Toxin Detection by a Miniaturized in Vitro Protein Expression Array

Cell-free protein synthesis in microfluidic 96-well plates

Cell-free protein synthesis (CFPS) enables rapid protein expression for the structural and functional characterization of proteins. Implementation of CFPS in a microfluidic platform has additional benefits such as reduced reaction volumes and simultaneous expression of multiple proteins. Here, we describe a microfluidic device that is composed of 96 continuous-exchange cell-free protein expression units and produces a protein synthesis yield up to 87 times higher than a conventional batch system.

Data Analysis Strategies for Protein Microarrays

Microarrays constitute a new platform which allows the discovery and characterization of proteins. According to different features, such as content, surface or detection system, there are many types of protein microarrays which can be applied for the identification of disease biomarkers and the characterization of protein expression patterns. However, the analysis and interpretation of the amount of information generated by microarrays remain a challenge. Further data analysis strategies are essential to obtain representative and reproducible results. Therefore, the experimental design is key, since the number of samples and dyes, among others aspects, would define the appropriate analysis method to be used. In this sense, several algorithms have been proposed so far to overcome analytical difficulties derived from fluorescence overlapping and/or background noise. Each kind of microarray is developed to fulfill a specific purpose. Therefore, the selection of appropriate analytical and data analysis strategies is crucial to achieve successful biological conclusions. In the present review, we focus on current algorithms and main strategies for data interpretation.

Experiment and mathematical modeling of gene expression dynamics in a cell-free system

Cell-free in vitro expression is increasingly important for high-throughput expression screening, high yield protein production and synthetic biology applications. Yet its potential for quantitative investigation of gene expression and regulatory circuits is limited by the availability of data on composition, kinetic rate constants and standardized computational tools for modeling. Here we report on calibration measurements and mathematical modeling of a reconstituted in vitro expression system. We measured a series of GFP expression and mRNA transcription time courses under various initial conditions and established the translation step as the bottle neck of in vitro protein synthesis. Cell-free translation was observed to expire after 3 h independent of initial template DNA concentration. We developed a minimalistic rate equation model and optimized its parameters by performing a concurrent fit to measured time courses. The model predicts the dependence of protein yield not only on template DNA concentration, but also on experimental timing and hence is a valuable tool to optimize yield strategies.

Continuous protein production in nanoporous, picolitre volume containers

The synthetic manufacture of functional proteins enables a bottom-up understanding of the workings of biological systems and opens new opportunities for the treatment of disease. Cell-free protein synthesis is a practical approach for enabling such manufacturing, however, it is typically carried out in fairly large volumes, when compared to a natural cell, leading to increases in cost and loss of efficiency. Here we demonstrate continuous cell free protein synthesis in arrays of cellular scale containers that continuously exchange energy and materials with their environment. A multiscale fabrication process allows the monolithic integration of nanoporous silicon containers within an addressable microfluidic network. Synthesis of enhanced green fluorescent protein (eGFP) in the containers continues beyond 24 h and yields more than twice the amount of protein, on a per volume basis, than conventional scale batch reactions. By mimicking the physical volume and controlled flux of a natural cell, the resulting "cell mimic" devices can enable fundamental studies of biological systems as well as serve applications related to the functional screening of proteins and the on-demand production of biologics.

Protein synthesis in a device with nanoporous membranes and microchannels

Cell-free protein synthesis (CFPS) is an alternative approach to cell-based recombinant protein production. It involves in vitro transcription and translation in a cell-free medium. In this work, we implemented CFPS in a plastic array device. Each unit in the array consisted of an inner well and an outer well. Two synthesis steps, gene transcription and protein translation, took place in the inner well, in which a cell-free medium was used to provide ribosomes and additional components necessary for protein synthesis. The outer well was concentric to the inner well and it functioned as a nutrient reservoir. A nanoporous membrane was sandwiched between the inner and outer wells for retaining the synthesized proteins and removing the reaction byproducts. A microfluidic channel was employed to connect these two wells for supplying fresh nutrients for longer reaction time and higher expression yield. Synthesis of luciferase was shown to last 8 times longer and yield 10 times more proteins than in a conventional container. The device also enables more than 2 orders of magnitude reduction in reagent consumption compared to a bench-top instrument. The effects of the membrane pore size and microfluidic channel on the protein production yield were also studied. The array device has potential to become a platform for parallel protein expression for proteomics applications, matching high-throughput gene discovery.

Nano-enabled synthetic biology

Biological systems display a functional diversity, density and efficiency that make them a paradigm for synthetic systems. In natural systems, the cell is the elemental unit and efforts to emulate cells, their components, and organization have relied primarily on the use of bioorganic materials. Impressive advances have been made towards assembling simple genetic systems within cellular scale containers. These biological system assembly efforts are particularly instructive, as we gain command over the directed synthesis and assembly of synthetic nanoscale structures. Advances in nanoscale fabrication, assembly, and characterization are providing the tools and materials for characterizing and emulating the smallest scale features of biology. Further, they are revealing unique physical properties that emerge at the nanoscale. Realizing these properties in useful ways will require attention to the assembly of these nanoscale components. Attention to systems biology principles can lead to the practical development of nanoscale technologies with possible realization of synthetic systems with cell-like complexity. In turn, useful tools for interpreting biological complexity and for interfacing to biological processes will result.