Dr Dayi Zhang

Lecturer

Profile

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.

Establishing reference conditions for lake water quality: a novel extrapolation approach
Xu, Y., Ma, C., Huo, S., Zhang, D., Xu, Z., Qian, G., Xi, B. 1/06/2014 In: Water Resources Management. 28, 8, p. 2161-2178. 11 p.
Journal article

Toxicity assessment and modeling of Moringa oleifera seeds in water purification by whole cell bioreporter
Al-Anizi, A.A., Hellyer, M.T., Zhang, D. 1/06/2014 In: Water Research. 56, p. 77-87. 11 p.
Journal article

Bacterial whole-cell biosensors for the detection of contaminants in water and soils
Zhang, D. 2014 In: Environmental microbiology. Humana Press p. 155-168. 14 p.
Chapter (peer-reviewed)

Functionalization and immobilization of whole cell bioreporters for the detection of environmental contamination
Chen, C., Zhang, D., Thornton, S.F., Duan, M., Luo, Y., Ding, A., Huang, W.E. 1/07/2013 In: Environmental Engineering and Management Journal. 12, 7, p. 1417-1422. 6 p.
Journal article

Whole cell bioreporter for the estimation of oil contamination
Li, C., Zhang, D., Song, Y., Jiang, B., Li, G., Huang, W.E. 07/2013 In: Environmental Engineering and Management Journal. 12, 7, p. 1353-1358. 6 p.
Journal article

Whole cell bioreporter application for rapid detection and evaluation of crude oil spill in seawater caused by Dalian oil tank explosion
Zhang, D., Ding, A., Cui, S., Hu, C., Thornton, S.F., Dou, J., Sun, Y., Huang, W.E. 1/03/2013 In: Water Research. 47, 3, p. 1191-1200. 10 p.
Journal article

Characterization and modeling of transcriptional cross-regulation in Acinetobacter baylyi ADP1
Zhang, D., Zhao, Y., He, Y., Wang, Y., Zhao, Y., Zheng, Y., Wei, X., Zhang, L., Li, Y., Jin, T., Wu, L., Wang, H., Davison, P.A., Xu, J., Huang, W.E. 07/2012 In: ACS Synthetic Biology. 1, 7, p. 274-283. 10 p.
Journal article

Whole-cell bacterial bioreporter for actively searching and sensing of alkanes and oil spills
Zhang, D., He, Y., Wang, Y., Wang, H., Wu, L., Aries, E., Huang, W.E. 01/2012 In: Microbial Biotechnology. 5, 1, p. 87-97. 11 p.
Journal article

Bacterial whole cell bioreporters in environmental health
Song, Y., Zhang, D., Polizzi, K., Zhang, E., Li, G., Huang, W. 2012 In: Biosensors and environmental health. Boca Raton, Fl. : Science Publishers Inc.
Chapter (peer-reviewed)

Functionalization of whole-cell bacterial reporters with magnetic nanoparticles
Zhang, D., Fakhrullin, R.F., Ozmen, M., Wang, H., Wang, J., Paunov, V.N., Li, G., Huang, W.E. 01/2011 In: Microbial Biotechnology. 4, 1, p. 89-97. 9 p.
Journal article

Synthetic biology approach for mining new enzymes from unculturable microorganisms
Wang, Y., Zhang, D., Huang, W.E. 04/2010
Meeting abstract

Bio-geological processes of nitrogen transport and transformation in the aeration zone and aquifer
Zhang, D., Li, G., Yang, Y.S., Zhang, X., Guo, H. 04/2009 In: Hydrological Sciences Journal. 54, 2, p. 316-326. 11 p.
Journal article

Effects of water table and fertilization management on nitrogen loading to groundwater
Guo, H., Li, G., Zhang, D., Zhang, X., Lu, C. 10/04/2006 In: Agricultural Water Management. 82, 1-2, p. 86-98. 13 p.
Journal article

Structure and function of slow release organic carbon source in groundwater in-situ denitrification
Zhang, D.Y., Li, G.H., Wang, Y., Zhou, G.Z. 2006 In: 5th World Water Congress. London : I W A PUBLISHING p. 105-113. 9 p.
Paper

A spatial research of denitrification and nitrification potential of agricultural soils in relation to fertilization practice
Guo, H., Li, G., Zhang, X., Yan, F., Zhang, D., Lu, C. 2003 In: Proceedings of the International Symposium on Water Resources and the Urban Environment . Beijing : CHINA ENVIRONMENTAL SCIENCE PRESS p. 179-185. 7 p.
Paper