Faculty of Science
Faculty of Science
UNIverse - Public Research Portal

Synthetic Systems (Nash)

Projects & Collaborations

15 found
Show per page
Project cover

Catch Bond Mediated Peristaltic Hydrogels

Research Project  | 2 Project Members

From the beating of our hearts, to the wave-like (peristaltic) motion of our intestines, the human body is a hive of activity. Dynamic processes are not only essential to our health but also to the differentiation, growth and regeneration of motile tissues, in particular, the intestines. Despite strong interest in the regeneration of intestinal tissue and gaining a clearer insight into the role of peristalsis in intestinal function, matrices used for the culture of intestinal organoids (IOs) and tissues are static. This limits their quality and viability and poses an obstacle to the accuracy of IO models and regenerative medicine. However, hydrogel matrices that exhibit the peristaltic motion required by intestinal tissues, specifically motion that is responsive to environmental cues, do not currently exist. Hydrogels cross-linked by responsive protein receptor-ligand (RL) complexes have the potential to harness the unique properties of their protein cross-links on the macroscale, including their response to mechanical and chemical stimulation. The main objective of the proposed research is to incorporate mechanoresponsive protein complexes into a hydrogel matrix, quantify their ability to alter the viscoelastic properties of the hydrogel as a function of environmental stimuli and assess the impact of this dynamic behaviour on cultured IOs. Combining microscale (AFM imaging and microrheology) and macroscale (rheology and mechanical testing) analytical techniques with biochemical characterisation (fluorescence microscopy and flow cytometry) and prior knowledge of biopolymer chemistry, I will rationally design biopolymer scaffolds, in which mechanically active proteins are embedded, and examine their responsive behaviour alongside their ability to support IO growth. By examining both the influence of the IOs on the hydrogel and that of the hydrogels on the IOs, knowledge of dynamic behaviour will be obtained in a cyclic manner that will permit tuning of the mechanical and chemical responsivity of the matrices to optimise dynamic behaviour and the impact on the cultured IOs. A rationally designed dynamic hydrogel that can adjust its viscoelastic behaviour in a periodic manner in response to local chemical and mechanical cues and support the growth of accurate and viable IOs will be the successful conclusion of this project. Insights gained in this study will lay the foundations for further exploration of responsive protein complexes in the design of dynamic cell culture matrices and their applicability to other organoid and tissue types, ultimately leading to significant leaps in organoid technology and regenerative medicine.

Project cover

MechanoBody

Research Project  | 1 Project Members

Directing nanoscale particles to strongly adhere to cancer cells and tissues under hydrodynamic flow in vivo is a challenging biophysical problem with important clinical implications. A common approach uses antibodies conjugated to nanoparticles to impart binding specificity, however, when exposed to mechanical shear stress antibodies are known to unbind at extremely low forces (<150 pN)1-3. This problem can occur even when antibodies are selected for high-affinity (e.g., KD < 1 nM) interactions at equilibrium. The goal of this research is therefore to engineer artificial binding proteins that form mechanically stable complexes with their target ligands for applications in nanoparticle-based drug delivery and bioimaging. I will focus on non-antibody (nAb) binding scaffolds (e.g., anticalin, affibody and DARPin) that will be optimized through two disparate yet complementary approaches: (1) geometrics and (2) genetics. By mechanically enhancing binding interactions, I will pioneer a new paradigm in the molecular engineering field called 'MechanoBodies' that will enable enhanced labelling and cargo delivery to cells under high shear stress.
Project cover

Exploring Sequence-Function Landscapes of Therapeutic Enzymes using Single-Cell Hydrogel Encapsulation and Deep Sequencing

Research Project  | 3 Project Members

The pharmaceutical industry is rapidly transitioning from small molecule therapeutics towards biologics. Among the various classes of biologics under development, therapeutic enzymes are gaining attention as molecular entities that can catalyze specific chemical reactions in the body to achieve a therapeutic effect. Therapeutic enzymes can be delivered systemically as full proteins or incorporated into gene therapies to transduce target cells with specific functionality in vivo. In these envisioned applications, understanding sequence-function relationships of therapeutic enzymes will play a crucial role. There is therefore an urgent need for improved methods for molecular analysis and enhancement of therapeutic enzymes. Naturally occurring enzyme sequences are typically not suitable as biopharmaceuticals due to general lack of stability, developability, and/or activity. In this context, molecular enhancement by improvement of colloidal stability, catalytic turnover rate, substrate binding affinity, and/or sensitivity to environmental conditions are essential steps in enabling therapeutic enzymes to reach their full potential. The establishment of rapid design, build, test, and learn (DBTL) cycles and the analysis of large-scale sequence-function relationships for therapeutic enzymes will be crucial for the advancement of leading therapeutic strategies.The Nash Lab at the University of Basel/ETH Zurich focuses on engineering and biophysics of artificial biomolecular systems. We recently developed an ultrahigh throughput enzyme screening strategy that outperforms multi-well robotic assays and automation by several orders of magnitude. We are now able to screen genetic libraries of catalytic enzymes using a one-pot reaction followed by fluorescence activated cell sorting (FACS). Our system is based on localized enzyme-triggered polymerization of a hydrogel capsule around individual yeast cells. Our goal is to utilize the ultrahigh throughput nature of this system to analyze sequence-function landscapes of enzymes on an unprecedented scale.