Biology subjects

Olsman, N.

Publications and source records attributed to Olsman, N..

7 recordsLinked to original sources

bioRxiv2026

Mapping Synthetic Circuit Design Space through Massively Parallel Measurement of Single-Cell Dynamics

Engineering predictable and robust gene-regulatory networks requires a quantitative understanding of how their dynamics depend on genetic design and environmental conditions. To investigate these relationships, we introduce BARRACUDA, a high-throughput platform that combines combinatorial assembly and programmable perturbations with lineage-resolved time-lapse imaging and optical pooled screening. Experiments using this platform follow approximately one million cell lineages, collectively sampling tens of thousands of circuit designs. We used BARRACUDA to investigate how the robustness of circuit behavior depends on molecular components and their interactions, combining quantitative dynamic measurements with precise genetic and environmental control. Antithetic integral feedback provided a model system linking a defined molecular architecture to theoretical predictions of robust adaptation. Through a hierarchy of increasingly complex libraries, we characterized individual components and used those measurements to model and interpret the dynamics of complete feedback circuits. Circuits built from wild-type inhibitory proteins rejected disturbances but also exhibited sustained overadaptation and fast disturbance-induced oscillations unexplained by a reduced control model. These discrepancies motivated a screen of de novo binders that retained inhibitory function while reducing host-stress response. Selected de novo binders supported strong feedback regulation and robust performance in the rebuilt circuits. Across more than 20,000 recovered feedback-circuit variants, binder identity and controller expression organized regimes of strong regulation and sustained oscillation. Counterintuitively, disturbances sometimes improved compensation rather than compromising it, consistent with nonlinear changes in feedback engagement. Together, these results show how structured libraries and massively parallel measurements of single-cell dynamics can test mechanistic theories across scales of circuit complexity, reveal missing biological interactions, and map the design space of gene-regulatory networks.

synthetic biology↗

bioRxiv2026

Inherited flagellar structures coordinate the onset of swimming among related E. coli cells

Bacteria commit to costly behaviors before they can benefit from them. In Escherichia coli, flagellar synthesis is expensive, yet the genes are expressed in stochastic pulses and only a small minority of pulses result in motility. Despite this noise, we find that lineage-related cells begin swimming at similar times, in groups of two to eight cells. Rare, high-amplitude pulses commit a single cell within one generation, but more commonly, pulses rise slowly and fail to trigger swimming before division. Rather than decaying, their output accumulates as cells inherit hook-basal bodies (HBBs) and continue to build new ones. This structural inheritance acts as a physical integrator, summing ongoing transcriptional activity across generations, so that an incomplete flagellar cascade is carried forward at division rather than lost. HBB accumulation sets when cells swim, and the anti-sigma factor FlgM sets how sharply. By holding late flagellar genes off until several HBBs have accumulated, FlgM makes motility depend steeply on early flagellar gene expression, so that relatives inheriting similar sets of HBBs become motile together. Without FlgM, this sharp dependence is largely lost, and activations of the full cascade do not reliably produce swimming. Together, our results show how the accumulation of a molecular machine integrates fluctuations, and how a checkpoint on its assembly sharpens them into a decision, setting both the speed and heritability of a behavioral trait.

systems biology↗

bioRxiv2021

A novel approach to comparative RNA-Seq does not support a conserved set of genes underlying animal regeneration

Molecular studies of animal regeneration typically focus on conserved genes and signaling pathways that underlie morphogenesis. To date, a holistic analysis of gene expression across animals has not been attempted, as it presents a suite of problems related to differences in experimental design and gene homology. By combining orthology analysis with a novel statistical method for testing gene enrichment across large datasets, we are able to test whether biological processes across organisms share transcriptional regulation. We applied this method to six publicly available RNA-seq datasets from diverse examples of animal regeneration. We recovered 160 conserved orthologous gene clusters, which are enriched in structural genes as opposed to those regulating morphogenesis. A breakdown of gene presence/absence provides only limited support for the conservation of pathways typically implicated in regeneration, such as Wnt signaling and cell pluripotency. Specifically, these pathways are only conserved if we allow gene paralogs to be interchangeable through evolution. Overall, our analysis does not support the hypothesis that a shared set of ancestral genes underlie regeneration mechanisms in animals. The methods described in this paper will be broadly applicable for studying the genetic underpinnings of traits across distantly related organisms.

evolutionary biology↗

bioRxiv2019

Antithetic integral feedback for the robust control of monostable and oscillatory biomolecular circuits

Biomolecular feedback systems are now a central application area of interest within control theory. While classical control techniques provide valuable insight into the function and design of both natural and synthetic biomolecular systems, there are certain aspects of biological control that have proven difficult to analyze with traditional methods. To this end, we describe here how the recently developed tools of dominance analysis can be used to gain insight into the nonlinear behavior of the antithetic integral feedback circuit, a recently discovered control architecture which implements integral control of arbitrary biomolecular processes using a simple feedback mechanism. We show that dominance theory can predict both monostability and periodic oscillations in the circuit, depending on the corresponding parameters and architecture. We then use the theory to characterize the robustness of the asymptotic behavior of this circuit in a nonlinear setting.Competing Interest StatementThe authors have declared no competing interest.View Full Text

synthetic biology↗

bioRxiv2018

Design Guidelines For Sequestration Feedback Networks

Integral control is commonly used in mechanical and electrical systems to ensure perfect adaptation. A proposed design of integral control for synthetic biological systems employs the sequestration of two biochemical controller species. The unbound amount of controller species captures the integral of the error between the current and the desired state of the system. However, implementing integral control inside bacterial cells using sequestration feedback has been challenging due to the controller molecules being degraded and diluted. Furthermore, integral control can only be achieved under stability conditions that not all sequestration feedback networks fulfill. In this work, we give guidelines for ensuring stability and good performance (small steady-state error) in sequestration feedback networks. Our guidelines provide simple tuning options to obtain a flexible and practical biological implementation of sequestration feedback control. Using tools and metrics from control theory, we pave the path for the systematic design of synthetic biological circuits.

synthetic biology↗

bioRxiv2018

Architectural Principles for Characterizing the Performance of Sequestration Feedback Networks

As we begin to design increasingly complex synthetic biomolecular systems, it is essential to develop rational design methodologies that yield predictable circuit performance. Here we apply theoretical tools from the theory of control and dynamical systems to yield practical insights into the architecture and function of a particular class of biological feedback circuit. Specifically, we show that it is possible to analytically characterize both the operating regime and performance tradeoffs of a sequestration feedback circuit architecture. Further, we demonstrate how these principles can be applied to inform the design process of a particular synthetic feedback circuit.

synthetic biology↗

bioRxiv2017

Hard Limits And Performance Tradeoffs In A Class Of Sequestration Feedback Systems

Feedback regulation is pervasive in biology at both the organismal and cellular level. In this article, we explore the properties of a particular biomolecular feedback mechanism implemented using the sequestration binding of two molecules. Our work develops an analytic framework for understanding the hard limits, performance tradeoffs, and architectural properties of this simple model of biological feedback control. Using tools from control theory, we show that there are simple parametric relationships that determine both the stability and the performance of these systems in terms of speed, robustness, steady-state error, and leakiness. These findings yield a holistic understanding of the behavior of sequestration feedback and contribute to a more general theory of biological control systems.

systems biology↗