Yolanda Schaerli

An engineered bacterial symbiont maps micron-scale sugar gradients in the honeybee gut

The paper engineers a bacterial biosensor to map micron-scale arabinose gradients in the honeybee gut, revealing heterogeneous nutrient distribution influenced by co-colonizing microbes.

Harnessing Escherichia coli motility to engineer bacterial Voronoi patterns

This study uses engineered Escherichia coli motility to control Voronoi patterns in 2D and 3D, generating programmable spatial structures.

An engineered multi-step differentiation program in Escherichia coli for self-organized spatial patterning

This paper engineers a multi-step differentiation program in E. coli to generate self-organized spatial patterns through symmetry breaking, paracrine, and autocrine signaling.

Competition between co-localized gut symbionts underlies inter-individual variation in the honeybee gut microbiota

The paper investigates competition between gut symbionts in honeybees, showing that spatial niche competition and bacterial factors influence microbiota variation.

Intracellularly Coupled Oscillators for Synthetic Biology

The paper proposes novel oscillator-based circuit designs for synthetic biology and models interactions of intracellularly coupled oscillators, predicting dynamic behaviors and potential applications in bacterial systems.

GRN_modeler: An Intuitive Tool for Constructing and Evaluating Gene Regulatory Networks and its Applications to Oscillators and a Light Biosensor

The paper introduces GRN_modeler, a user-friendly tool for constructing and evaluating gene regulatory networks, demonstrating its application in designing oscillators and a light biosensor in E. coli.

Let there be multifunctionality: Uncovering the criticality zoo of the AC-DCgenetic circuit

The paper analyzes the AC-DC genetic circuit to show it can exhibit diverse multifunctional dynamics, including coexisting oscillations and multistability, challenging traditional views of network constraints.

Engineering Intercellular Communication using M13 Phagemid and CRISPR-based Gene Regulation for Multicellular Computing in Escherichia coli

This paper develops a method for intercellular communication in E. coli using M13 phagemids and CRISPR-based gene regulation to build logic gates for multicellular computing.

Engineering microbial consortia: uptake and leakage ratedifferentially shape community arrangement and composition

This study shows that amino acid uptake and leakage rates determine microbial community structure and composition in synthetic E. coli consortia.

From resonance to chaos: modulating spatiotemporal patterns through a synthetic optogenetic oscillator

The paper designs and studies a synthetic optogenetic oscillator in E. coli, demonstrating complex spatiotemporal patterns including synchronization, resonance, and chaos under periodic light exposure.

Synthetic gene circuits combining CRISPR interference and CRISPR activation in E. coli: importance of equal guide RNA binding affinities to avoid context-dependent effects

The paper shows that using the same guide RNA structure for CRISPRi and CRISPRa in E. coli prevents context-dependent effects, ensuring predictable gene circuit behavior.

Synthetic genotype networks

The paper constructs synthetic genotype networks of gene regulatory networks in E. coli to study robustness and evolvability in genotype-phenotype maps.

Engineering a symbiont as a biosensor for the honey bee gut environment

The paper develops a biosensor in the honey bee gut bacterium to detect IPTG exposure through fluorescent protein expression, enabling non-invasive fecal sampling.

Multistable and dynamic CRISPRi-based synthetic circuits

This paper designs and demonstrates CRISPRi-based synthetic gene circuits in E. coli, including an oscillator, bistable switch, and stripe pattern-forming IFFL, showing the potential of CRISPRi for dynamic and multistable circuit construction.

Controlling spatiotemporal pattern formation in a concentration gradient with a synthetic toggle switch

This study builds a synthetic toggle switch in E. coli to control spatiotemporal gene expression patterns using diffusible molecules and mathematical modeling.

A framework for the modular and combinatorial assembly of synthetic gene circuits

The paper introduces a modular cloning framework for assembling synthetic gene circuits in E. coli, reducing construction time and costs through a two-step Gibson assembly process.

The mechanisms of gene regulatory networks constrain evolution: A lesson from synthetic circuits

The paper shows that different gene regulatory networks in E. coli constrain phenotypic variation differently, even when producing the same phenotype.