs in a variety of disease settings.

bioengineering↗

bioRxiv2018

Whence Lotka-Volterra? Conservation Laws and Integrable Systems in Ecology.

Competition in ecology is often modeled in terms of direct, negative effects of one individual on another. An example is logistic growth, modeling the effects of intraspecific competition, while the Lotka-Volterra equations for competition extend this to systems of multiple species, with varying strengths of intra- and inter-specific competition. These equations are a classic and well-used staple of quantitative ecology, providing a framework to understand species interactions, species coexistence, and community assembly. They can be derived from an assumption of random mixing of organisms, and an outcome of each interaction that removes one or more individuals. However, this framing is some-what unsatisfactory, and ecologists may prefer to think of phenomenological equations for competition as deriving from competition for a set of resources required for growth, which in turn may undergo their own complex dynamics. While it is intuitive that these frameworks are connected, and the connection is well-understood near to equilibria, here we ask the question: when can consumer dynamics alone become an exact description of a full system of consumers and resources? We identify that consumer-resource systems with this property must have some kind of redundancy in the original description, or equivalently there is one or more conservation laws for quantities that do not change with time. Such systems are known in mathematics as integrable systems. We suggest that integrability in consumer-resource dynamics can only arise in cases where each species in an assemblage requires a distinct and unique combination of resources, and even in these cases it is not clear that the resulting dynamics will lead to Lotka-Volterra competition.\n\nI acknowledge the Simons Foundation Grant #376199 and the McDonnell Foundation Grant #220020439.

ecology↗

bioRxiv2018

Born to run? Quantifying the balance of prior bias and new information in prey escape decisions

Animal behaviors can often be challenging to model and predict, though optimality theory has improved our ability to do so. While many qualitative predictions of behavior exist, accurate quantitative models, tested by empirical data, are often lacking. This is likely due to variation in biases across individuals and variation in the way new information is gathered and used. We propose a modeling framework based on a novel interpretation of Bayes theorem to integrate optimization of energetic constraints with both prior biases and specific sources of new information gathered by individuals. We present methods for inferring distributions of prior biases within populations rather than assuming known priors, as is common in Bayesian approaches to modelling behavior, and for evaluating the goodness of fit of overall model descriptions. We apply this framework to predict optimal escape during predator-prey encounters, based on prior biases and variation in what information prey use. Using this approach we collected and analyzed data characterizing white-tailed deer (Odocoileus virginianus) escape behavior in response to human approaches. We found that distance to predator alone was not sufficient for predicting deer flight response, and have shown that the inclusion of additional information is necessary. Additionally, we compared differences in the inferred distributions of prior biases across different populations and discuss the possible role of human activity in influencing these distributions.

ecology↗

bioRxiv2018

Stability Criteria for Complex Microbial Communities

Competition and mutualism are inevitable processes in microbial ecology, and a central question is which and how many taxa will persist in the face of these interactions. Ecological theory has demonstrated that when direct, pairwise interactions among a group of species are too numerous, or too strong, then the coexistence of these species will be unstable to any slight perturbation. This instability worsens when mutualistic interactions complement competition. Here, we refine and to some extent overturn that understanding, by considering explicitly the resources that microbes consume and produce. In contrast to more complex organisms, microbial cells consume primarily abiotic resources, and mutualistic interactions are often mediated by these same abiotic resources through the mechanism of cross-feeding. Our model therefore considers the consumption and production of a set of abiotic resources by a group of microbial species. We show that if microbes consume, but do not produce resources, then any positive equilibrium will always be stable to small perturbations. We go on to show that in the presence of crossfeeding, stability is no longer guaranteed. However, stability still holds when mutualistic interations are either symmetric, or sufficiently weak.

ecology↗