Design and Functional Assembly of Synthetic Biological Parts and Devices

Programming living cells with synthetic gene circuits to perform desired tasks has been a major theme in the emerging field of synthetic biology. However, gene circuit engineering currently lacks the same predictability and reliability as seen in other mature engineering disciplines. This thesis focuses on the design and engineering of novel modular and orthogonal biological devices, and the predictable functional assembly of modular biological elements (BioParts) into customisable larger biological devices. The thesis introduces the design methodology for engineering modular and orthogonal biological devices. A set of modular biological devices with digital logic functions, including the AND, NOT and combinatorial NAND gates, were constructed and quantitatively characterised. In particular, a novel genetic AND gate was engineered in Escherichia coli by redesigning the natural HrpR/HrpS heteroregulation motif in the hrp system of Pseudomonas syringae. The AND gate is orthogonal to E. coli chassis, and employs the alternative σ54-dependent gene transcription to achieve tight transcriptional control. Results obtained show that context has a large impact on part and device behaviour, established through the systematic characterisation of a series of biological parts and devices in various biophysical and genetic contexts. A new, effective strategy is presented for the assembly of BioParts into functional customised systems using engineered ‘incontext’ characterised modules aided by modelling, which can significantly increase the predictability of circuit construction by characterising the component parts and modules in the same biophysical and genetic contexts as anticipated in their final systems. Finally, the thesis presents the design and construction of an application-oriented integrated system – the cell density-dependent microbe-based biosensor. The in vivo biosensor was programmed to be able to integrate its own cell density signal through an engineered cell-cell communication module and a second environmental signal through an environment-responsive promoter in the logic AND manner, with GFP as the output readout

Offset quantum-well method for tunable distributed Bragg reflector lasers and electro-absorption modulated distributed feedback lasers

A two-section offset quantum-well structure tunable laser with a tuning range of 7 nm was fabricated using offset quantum-well method. The distributed Bragg reflector (DBR) was realized just by selectively wet etching the multiquantum-well (MQW) layer above the quaternary lower waveguide. A threshold current of 32 mA and an output power of 9 mW at 100 mA were achieved. Furthermore, with this offset structure method, a distributed feedback (DFB) laser was integrated with an electro-absorption modulator (EAM), which was capable of producing 20 dB of optical extinction

Applied Technologies and Prospects of Conformance Control Treatments in China

China is the largest user of chemical-based conformance control treatments and a series of technologies have been successfully developed and deployed in recent years. This paper first shows the milestones of development and application of conformance control technologies in China. Then integrated conformance control technologies are reviewed followed by the lessons we have learned, and then a few major specific conformance control technologies are addressed, including tracer injection and channels explanation, potentiometric testing to identify areal sweep efficiency, Pressure Index (PI) decisionmaking technology to select well candidate, complementary decision-making technology to select well candidate and design application parameters, and major chemicals for in-depth fluid diversion technologies. In addition, this paper also describes the principles and applications of some promising technologies of combined chemical-based conformance treatment with other EOR/IOR process, including the combination technology of surfactant and water shutoff, profile control and mini-scale surfactant flooding, acid treatment and profile control treatment. Finally, this paper summarizes the problems and challenges faced by mature water flooded oilfields in China. Based on recent well tests, tracer testing and interpretation, and previous water control treatment experience, it appears that channels or high permeability streaks are common in mature water flooded oilfields. Some research directions and promising technologies are suggested

Tools and Principles for Microbial Gene Circuit Engineering

AbstractSynthetic biologists aim to construct novel genetic circuits with useful applications through rational design and forward engineering. Given the complexity of signal processing that occurs in natural biological systems, engineered microbes have the potential to perform a wide range of desirable tasks that require sophisticated computation and control. Realising this goal will require accurate predictive design of complex synthetic gene circuits and accompanying large sets of quality modular and orthogonal genetic parts. Here we present a current overview of the versatile components and tools available for engineering gene circuits in microbes, including recently developed RNA-based tools that possess large dynamic ranges and can be easily programmed. We introduce design principles that enable robust and scalable circuit performance such as insulating a gene circuit against unwanted interactions with its context, and we describe efficient strategies for rapidly identifying and correcting causes of failure and fine-tuning circuit characteristics