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Dr Dayi Zhang

Formerly at Lancaster University


My main research area focuses on the environmental monitoring and assessment of contaminated sites, as well as their ecological impacts on microbial communities.

  • Application of whole cell bioreporter in environmental monitoring

Whole cell bioreporters are biological sensing devices with living microorganisms, which have been demonstrated as a useful and complementary tool to conventional chemical and physical analytical method for environmental monitoring. With engineered sensing element, usually regulatory proteins, the whole cell bioreporter can specifically recognize the environmental chemicals and promote reporter genes to express detectable signals in the presence of contaminants.

  • Bioavailability and ecotoxicity estimation for environmental assessment

Of all types of pollutants in the environment, their bioavailable proportion has significant ecotoxic impacts on ecological system and microbial communities. The frequent environmental accidents require a rapid detection of toxicity and bioavailability of contaminated water and sediments for effective risk assessments and support management decisions. Traditional chemistry and toxicity analyses for such complex organic mixtures could be laborious, time-consuming and costly, which face a challenge to achieving a fast and in situ assessment. Whole cell bioreporters can therefore be an effective tool in this respect as a complementary tool to traditional chemical analysis and ecotoxicological assessment of mixed compounds in environmental samples.

  • Environmental microbiology

Though microorganisms are ubiquitous and account for nearly half of the total biomass on earth, more than 99% of microorganisms were unculturable or at least as-yet-uncultured. Those uncultivable microorganisms play important roles in ecological system but their functions are hard to be identified and characterized due to the uncultivable challenges. Conventional tools of stable isotope probing (SIP) and metagenomic can reveal the potential functional species and genes related to specific biochemical process. However, they suffered from distinguishing respective roles between identified species or link them with their functional genes at single cell level. A novel toolbox of magnetic nanoparticles (MNPs) and Raman micro-spectroscopy can initiate a marker free, low cost and culture-independent approach to provide detailed insights into the uncultivable microorganisms and characterize their ecological roles.

  • Biotechnology and synthetic biology

As a systematic approach, synthetic biology aims to design and rewire existing and new biological parts, devices, and systems for useful purposes. The current main challenges of synthetic biology include developing reliable and robust chassis, standardisation of bio-parts and logic gate assembly. With the novel and directed evolutionary tools, Acinetobacter baylyi performs as a perfect candidate for all the challenges when addressed on environmental issues, such as contamination assessment and bioremediation.

  • Gene regulation mechanisms

Quantitative gene regulation behavior, especially real-time dynamics, is important for synthetic biological prediction, design and approach for the metabolite pathway and energy flow. Gene expression is such a complex stochastic event that random timing and discrete nature of bioprocess associated with synthesis/decay rate of mRNA and protein, where stochastic effects cannot be ignored. Here we describe a real-time quantum gene expression model to reveal on-or-off gene status of DNA, demonstrating that stochastic cellular phenotypic variation, which is usually considered as the result of gene expression (intrinsic noise) and cellular components fluctuation (extrinsic noise). Finite gene states are switched by collision frequency and bonding strength of regulator, causing discontiguous gene burst in single copy chromosome system. Such quantum DNA status causes principle gene expression stochastic, while the DNA bonding probability and strength for both activator and repressor depend on the energy gap between regulator monomer and regulator-DNA holoenzyme. With the quantum mechanisms, the stochastic gene expression behavior at real time and single cell level can be revealed with the Markov processed dynamics. The amplitude of noise at protein level is controlled by both distributed quantum gene states. Genetically identical cells exposed to the same environmental conditions are predicted and observed to show significant variation in molecular content and marked differences in phenotypic characteristics due to DNA quantum pattern.

Research overview

My main research area focuses on the environmental monitoring and assessment of contaminated sites, as well as their ecological impacts on microbial communities. Key interests are:

● Application of whole cell bioreporter in environmental monitoring

● Bioavailability and ecotoxicity estimation for environmental assessment

● Environmental microbiology

● Biotechnology and synthetic biology

● Gene regulation mechanisms


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