Phase Referencing in Optical Interferometry

One of the aims of next generation optical interferometric instrumentation is to be able to make use of information contained in the visibility phase to construct high dynamic range images. Radio and optical interferometry are at the two extremes of phase corruption by the atmosphere. While in radio it is possible to obtain calibrated phases for the science objects, in the optical this is currently not possible. Instead, optical interferometry has relied on closure phase techniques to produce images. Such techniques allow only to achieve modest dynamic ranges. However, with high contrast objects, for faint targets or when structure detail is needed, phase referencing techniques as used in radio interferometry, should theoretically achieve higher dynamic ranges for the same number of telescopes. Our approach is not to provide evidence either for or against the hypothesis that phase referenced imaging gives better dynamic range than closure phase imaging. Instead we wish to explore the potential of this technique for future optical interferometry and also because image reconstruction in the optical using phase referencing techniques has only been performed with limited success. We have generated simulated, noisy, complex visibility data, analogous to the signal produced in radio interferometers, using the VLTI as a template. We proceeded with image reconstruction using the radio image reconstruction algorithms contained in AIPS IMAGR (CLEAN algorithm). Our results show that image reconstruction is successful in most of our science cases, yielding images with a 4 milliarcsecond resolution in K band. (abridged)Comment: 11 pages, 36 figure

Phase closure image reconstruction for future VLTI instrumentation

Classically, optical and near-infrared interferometry have relied on closure phase techniques to produce images. Such techniques allow us to achieve modest dynamic ranges. In order to test the feasibility of next generation optical interferometers in the context of the VLTI-spectro-imager (VSI), we have embarked on a study of image reconstruction and analysis. Our main aim was to test the influence of the number of telescopes, observing nights and distribution of the visibility points on the quality of the reconstructed images. Our results show that observations using six Auxiliary Telescopes (ATs) during one complete night yield the best results in general and is critical in most science cases; the number of telescopes is the determining factor in the image reconstruction outcome. In terms of imaging capabilities, an optical, six telescope VLTI-type configuration and ~200 meter baseline will achieve 4 mas spatial resolution, which is comparable to ALMA and almost 50 times better than JWST will achieve at 2.2 microns. Our results show that such an instrument will be capable of imaging, with unprecedented detail, a plethora of sources, ranging from complex stellar surfaces to microlensing events

Models for Cell-Free Synthetic Biology: Make Prototyping Easier, Better, and Faster

Cell-free TX-TL is an increasingly mature and useful platform for prototyping, testing, and engineering biological parts and systems. However, to fully accomplish the promises of synthetic biology, mathematical models are required to facilitate the design and predict the behavior of biological components in cell-free extracts. We review here the latest models accounting for transcription, translation, competition, and depletion of resources as well as genome scale models for lysate-based cell-free TX-TL systems, including their current limitations. These models will have to find ways to account for batch-to-batch variability before being quantitatively predictive in cell-free lysate-based platforms

Burden-driven feedback control of gene expression

Cells use feedback regulation to ensure robust growth despite fluctuating demands for resources and differing environmental conditions. However, the expression of foreign proteins from engineered constructs is an unnatural burden that cells are not adapted for. Here we combined RNA-seq with an in vivo assay to identify the major transcriptional changes that occur in Escherichia coli when inducible synthetic constructs are expressed. We observed that native promoters related to the heat-shock response activated expression rapidly in response to synthetic expression, regardless of the construct. Using these promoters, we built a dCas9-based feedback-regulation system that automatically adjusts the expression of a synthetic construct in response to burden. Cells equipped with this general-use controller maintained their capacity for native gene expression to ensure robust growth and thus outperformed unregulated cells in terms of protein yield in batch production. This engineered feedback is to our knowledge the first example of a universal, burden-based biomolecular control system and is modular, tunable and portable

Cell-free systems: Gene expression outside of the cell

Doctora

Active learning cell free protein production optimization

Presentation for the American Institute of Chemical Engineers with the company Beckman

Protein synthesis in cell free systems

Doctoral1. Description of Cell Free Systems: An open system to study biology2 Understand living organisms: functions preserved in cell free systems3 Building artificial cells: reconstruct f unctions defective in cell free system

Relationship between protein production and cell physiology

International audienceUnderstand and use the relationship between protein production and cell physiology (growth-rate dependent) for synthetic biolog

Active learning leads to highly efficient predictions in cell-free systems

Bioengineering community naturehttps://go.nature.com/3cxhJbJCell-free systems are widely used for fundamental molecular biology, for applications in genetic engineering, in metabolic engineering or in medical diagnostics and for a better understanding in the origin of life1,2,3. Cell-free systems present many advantages for synthetic biology through high-throughput characterization and prototyping of natural and synthetic circuits. Over the last decade, the cell-free community developed multiple protocols to simplify lysate preparation and maximize protein production in vitro. The lysate-based transcription-translation cell-free systems (TXTL) using E. coli can currently be prepared in a few days via chemical or physical disruption of the cellular membrane and mixed with an energy buffer

Maximization of production in cell-free systems

International audienc