Biology subjects

Victoria Hsiao

Publications and source records attributed to Victoria Hsiao.

3 recordsLinked to original sources

bioRxiv2016

The role of single occupancy effects on integrase dynamics in a cell-free system

Phage integrase-based circuits are an alternative approach to relying on transcriptional and translational repression for biomolecular circuits. Previous research has shown that circuits based on integrases can perform a variety of functions, including counters, Boolean logic operators, memory modules and temporal event detectors. It is therefore essential to develop a principled theoretical and experimental framework for the design, implementation and study of such circuits. One of the fundamental questions that such a framework should address concerns the functionality limitations and temporal dynamics of the integrases as regulatory elements. Here, we test the functionality of several large serine integrases from a recently published library in a cell-free transcription-translation (TX-TL) platform. Additionally, we use a combination of experimental data and models to investigate integrase dynamics as a function of enzyme concentration and number of binding sites.\n\nWe report that sequestration of integrase molecules, either in the form of monomers or dimers, by the integrase's own binding sites dominates integrase dynamics, and that the delay in the activation of the reporter is negatively correlated with integrase plasmid concentration. We have validated our sequestration hypothesis by building a model with MATLABs SimBiology toolbox, and running simulations with various integrase and binding sites concentrations. The simulation results qualitatively match the experimental results, and offer further insights into the system.

Synthetic Biology↗

bioRxiv2015

A population-based temporal logic gate for timing and recording chemical events

Single-cell bacterial sensors have numerous applications in human health monitoring, environmental chemical detection, and materials biosynthesis. Such bacterial devices need not only the capability to differentiate between combinations of inputs, but also the ability to process signal timing and duration. In this work, we present a two-input temporal logic gate that can sense and record the order of the inputs, the timing between inputs, and the duration of input pulses. The temporal logic gate design relies on unidirectional DNA recombination with bacteriophage integrases to detect and encode sequences of input events. When implemented in a chromosomally-modified E. coli strain, we can utilize stochastic single cell responses to predict overall heterogeneous population behavior. We show that a stochastic model can be used to predict final population distributions of this E. coli strain, and thus that final differentiated sub-populations can be used to deduce the timing and duration of transient chemical events.

Synthetic Biology↗

bioRxiv2013

Design and implementation of a synthetic biomolecular concentration tracker

As a field, synthetic biology strives to engineer increasingly complex artificial systems in living cells. Active feedback in closed loop systems offers a dynamic and adaptive way to ensure constant relative activity independent of intrinsic and extrinsic noise. In this work, we design, model, and implement a biomolecular concentration tracker, in which an output protein tracks the concentration of an input protein. Synthetic modular protein scaffold domains are used to colocalize a two-component system, and a single negative feedback loop modulates the production of the output protein. Using a combination of model and experimental work, we show that the circuit achieves real-time protein concentration tracking in Escherichia coli and that steady state outputs can be tuned.

Synthetic Biology↗