Zhongrui Zhou

Bio: Zhongrui Zhou is an academic researcher from University of California, Berkeley. The author has contributed to research in topics: Bioremediation & Soil microbiology. The author has an hindex of 2, co-authored 4 publications receiving 9 citations.

Horizontal 'gene drives' harness indigenous bacteria for bioremediation.

Abstract: Engineering bacteria to clean-up oil spills is rapidly advancing but faces regulatory hurdles and environmental concerns. Here, we develop a new technology to harness indigenous soil microbial communities for bioremediation by flooding local populations with catabolic genes for petroleum hydrocarbon degradation. Overexpressing three enzymes (almA, xylE, p450cam) in Escherichia coli led to degradation of 60–99% of target hydrocarbon substrates. Mating experiments, fluorescence microscopy and TEM revealed indigenous bacteria could obtain these vectors from E. coli through several mechanisms of horizontal gene transfer (HGT), including conjugation and cytoplasmic exchange through nanotubes. Inoculating petroleum-polluted sediments with E. coli carrying the vector pSF-OXB15-p450camfusion showed that the E. coli cells died after five days but a variety of bacteria received and carried the vector for over 60 days after inoculation. Within 60 days, the total petroleum hydrocarbon content of the polluted soil was reduced by 46%. Pilot experiments show that vectors only persist in indigenous populations when under selection pressure, disappearing when this carbon source is removed. This approach to remediation could prime indigenous bacteria for degrading pollutants while providing minimal ecosystem disturbance.

Horizontal ‘gene drives’ harness indigenous bacteria for bioremediation

Abstract: Engineering bacteria to clean-up oil spills is rapidly advancing but faces regulatory hurdles and environmental concerns. Here, we develop a new technology to harness indigenous soil microbial communities for bioremediation by flooding local populations with catabolic genes for petroleum hydrocarbon degradation. Overexpressing three enzymes (almA, xylE, p450cam) in E.coli led to degradation rates of 60-99% of target hydrocarbon substrates. Mating experiments, fluorescence microscopy and TEM revealed indigenous bacteria could obtain these vectors from E.coli through several mechanisms of horizontal gene transfer (HGT), including conjugation and cytoplasmic exchange through nanotubes. Inoculating petroleum-polluted sediments with E.coli carrying the vector pSF-OXB15-p450camfusion showed that the E.coli die after five days but a variety of bacteria received and carried the vector for over 60 days after inoculation. Within 60 days, the total petroleum hydrocarbon content of the polluted soil was reduced by 46%. Pilot experiments show that vectors only persist in indigenous populations when “useful,” disappearing when this carbon source is removed. This approach to remediation could prime indigenous bacteria for degrading pollutants while providing minimal ecosystem disturbance.

Conjugation-dependent "gene drives" harness indigenous bacteria for bioremediation

Abstract: Engineering bacteria to clean-up oil spills is rapidly advancing but faces regulatory hurdles and environmental concerns. Here, we develop a new technology to harness indigenous soil microbial communities for bioremediation by flooding local populations with catabolic genes for petroleum hydrocarbon degradation. Overexpressing three enzymes (almA, xylE, p450cam) in E.coli led to degradation rates of 60-99% of target hydrocarbon substrates. Mating experiments, fluorescence microscopy and TEM revealed indigenous bacteria could obtain these vectors from E.coli through conjugation. Inoculating petroleum-polluted sediments from a former refinery with engineered E.coli showed that the E.coli die after five days but a variety of bacteria received and carried the vector for over 120 days after inoculation. This approach could prime indigenous bacteria for degrading pollutants while providing minimal ecosystem disturbance.

Detecting the state of drowsiness induced by propofol by spatial filter and machine learning algorithm on EEG recording

Abstract: To accurately measure the depth of anesthesia has been a challenge for both anesthesiologists and engineers who work on developing tools of measurements. This study aims to use a machine-learning algorithm to predict the drowsy state, a transitional depth of sedation during propofol anesthesia. The data used in this study were scalp EEG (electroencephalogram) recordings selected from the University of Cambridge Repository. Raw EEG recordings were preprocessed into power spectrum matrices one second per sample. A total of 170 samples (110 awake samples and 60 drowsy samples) were used. A CNN (Convolutional Neural Network) for the MNIST (Modified National Institute of Standards and Technology) dataset was applied on these EEG power spectrum matrices. Due to the small dataset volume, Leave-One-Out cross-validation was used to train the data. Results of the training accuracy reached 99.69%. And test accuracy averaged 96.47%. Overall, the model is able to predict the state of drowsiness during propofol anesthesia. This provides the potential to develop EEG monitoring devices with closed-loop feedback of such a machine learning algorithm that controls the titration of the dosage of anesthetic administration and the depth of anesthesia.

Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities.

Abstract: Global environmental contamination with a complex mixture of xenobiotics has become a major environmental issue worldwide Many xenobiotic compounds severely impact the environment due to their high toxicity, prolonged persistence, and limited biodegradability Microbial-assisted degradation of xenobiotic compounds is considered to be the most effective and beneficial approach Microorganisms have remarkable catabolic potential, with genes, enzymes, and degradation pathways implicated in the process of biodegradation A number of microbes, including Alcaligenes, Cellulosimicrobium, Microbacterium, Micrococcus, Methanospirillum, Aeromonas, Sphingobium, Flavobacterium, Rhodococcus, Aspergillus, Penecillium, Trichoderma, Streptomyces, Rhodotorula, Candida, and Aureobasidium, have been isolated and characterized, and have shown exceptional biodegradation potential for a variety of xenobiotic contaminants from soil/water environments Microorganisms potentially utilize xenobiotic contaminants as carbon or nitrogen sources to sustain their growth and metabolic activities Diverse microbial populations survive in harsh contaminated environments, exhibiting a significant biodegradation potential to degrade and transform pollutants However, the study of such microbial populations requires a more advanced and multifaceted approach Currently, multiple advanced approaches, including metagenomics, proteomics, transcriptomics, and metabolomics, are successfully employed for the characterization of pollutant-degrading microorganisms, their metabolic machinery, novel proteins, and catabolic genes involved in the degradation process These technologies are highly sophisticated, and efficient for obtaining information about the genetic diversity and community structures of microorganisms Advanced molecular technologies used for the characterization of complex microbial communities give an in-depth understanding of their structural and functional aspects, and help to resolve issues related to the biodegradation potential of microorganisms This review article discusses the biodegradation potential of microorganisms and provides insights into recent advances and omics approaches employed for the specific characterization of xenobiotic-degrading microorganisms from contaminated environments

Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology.

Abstract: Continuous contamination of the environment with xenobiotics and related recalcitrant compounds has emerged as a serious pollution threat. Bioremediation is the key to eliminating persistent contaminants from the environment. Traditional bioremediation processes show limitations, therefore it is necessary to discover new bioremediation technologies for better results. In this review we provide an outlook of alternative strategies for bioremediation via synthetic biology, including exploring the prerequisites for analysis of research data for developing synthetic biological models of microbial bioremediation. Moreover, cell coordination in synthetic microbial community, cell signaling, and quorum sensing as engineered for enhanced bioremediation strategies are described, along with promising gene editing tools for obtaining the host with target gene sequences responsible for the degradation of recalcitrant compounds. The synthetic genetic circuit and two-component regulatory system (TCRS)-based microbial biosensors for detection and bioremediation are also briefly explained. These developments are expected to increase the efficiency of bioremediation strategies for best results.

Bioelectronic control of a microbial community using surface-assembled electrogenetic cells to route signals.

Abstract: We developed a bioelectronic communication system that is enabled by a redox signal transduction modality to exchange information between a living cell-embedded bioelectronics interface and an engineered microbial network. A naturally communicating three-member microbial network is 'plugged into' an external electronic system that interrogates and controls biological function in real time. First, electrode-generated redox molecules are programmed to activate gene expression in an engineered population of electrode-attached bacterial cells, effectively creating a living transducer electrode. These cells interpret and translate electronic signals and then transmit this information biologically by producing quorum sensing molecules that are, in turn, interpreted by a planktonic coculture. The propagated molecular communication drives expression and secretion of a therapeutic peptide from one strain and simultaneously enables direct electronic feedback from the second strain, thus enabling real-time electronic verification of biological signal propagation. Overall, we show how this multifunctional bioelectronic platform, termed a BioLAN, reliably facilitates on-demand bioelectronic communication and concurrently performs programmed tasks.

Synthetically engineered microbial scavengers for enhanced bioremediation.

Abstract: Microbial bioremediation has gained attention as a cheap, efficient, and sustainable technology to manage the increasing environmental pollution. Since microorganisms in nature are not evolved to degrade pollutants, there is an increasing demand for developing safer and more efficient pollutant-scavengers for enhanced bioremediation. In this review, we introduce the strategies and technologies developed in the field of synthetic biology and their applications to the construction of microbial scavengers with improved efficiency of biodegradation while minimizing the impact of genetically engineered microbial scavengers on ecosystems. In addition, we discuss recent achievements in the biodegradation of fastidious pollutants, greenhouse gases, and microplastics using engineered microbial scavengers. Using synthetic microbial scavengers and multidisciplinary technologies, toxic pollutants could be more easily eliminated, and the environment could be more efficiently recovered.

Current insights into the microbial degradation for butachlor: strains, metabolic pathways, and molecular mechanisms

Abstract: The herbicide butachlor has been used in huge quantities worldwide, affecting various environmental systems. Butachlor residues have been detected in soil, water, and organisms, and have been shown to be toxic to these non-target organisms. This paper briefly summarizes the toxic effects of butachlor on aquatic and terrestrial animals, including humans, and proposes the necessity of its removal from the environment. Due to long-term exposure, some animals, plants, and microorganisms have developed resistance toward butachlor, indicating that the toxicity of this herbicide can be reduced. Furthermore, we can consider removing butachlor residues from the environment by using such butachlor-resistant organisms. In particular, microbial degradation methods have attracted much attention, with about 30 kinds of butachlor-degrading microorganisms have been found, such as Fusarium solani, Novosphingobium chloroacetimidivorans, Chaetomium globosum, Pseudomonas putida, Sphingomonas chloroacetimidivorans, and Rhodococcus sp. The metabolites and degradation pathways of butachlor have been investigated. In addition, enzymes associated with butachlor degradation have been identified, including CndC1 (ferredoxin), Red1 (reductase), FdX1 (ferredoxin), FdX2 (ferredoxin), Dbo (debutoxylase), and catechol 1,2 dioxygenase. However, few reviews have focused on the microbial degradation and molecular mechanisms of butachlor. This review explores the biochemical pathways and molecular mechanisms of butachlor biodegradation in depth in order to provide new ideas for repairing butachlor-contaminated environments. • Biodegradation is a powerful tool for the removal of butachlor. • Dechlorination plays a key role in the degradation of butachlor. • Possible biochemical pathways of butachlor in the environment are described.