Biology subjects

Riedel-Kruse, I. H.

Publications and source records attributed to Riedel-Kruse, I. H..

4 recordsLinked to original sources

bioRxiv2018

Polygonal motion and adaptable phototaxis via flagellar beat switching in Euglena gracilis

Biological microswimmers exhibit versatile strategies for sensing and navigating their environment 1-7, e.g., run-and-tumble 2 and curvature modulation 3. Here we report a striking behavior of Euglena gracilis, where Euglena cells swim in polygonal trajectories due to exposure to increasing light intensities. While smoothly curved trajectories are common for microswimmers 3, 8, such quantized ones have not been reported previously. This polygonal behavior emerges from periodic switching between the flagellar beating patterns of helical swimming 6, 9 and spinning 10 behaviors. We develop and experimentally validate a biophysical model that describes the phase relationship between the eyespot, cell orientation, light detection, and cellular reorientation, that accounts for all three behavioral states. Coordinated switching between these behaviors allows ballistic, superdiffusive, diffusive, or subdiffusive motion 11,12 (i.e., the tuning of the diffusion constant over 3 orders of magnitude) and enables navigation in structured light fields, e.g., edge avoidance and gradient descent. This feedback-control links multiple system scales (flagellar beats, cellular behaviors, phototaxis strategies) with implications for other natural and synthetic microswimmers 13.

biophysics↗

bioRxiv2017

A genetically encoded adhesin toolbox for programming multicellular morphologies and patterns

Synthetic multicellular systems hold promise for understanding natural development of biofilms and higher organisms1,2, as well as for engineering complex multi-component metabolic pathways2,3 and materials4. However, such efforts will require tools to adhere cells into defined morphologies and patterns, and these tools are currently lacking1,5,6. Here we report the first 100% genetically encoded synthetic platform for modular cell-cell adhesion in Escherichia coli, which provides control over multicellular self-assembly. Adhesive selectivity is provided by a library of outer membrane-displayed nanobody7,8 and antigen peptides with orthogonal intra-library specificities, while affinity is controlled by intrinsic adhesin affinity, competitive inhibition, and inducible expression. We demonstrate the resulting capabilities for rational design of well-defined morphologies and patterns through homophilic and heterophilic interactions, lattice-like self-assembly, phase separation, differential adhesion, and sequential layering. This adhesion toolbox, compatible with synthetic biology standards9, will enable construction of high-level multicellular designs and shed light on the evolutionary transition to multicellularity6,10.

synthetic biology↗

bioRxiv2017

Bioty: A cloud-based development toolkit for programming experiments and interactive applications with living cells

Recent advancements in life-science instrumentation and automation enable entirely new modes of human interaction with microbiological processes and corresponding applications for science and education through biology cloud labs. A critical barrier for remote life-science experimentation is the absence of suitable abstractions and interfaces for programming living matter. To this end we conceptualize a programming paradigm that provides stimulus control functions and sensor control functions for realtime manipulation of biological (physical) matter. Additionally, a simulation mode facilitates higher user throughput, program debugging, and biophysical modeling. To evaluate this paradigm, we implemented a JavaScript-based web toolkit, Bioty, that supports realtime interaction with swarms of phototactic Euglena cells hosted on a cloud lab. Studies with remote users demonstrate that individuals with little to no biology knowledge and intermediate programming knowledge were able to successfully create and use scientific applications and games. This work informs the design of programming environments for controlling living matter in general and lowers the access barriers to biology experimentation for professional and citizen scientists, learners, and the lay public.\n\nSignificance StatementBiology cloud labs are an emerging approach to lower access barriers to life-science experimentation. However, suitable programming approaches and user interfaces are lacking, especially ones that enable the interaction with the living matter itself - not just the control of equipment. Here we present and implement a corresponding programming paradigm for realtime interactive applications with remotely housed biological systems, and which is accessible and useful for scientists, programmers and lay people alike. Our user studies show that scientists and non-scientists are able to rapidly develop a variety of applications, such as interactive biophysics experiments and games. This paradigm has the potential to make first-hand experiences with biology accessible to all of society and to accelerate the rate of scientific discovery.

bioengineering↗

bioRxiv2017

Biofilm Lithography: High-resolution cell patterning via optogenetic adhesin expression

Bacterial biofilms represent a promising opportunity for engineering of microbial communities. However our ability to control spatial structure in biofilms remains limited. Here we engineer Escherichia coli with a light-activated transcriptional promoter to optically regulate adhesin gene expression. When illuminated with patterned blue light, long-term viable biofilms with spatial resolution down to 25m can be formed on a variety of substrates and inside enclosed culture chambers without the need for surface pretreatment. A biophysical model suggests the patterning mechanism involves stimulation of transiently surface-adsorbed cells, lending new evidence to a previously proposed role of adhesin expression during natural biofilm maturation. Overall, this tool - termed Biofilm Lithography - has distinct advantages over existing cell-depositing and patterning methods and provides the ability to grow structured biofilms, with applications towards an improved understanding natural biofilm communities, as well as the engineering of living biomaterials and bottom-up approaches to microbial consortia design.

synthetic biology↗