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Open Access Publications from the University of California

This series is home to publications and data sets from the Bourns College of Engineering at the University of California, Riverside.

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Center for Environmental Research and Technology

Cover page of Cometabolism of 17α-ethynylestradiol by nitrifying bacteria depends on reducing power availability and leads to elevated nitric oxide formation.

Cometabolism of 17α-ethynylestradiol by nitrifying bacteria depends on reducing power availability and leads to elevated nitric oxide formation.

(2021)

17α-ethynylestradiol (EE2) is a priority emerging contaminant (EC) in diverse environments that can be cometabolized by ammonia oxidizing bacteria (AOB). However, its transformation kinetics and the underlying molecular mechanism are unclear. In this study, kinetic parameters, including maximum specific EE2 transformation rate, EE2 half-saturation coefficient, and EE2transformation capacity of AOBwere obtained by using the model AOB strain, Nitrosomonas europaea 19718. The relationship between EE2 cometabolism and ammonia oxidation was divided into three phases according to reducing power availability, namely "activation", "coupling", and "saturation". Specifically, there was a universal lag of EE2 transformation after ammonia oxidation was initiated, suggesting that sufficient reducing power (approximately 0.95 ± 0.06 mol NADH/L) was required to activate EE2 cometabolism. Interestingly, nitric oxide emission increased by 12 ± 2% during EE2 cometabolism, along with significantly upregulated nirK cluster genes. The findings are of importance to understanding the cometabolic behavior and mechanism of EE2 in natural and engineered environments. Maintaining relatively high and stable reducing power supply from ammonia oxidation can potentially improve the cometabolic removal of EE2 and other ECs during wastewater nitrification processes.

Cover page of Near-Quantitative Defluorination of Perfluorinated and Fluorotelomer Carboxylates and Sulfonates with Integrated Oxidation and Reduction.

Near-Quantitative Defluorination of Perfluorinated and Fluorotelomer Carboxylates and Sulfonates with Integrated Oxidation and Reduction.

(2021)

The UV-sulfite reductive treatment using hydrated electrons (eaq-) is a promising technology for destroying perfluorocarboxylates (PFCAs, CnF2n+1COO-) in any chain length. However, the C-H bonds formed in the transformation products strengthen the residual C-F bonds and thus prevent complete defluorination. Reductive treatments of fluorotelomer carboxylates (FTCAs, CnF2n+1-CH2CH2-COO-) and sulfonates (FTSAs, CnF2n+1-CH2CH2-SO3-) are also sluggish because the ethylene linker separates the fluoroalkyl chain from the end functional group. In this work, we used oxidation (Ox) with hydroxyl radicals (HO•) to convert FTCAs and FTSAs to a mixture of PFCAs. This process also cleaved 35-95% of C-F bonds depending on the fluoroalkyl chain length. We probed the stoichiometry and mechanism for the oxidative defluorination of fluorotelomers. The subsequent reduction (Red) with UV-sulfite achieved deep defluorination of the PFCA mixture for up to 90%. The following use of HO• to oxidize the H-rich residues led to the cleavage of the remaining C-F bonds. We examined the efficacy of integrated oxidative and reductive treatment of n = 1-8 PFCAs, n = 4,6,8 perfluorosulfonates (PFSAs, CnF2n+1-SO3-), n = 1-8 FTCAs, and n = 4,6,8 FTSAs. A majority of structures yielded near-quantitative overall defluorination (97-103%), except for n = 7,8 fluorotelomers (85-89%), n = 4 PFSA (94%), and n = 4 FTSA (93%). The results show the feasibility of complete defluorination of legacy PFAS pollutants and will advance both remediation technology design and water sample analysis.

Cover page of Biotransformation of lincomycin and fluoroquinolone antibiotics by the ammonia oxidizers AOA, AOB and comammox: A comparison of removal, pathways, and mechanisms.

Biotransformation of lincomycin and fluoroquinolone antibiotics by the ammonia oxidizers AOA, AOB and comammox: A comparison of removal, pathways, and mechanisms.

(2021)

In this study, we evaluated the biotransformation mechanisms of lincomycin (LIN) and three fluoroquinolone antibiotics (FQs), ciprofloxacin (CFX), norfloxacin (NFX), and ofloxacin (OFX), which regularly enter aquatic environments through human activities, by different ammonia-oxidizing microorganisms (AOM). The organisms included a pure culture of the complete ammonia oxidizer (comammox) Nitrospira inopinata, an ammonia oxidizing archaeon (AOA) Nitrososphaera gargensis, and an ammonia-oxidizing bacterium (AOB) Nitrosomonas nitrosa Nm90. The removal of these antibiotics by the pure microbial cultures and the protein-normalized biotransformation rate constants indicated that LIN was significantly co-metabolically biotransformed by AOA and comammox, but not by AOB. CFX and NFX were significantly co-metabolized by AOA and AOB, but not by comammox. None of the tested cultures transformed OFX effectively. Generally, AOA showed the best biotransformation capability for LIN and FQs, followed by comammox and AOB. The transformation products and their related biotransformation mechanisms were also elucidated. i) The AOA performed hydroxylation, S-oxidation, and demethylation of LIN, as well as nitrosation and cleavage of the piperazine moiety of CFX and NFX; ii) the AOB utilized nitrosation to biotransform CFX and NFX; and iii) the comammox carried out hydroxylation, demethylation, and demethylthioation of LIN. Hydroxylamine, an intermediate of ammonia oxidation, chemically reacted with LIN and the selected FQs, with removals exceeding 90%. Collectively, these findings provide important fundamental insights into the roles of different ammonia oxidizers and their intermediates on LIN and FQ biotransformation in nitrifying environments including wastewater treatment systems.

Cover page of Modeling multi-species RNA modification through multi-task curriculum learning.

Modeling multi-species RNA modification through multi-task curriculum learning.

(2021)

N6-methyladenosine (m6A) is the most pervasive modification in eukaryotic mRNAs. Numerous biological processes are regulated by this critical post-transcriptional mark, such as gene expression, RNA stability, RNA structure and translation. Recently, various experimental techniques and computational methods have been developed to characterize the transcriptome-wide landscapes of m6A modification for understanding its underlying mechanisms and functions in mRNA regulation. However, the experimental techniques are generally costly and time-consuming, while the existing computational models are usually designed only for m6A site prediction in a single-species and have significant limitations in accuracy, interpretability and generalizability. Here, we propose a highly interpretable computational framework, called MASS, based on a multi-task curriculum learning strategy to capture m6A features across multiple species simultaneously. Extensive computational experiments demonstrate the superior performances of MASS when compared to the state-of-the-art prediction methods. Furthermore, the contextual sequence features of m6A captured by MASS can be explained by the known critical binding motifs of the related RNA-binding proteins, which also help elucidate the similarity and difference among m6A features across species. In addition, based on the predicted m6A profiles, we further delineate the relationships between m6A and various properties of gene regulation, including gene expression, RNA stability, translation, RNA structure and histone modification. In summary, MASS may serve as a useful tool for characterizing m6A modification and studying its regulatory code. The source code of MASS can be downloaded from https://github.com/mlcb-thu/MASS.

Cover page of Emerging Technologies for Monitoring Plant Health in Vivo.

Emerging Technologies for Monitoring Plant Health in Vivo.

(2021)

In the coming decades, increasing agricultural productivity is all-important. As the global population is growing rapidly and putting increased demand on food supply, poor soil quality, drought, flooding, increasing temperatures, and novel plant diseases are negatively impacting yields worldwide. One method to increase yields is plant health monitoring and rapid detection of disease, nutrient deficiencies, or drought. Monitoring plant health will allow for precise application of agrichemicals, fertilizers, and water in order to maximize yields. In vivo plant sensors are an emerging technology with the potential to increase agricultural productivity. In this mini-review, we discuss three major approaches of in vivo sensors for plant health monitoring, including genetic engineering, imaging and spectroscopy, and electrical.

Cover page of Encapsulating Polyethyleneimine-DNA Nanoplexes into PEGylated Biodegradable Microparticles Increases Transgene Expression In Vitro and Reduces Inflammatory Responses In Vivo.

Encapsulating Polyethyleneimine-DNA Nanoplexes into PEGylated Biodegradable Microparticles Increases Transgene Expression In Vitro and Reduces Inflammatory Responses In Vivo.

(2021)

Encapsulating genetic material into biocompatible polymeric microparticles is a means to improving gene transfection while simultaneously decreasing the tendency for inflammatory responses; and can be advantageous in terms of delivering material directly to the lungs via aerosolization for applications such as vaccinations. In this study, we investigated the advantages of using polymeric microparticles carrying the luciferase reporter gene in increasing transfection efficiency in the readily transfectable HEK293 cell line and the difficult to transfect RAW264.7 cell line. The results indicated that there was a limit to the ratio of nitrogen in polyethylenimine (PEI) to phosphate in DNA (N/P ratio) beyond which further increases in transgene expression no longer, or only marginally, occurred. Microparticles encapsulating PEI:DNA nanoplexes induced cellular toxicity in a dose-dependent manner. PEGylation increased transgene expression, likely related to enhanced degradation of particles. Furthermore, intra-tracheal instillation in rats allowed us to investigate the inflammatory response in the lung as a function of PEGylation, porosity, and size. Porosity did not influence cell counts in bronchoalveolar lavage fluid in the absence of PEG, but in particles containing PEG, non-porous particles recruited fewer inflammatory cells than their porous counterparts. Finally, both 1 μm and 10 μm porous PLA-PEG particles recruited more neutrophils than 4 μm particles. Thus, we have shown that PEGylation and lack of porosity are advantageous for faster release of genetic cargo from microparticles and a reduced inflammatory response, respectively.

Cover page of Bubble dynamics of laser-induced cavitation in plasmonic gold nanorod solutions and the relative effect of surface tension and viscosity

Bubble dynamics of laser-induced cavitation in plasmonic gold nanorod solutions and the relative effect of surface tension and viscosity

(2021)

Laser-induced cavitation (LIC) bubbles and the shockwaves they form upon collapse are destructive to nearby solid boundaries, making them of interest for biomedical and industrial applications. Furthermore, the LIC bubbles provide spatial control that can be tuned by the bubble size, collapse time and shockwave intensity. The inclusion of plasmonic nanoparticles, such as gold nanoparticles (GNP) in the liquids where LIC bubbles are formed, can further enhance the absorption of light, allowing for bubble formation at lower laser energies. However, the effect of the physical properties of such liquids on LIC bubble dynamics remains unknown. In this study, the dynamics of LIC bubbles in water–ethanol, water-glycerol, and water-GNP solutions were investigated by simultaneous high-speed shadowgraphy and spatial transmittance modulation. The first set of experiments demonstrated that LIC bubbles induced in the GNP solutions led to more efficient cavitation formation with lower fluence compared to solutions without GNPs, thereby producing higher-intensity pressure waves. A second set of experiments was conducted to determine the surface tension of GNP solutions at room temperature and was found to be 70.62 mN/m. With this information, and the corresponding values reported in the literature for ethanol and glycerol, we aimed at discerning the role of surface tension and viscosity on the dynamics of LIC bubbles, apart from the enhanced optical absorption of the GNP solutions. We observed that the optical breakdown threshold for plasma formation was reduced by 18% in GNP solutions as compared to DI water and 10.4% compared to ethanol, and the intensity of initial shockwaves in the GNP solutions was much higher than those in DI water. This enhanced intensity of shockwaves in GNP solutions compared to DI water opens a new avenue for the enhancement of cancer cell treatment and anti-bacterial applications in the biomedical field and the enhancement of the laser ablation technique in the industrial setting.

Cover page of Predicting Solute Transport Through Green Stormwater Infrastructure With Unsteady Transit Time Distribution Theory

Predicting Solute Transport Through Green Stormwater Infrastructure With Unsteady Transit Time Distribution Theory

(2021)

In this study, we explore the use of unsteady transit time distribution (TTD) theory to model solute transport in biofilters, a popular form of nature-based or “green” storm water infrastructure (GSI). TTD theory has the potential to address many unresolved challenges associated with predicting pollutant fate and transport through these systems, including unsteadiness in the water balance (time-varying inflows, outflows, and storage), unsteadiness in pollutant loading, time-dependent reactions, and scale-up to GSI networks and urban catchments. From a solution to the unsteady age conservation equation under uniform sampling, we derive an explicit expression for solute breakthrough during and after one or more storm events. The solution is calibrated and validated with breakthrough data from 17 simulated storms at a field-scale biofilter test facility in Southern California, using bromide as a conservative tracer. TTD theory closely reproduces bromide breakthrough concentrations, provided that lateral exchange with the surrounding soil is accounted for. At any given time, according to theory, more than half of the water in storage is from the most recent storm, while the rest is a mixture of penultimate and earlier storms. Thus, key management endpoints, such as the pollutant treatment credit attributable to GSI, are likely to depend on the evolving age distribution of water stored and released by these systems.

Cover page of Development of an Interdigitated Electrode-Based Disposable Enzyme Sensor Strip for Glycated Albumin Measurement.

Development of an Interdigitated Electrode-Based Disposable Enzyme Sensor Strip for Glycated Albumin Measurement.

(2021)

Glycated albumin (GA) is an important glycemic control marker for diabetes mellitus. This study aimed to develop a highly sensitive disposable enzyme sensor strip for GA measurement by using an interdigitated electrode (IDE) as an electrode platform. The superior characteristics of IDE were demonstrated using one microelectrode of the IDE pair as the working electrode (WE) and the other as the counter electrode, and by measuring ferrocyanide/ferricyanide redox couple. The oxidation current was immediately reached at the steady state when the oxidation potential was applied to the WE. Then, an IDE enzyme sensor strip for GA measurement was prepared. The measurement of fructosyl lysine, the protease digestion product of GA, exhibited a high, steady current immediately after potential application, revealing the highly reproducible measurement. The sensitivity (2.8 nA µM-1) and the limit of detection (1.2 µM) obtained with IDE enzyme sensor strip were superior compared with our previously reported sensor using screen printed electrode. Two GA samples, 15 or 30% GA, corresponding to healthy and diabetic levels, respectively, were measured after protease digestion with high resolution. This study demonstrated that the application of an IDE will realize the development of highly sensitive disposable-type amperometric enzyme sensors with high reproducibility.