Biology subjects

Frei, T.

Publications and source records attributed to Frei, T..

4 recordsLinked to original sources

bioRxiv2024

Multi-Layer Autocatalytic Feedback Enables Integral Control Amidst Resource Competition and Across Scales

Integral feedback control strategies have proven effective in regulating protein expression in unpredictable cellular environments. These strategies, grounded in model-based designs and control theory, have advanced synthetic biology applications. Autocatalytic integral feed-back controllers, utilizing positive autoregulation for integral action, are particularly promising due to their similarity to natural behaviors like self-replication and positive feedback seen across biological scales. However, their effectiveness is often hindered by resource competition and context-dependent couplings. This study addresses these challenges with a multi-layer feedback strategy, enabling population-level integral feedback and multicellular integrators. We provide a generalized mathematical framework for modeling resource competition in complex genetic networks, supporting the design of intracellular control circuits. Our controller motif demonstrated precise regulation in tasks ranging from gene expression control to population growth in multi-strain communities. We also explore a variant capable of ratiometric control, proving its effectiveness in managing gene ratios and co-culture compositions in engineered microbial ecosystems. These findings offer a versatile approach to achieving robust adaptation and homeostasis from subcellular to multicellular scales.

synthetic biology↗

bioRxiv2024

Dermatological plants and their uses in the Receptarium of Burkhard III from Hallwyl from 16th century Switzerland: Data mining a historical text and preliminary in vitro screening

Ethnopharmacological relevanceHistorical texts on materia medica can be an attractive source of ethnopharmacological information. In recent decades, various research groups have investigated corresponding resources from Europe and the Mediterranean region, pursuing different objectives. Regardless of the method used in such a work, the indexing of textual information and its conversion into data sets useful for further investigations represents a significant challenge. Aim of the studyFirst of all, this study aims to systematically catalogue pharmaco-botanical information in the Receptarium of Burkhard from Hallwyl (RBH) in order to identify candidate plants in a targeted manner. Secondly, the potential of RBH as a resource for pharmacological investigations will be assessed by means of a preliminary in vitro screening. Materials and methodsWe developed a relational database for the systematic recording of the parameters composing the medical recipes contained in the historical text. Focusing on dermatological recipes, we explored the mentioned plants and their uses by drawing on specific literature. The botanical identities (candidate species) suggested in the literature for the historical plant names were rated based on their plausibility of being the correct attribution. The historical uses were interpreted by consulting medical-historical and modern clinical literature. For the subsequent in vitro screening, we selected candidate species used in recipes directed at the treatment of inflammatory or infectious skin disorders and wounds. Plants were collected in Switzerland and their hydroethanolic crude extracts tested for possible cytotoxic effects and for their potential to modulate the release of IL-6 and TNF in LPS-stimulated whole blood and PBMCs. ResultsThe historical text analysis points up the challenges associated with the assessment of historical plant names. Often two or more plant species are available as candidates for each of the 161 historical plant names counted in the 200 dermatological recipes in RBH. At the same time, the 56 medicinal uses mentioned in these recipes illustrate, that the details provided in the text about the skin problem in question enable conclusions to be drawn based on which the presumed underlying medical condition and its pharmacological basis can be narrowed down. On this basis, 11 candidate species were selected for in vitro screening, four of which were used in RBH in herbal simple recipes and seven in a herbal compound formulation. None of the extracts tested showed a noteworthy effect on cell viability except for the sample of Sanicula europaea. Extracts were tested at 50 {micro}g/mL in the whole blood assay, where especially Vincetoxicum hirundinaria or Solanum nigrum showed inhibitory or stimulatory activities. In the PBMC assay, the root of Vincetoxicum hirundinaria revealed a distinct inhibitory effect on IL-6 release (IC50 of 3.6 {micro}g/mL). ConclusionsUsing the example of RBH, this study illustrates a possible ethnopharmacological path from unlocking the historical text and its subsequent analysis, through the selection and collection of plant candidates to their in vitro investigation. Fully documenting our approach to the analysis of historical texts, we hope to contribute to the discussion on solutions for the digital indexing of premodern information on the use of plants or other natural products.

pharmacology and toxicology↗

bioRxiv2020

Genetically Engineered Integral Feedback Controllers for Robust Perfect Adaptation in Mammalian Cells

To support their survival, cells adapt to environmental disturbances by maintaining a constant internal milieu. Robust perfect adaptation is a strategy that utilizes integral feedback to promote adaptation by robustly driving regulated physiological variables to their pre-disturbance levels. Present in natural systems, this stringent regulatory strategy promises to enable the engineering of sophisticated genetic programs with diverse applications. Here, we present the first synthetic implementations of integral and proportional-integral feedback controllers in mammalian cells. We show that the integral controller robustly and precisely maintains a desired level of a transcription factor, in spite of induced disturbances and network perturbations. Augmenting proportional feedback reduces stochastic variability while maintaining robust perfect adaptation. We demonstrate the benefits of these controllers in mitigating the impact of resource burden and investigate their use in cell therapy. The synthetic biological realization of robust perfect adaptation holds promise for substantial advances in industrial biotechnology and cell-based therapies.

synthetic biology↗

bioRxiv2019

Characterization, modelling and mitigation of gene expression burden in mammalian cells

Despite recent advances in genome engineering, the design of genetic circuits in mammalian cells is still painstakingly slow and fraught with inexplicable failures. Here we demonstrate that competition for limited transcriptional and translational resources dynamically couples otherwise independent co-expressed exogenous genes, leading to diminished performance and contributing to the divergence between intended and actual function. We also show that the expression of endogenous genes is likewise impacted when genetic payloads are expressed in the host cells. Guided by a resource-aware mathematical model and our experimental finding that post-transcriptional regulators have a large capacity for resource redistribution, we identify and engineer natural and synthetic miRNA-based incoherent feedforward loop (iFFL) circuits that mitigate gene expression burden. The implementation of these circuits features the novel use of endogenous miRNAs as integral components of the engineered iFFL device, a versatile hybrid design that allows burden mitigation to be achieved across different cell-lines with minimal resource requirements. This study establishes the foundations for context-aware prediction and improvement of in vivo synthetic circuit performance, paving the way towards more rational synthetic construct design in mammalian cells.

synthetic biology↗