Waterloo Research

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Now showing 1 - 20 of 2921

Navigating food futures post-disaster: the intersectional politics of race, gender, disability and access
(Informa UK, 2025-10-01) Diaz, Ileana I.
A historically devastating series of climatic events in September 2017 transformed lives in Puerto Rico and its diaspora. The impacts of Hurricanes Irma and Maria ruptured the functionality of lifeways in unprecedented forms. The events also characterize the longest disaster response muddle in the history of the United States. This focused case study investigates the ways that individuals navigate their island food system in a post-disaster context. It explores the political, social and economic circumstances which inform various experiences of food insecurity, hunger, gendered vulnerabilities, disability and the role that layered structural inequity plays in producing unequal access to food. Based on news media, photographic analysis and in-depth interviews conducted with those who lived through both hurricanes, an evidence-informed intersectional analysis is produced. Scaffolding the research conceptually through an intersectionality and Afro-diasporic futures epistemology, this paper contributes a geographical and feminist analysis to the study of disasters in relation to food insecurity. Markedly, people living with disabilities and women participants reported increased challenges to disaster recovery and resilience. Parents were found to be the most food insecure. Research findings show that gender, race, disability and income play a pivotal role in shaping food access and long-term wellbeing in post-disaster contexts. -----
Self-assembled manganese phthalocyanine nanoparticles with enhanced peroxidase-like activity for anti-tumor therapy Research Article Published: 29 September 2021
(2021-09-29) Wang, Jinghan; Gao, Shanqing; Wang, Xiao; Zhang, Haozhen; Ren, Xitong; Liu, Juewen; Bai, Feng
The use of functional nanoparticles as peroxidase-like (POD-like) catalyst has recently become a focus of research in cancer therapy. Phthalocyanine is a macrocyclic conjugated metal ligand, which is expected to achieve a high POD-like catalytic activity, generating free radicals and inhibiting the proliferation of cancer cells. In this paper, we synthesized phthalocyanine nanocrystals with different structures through noncovalent self-assembly confined within micro-emulsion droplets, and manganese phthalocyanine (MnPc) possessing a metal-N-C active center was used as the building block. These nano-assemblies exhibit shape-dependent POD-like catalytic activities, because the emulsifier and MnPc co-mixed assembly reduced the close packing between MnPc molecules and exposed more active sites. The assembly had a water-dispersed nanostructure, which is conducive to accumulation at tumor sites through the enhanced permeability and retention effect (EPR). Because of a highly efficient microenvironmental response, the assembly showed higher catalytic activity only emerged under the acidic tumor-like microenvironment, but caused less damage to normal tissues in biomedical applications. In vivo and in vitro catalytic therapy tests showed excellent anti-tumor effects. This work explored a new way for the application of metal-organic macromolecules such as MnPc as nanozymes for catalytic tumor therapy.
Hypothesis Testing of Multivariate Biomechanical Responses using Statistical Parametric Mapping and Arc-Length Re-Parameterization
(Springer Nature, 2025-07-14) Hartlen, Devon C.; Cronin, Duane S.
Detection of differences between experimental biomechanical data sets is critical to quantify effects and their significance. Many forms of biomechanical data are continuous and multivariate in nature, yet contemporary statistical analysis and hypothesis testing most often utilize single-value scalar metrics. However, reducing continuous responses to single-value scalar metrics can introduce bias and eliminate much of the physical context of a response. This study proposes a methodology to perform hypothesis testing directly on continuous multivariate experimental data sets. The methodology couples arc-length re-parameterization with statistical parametric mapping (SPM) to provide a general framework that can be applied to many of the response types found in biomechanics, including sets of responses that do not terminate at a common coordinate or are hysteretic, such as load-unload data. The arc-length-based SPM methodology was applied to three literature data sets representing a cross-section of the types of responses encountered in biomechanics. In each case, the arc-length-based SPM methodology produced results that agreed with contemporary statistical techniques while providing quantification and identification of statistically significant differences between the data sets. The proposed method provided important contextual information and a deeper understanding of the underlying behaviour of a dataset that would otherwise be missed using contemporary single-value scalar metric statistical techniques, such as highlighting specific response features that drive differences between datasets.
Nucleobase, nucleoside, nucleotide, and oligonucleotide coordinated metal ions for sensing and biomedicine applications
(Springer Nature, 2021-04-19) Zhou, Jiaojiao; Han, Heyou; Liu, Juewen
Metal ions play critical roles in chemical, biological, and environmental processes. Various biomolecules have the ability to coordinate with metal ions and form various materials. Nucleobases, nucleosides, and nucleotides, as the essential components of DNA, have emerged as a useful building block for the construction of functional nanomaterials. In recent years, DNA oligonucleotides have also been used for this purpose. We herein review the strategies for the synthesis of soft nanomaterials through the assembly of nucleotides (or DNA) and metal ions to yield various nanoparticles, fibers, and hydrogels. Such coordination methods are simple to operate and can be carried out under ambient conditions. The luminescent, catalytic, and molecular recognition properties of these coordination materials are described with representative recent examples. Their applications ranging from biosensing, enzyme encapsulation, catalysis, templated shell growth to cancer therapy are highlighted. Finally, challenges of this field and future perspectives are discussed.
Critical evaluation of aptamer binding for biosensor designs
(Elsevier, 2021-11-13) Zhao, Yichen; Yavari, Kayvan; Liu, Juewen
Over the last three decades, numerous aptamer-based biosensors have been reported. The basis of these sensors is the selective binding of target analytes by aptamers. In the last few years, a number of papers have been published questioning the binding ability of some popular aptamers such as those documented for As(III), ampicillin, chloramphenicol, isocarbophos, phorate and dopamine. In this article, these papers are reviewed, and the binding assays are described, which may provide possible reasons for obtaining false positive aptamers. Additionally, relevant aptamer selection methods and typical characterization steps are described. It is found that for small molecular targets, using an immobilized library might result in better aptamers. Furthermore, the importance of carefully designed controls to ensure the quality of binding assays is discussed, especially in the case of mutated nonbinding aptamers. Only then, with fully validated aptamers, can subsequent biosensor design bring about meaningful results.
Deployment of functional DNA-based biosensors for environmental water analysis
(Elsevier, 2022-04-14) Zhao, Yichen; Yavari, Kayvan; Wang, Yihao; Pi, Kunfu; Van Cappellen, Philippe; Liu, Juewen
Various functional DNA molecules have been used for the detection of environmental contaminants in water, but their practical applications have been limited. To address this gap, this review highlights the efforts to develop field-deployable water quality biosensors. The biosensor devices include microfluidic, lateral flow and paper-based devices, and other novel ideas such as the conversion of glucometers for the detection of environmental analytes. In addition, we also review DNA-functionalized hydrogels and their use in diffusive gradients in thin films (DGT) devices. We classify the sensors into one-step and two-step assays and discuss their practical implications. While the review is focused on works reported in the last five years, some classic early works are cited as well. Overall, most of the existing work only tested spiked water samples. Future work needs to shift to real environmental samples and the comparison of DNA-based sensors to standard analytical methods.
Signaling Kinetics of DNA and Aptamer Biosensors Revealing Graphene Oxide Surface Heterogeneity
(Springer Nature, 2021-12-16) Huang, Po-Jung Jimmy; Liu, Juewen
Adsorption of fluorescently labeled DNA and aptamer probes to graphene oxide (GO) has been one of the most popular methods for developing biosensors. In the presence of target analytes, the quenched fluorescence would recover. In this work, we followed the kinetics of the reactions and found that the fluorescence would eventually drop after an initial increase, and this was attributed to the re-adsorption of the desorbed probe DNA molecules. Both a DNA probe and an aptamer for adenosine were used. This re-adsorption was attributed to the surface heterogeneity of GO, and the DNA probes desorbed from relatively weaker binding sites were re-adsorbed on the stronger binding sites. This re-adsorption can be avoided by extensive washing the samples, and also by blocking the GO surface or by heating. This fundamental understanding is important for achieving a stable signal of such biosensors.
Adsorption of Linear and Spherical DNA Oligonucleotides onto Microplastics
(American Chemical Society, 2022-01-30) Zandieh, Mohamad; Patel, Kshiti; Liu, Juewen
Microplastic pollution of water and food chains can endanger human health. It has been reported that environmental DNA can be carried by microplastics and spread into the ecosystem. To better comprehend the interactions between microplastics and DNA, we herein investigated the adsorption of DNA oligonucleotides on a few important microplastics. The microplastics were prepared using common plastic objects made of polyethylene (PE), polypropylene (PP), polystyrene (PS), polyvinyl chloride (PVC), composite of PS/PVC, and polyethylene terephthalate (PET). The effect of environmentally abundant metal ions such as Na+, Mg2+, and Ca2+ on the adsorption was also studied. Among the microplastics, PET and PS had the highest efficiency for the adsorption of linear DNA, likely due to the interactions provided by their aromatic rings. The study of DNA desorption from PET revealed the important role of hydrogen bonding and metal-mediated adsorption, while van der Waals force and hydrophobic interactions were also involved in the adsorption mechanism. The adsorption of spherical DNA (SNA) made of a high density of DNA coated on gold nanoparticles (AuNPs) was also studied, where the adsorption affinity order was found to be PET > PS/PVC > PS. Moreover, a tighter DNA adsorption was achieved in the presence of Ca2+ and Mg2+ compared to Na+.
Selection of Aptamers for Sensing Caffeine and Discrimination of Its Three Single Demethylated Analogues
(American Chemical Society, 2022-02-10) Huang, Po-Jung Jimmy; Liu, Juewen
With the growing consumption of caffeine-containing beverages, detection of caffeine has become an important biomedical, bioanalytical, and environmental topic. We herein isolated four high-quality aptamers for caffeine with dissociation constants ranging from 2.2 to 14.6 μM as characterized using isothermal titration calorimetry. Different binding patterns were obtained for the three single demethylated analogues: theobromine, theophylline, and paraxanthine, highlighting the effect of the molecular symmetry of the arrangement of the three methyl groups in caffeine. A structure-switching fluorescent sensor was designed showing a detection limit of 1.2 μM caffeine, which reflected the labeled caffeine concentration within 6.1% difference for eight commercial beverages. In 20% human serum, a detection limit of 4.0 μM caffeine was achieved. With the four aptamer sensors forming an array, caffeine and the three analogues were well separated from nine other closely related molecules.
Homogeneous assays for aptamer-based ethanolamine sensing: no indication of target binding
(Royal Society of Chemistry, 2022-02-11) Ding, Yuzhe; Liu, Xun; Huang, Po-Jung Jimmy; Liu, Juewen
Ethanolamine is an important analyte for environmental chemistry and biological sciences. A few DNA aptamers were previously reported for binding ethanolamine with a dissociation constant (Kd) as low as 9.6 nM. However, most of the previous binding assays and sensing work used either immobilized ethanolamine or immobilized aptamers. In this work, we studied three previously reported DNA sequences, two of which were supposed to bind ethanolamine while the other could not bind. Isothermal titration calorimetry revealed no binding for any of these sequences. In addition, due to their guanine-rich sequences, thioflavin T was used as a probe. Little fluorescence change was observed with up to 1 μM ethanolamine. Responses within the millimolar range of ethanolamine were attributed to the general fluorescence quenching effect of ethanolamine instead of aptamer binding. Finally, after studying the adsorption of ethanolamine to gold nanoparticles (AuNPs), we confirmed the feasibility of using AuNPs as a probe when the concentration of ethanolamine was below 0.1 mM. However, no indication of specific aptamer binding was observed by comparing the three DNA sequences for their color changing trends. This work articulates the importance of careful homogeneous binding assays using free target molecules.
Adsorption of DNA Oligonucleotides by Self-Assembled Metalloporphyrin Nanomaterials
(American Chemical Society, 2022-03-08) Wang, Jinghan; Wang, Zhen; Huang, Po-Jung Jimmy; Bai, Feng; Liu, Juewen
Porphyrin assemblies have controllable morphology, high biocompatibility, and good optical properties and were widely used in biomedical diagnosis and treatment. With the development of DNA biotechnology, combining DNA with porphyrin assemblies can broaden the biological applications of porphyrins. Porphyrin assemblies can serve as nanocarriers for DNA, although the fundamental interactions between them are not well understood. In this work, zinc meso-tetra(4-pyridyl)porphyrin (ZnTPyP) assemblies were prepared in the presence of various surfactants and at different pH values, yielding a variety of aggregation forms. Among them, the hexagonal stacking form exposes more pyridine substituents, and the hydrogen bonding force between the substituents and the DNA bases allows the DNA to be quickly adsorbed on the surface of the assemblies. The effects of DNA sequence and length were systematically tested. In particular, the adsorption of duplex DNA was less efficient compared to the adsorption of single-stranded DNA. This fundamental study is useful for the further combination of DNA and porphyrin assemblies to prepare new functional hybrid nanomaterials.
Surface Science of Nanozymes and Defining a Nanozyme Unit
(American Chemical Society, 2022-03-15) Zandieh, Mohamad; Liu, Juewen
The field of nanozyme aims to use nanomaterials to replace protein-based enzymes. Nanozymes have attracted extensive interest because of their stability, cost-effectiveness, and versatility. While the focus of the nanozyme field has mainly been the discovery of new nanozyme materials and the exploration of their analytical, biomedical, and environmental applications, the number of fundamental studies is growing. Nanozymes are related to two important fields: enzymology and heterogeneous catalysis. Although fitting nanozyme kinetic data to the Michaelis–Menten kinetics is a very common practice, using the surface science methods of heterogeneous catalysis can provide insights about their catalytic mechanisms. The definition of a nanozyme unit is critical to understanding and comparing nanozyme activities. In this perspective, we articulate the use of a surface science approach to study nanozymes and discuss the various application scenarios of using different nanozyme units.
Selection of DNA Aptamers for Sensing Uric Acid in Simulated Tears
(Chemistry Europe: European Chemical Sciences Publishing, 2022-03-30) Liu, Yibo; Liu, Juewen
Uric acid is a biomarker for a range of diseases and hyperuricemia is the cause of many diseases including gout. While most biosensors for detecting uric acid relied on enzymatic reactions, in this work a library-immobilization method was used to obtain DNA aptamers for uric acid. After 18 rounds of selection, two representative aptamers were obtained with a Kd around 1.2 μM measured by isothermal titration calorimetry (ITC). Based on their difference in binding to xanthine, which differs from uric acid by only one oxygen atom, these two aptamers have different binding orientations to uric acid. ITC also indicated that the UA-1 aptamer specifically required a high concentration of Na+ for binding, which cannot be replaced by Li+, K+ or Mg2+. Combined ITC and fluorescence spectroscopy data indicated the need of three Na+ ions, which explained the requirement of a high Na+ concentration. The UA-1 aptamer was engineered into a fluorescent biosensor based on the strand-displacement reaction, resulting in a limit of detection of 90 nM uric acid. This sensor was also tested in simulated tears with a limit of detection of 350 nM uric acid.
DNA coated CoZn-ZIF metal-organic frameworks for fluorescent sensing guanosine triphosphate and discrimination of nucleoside triphosphates
(Elsevier, 2022-05-15) Wang, Zhen; Zhou, Xumei; Han, Jing; Xie, Gang; Liu, Juewen
Imidazole-based metal-organic frameworks (MOFs) are easy to prepare as well-dispersed nanoparticles, which have attracted a lot of interest in sensing. Metal substitution is an effective way to regulate the composition and performance of MOFs. Herein, by tuning the contents of Co and Zn, a series of homobimetallic CoxZn100-x-ZIF (x = 0–100) were synthesized. Using a fluorescently-labeled DNA oligonucleotide probe, guanosine triphosphate (GTP) can readily displace the adsorbed DNA from Co50Zn50-ZIF, resulting in over 30-fold fluorescence enhancement with 1 mM GTP. Co80Zn20-ZIF could specifically recognize adenosine triphosphate (ATP), whereas Co65Zn35-ZIF and Co20Zn80-ZIF responded to both ATP and GTP. For comparison, Co50Ni50-ZIF and Co50Cu50-ZIF were also prepared, but none of them were selective for any of the molecules, indicating a synergetic effect of cobalt and zinc in Co50Zn50-ZIF for the selective recognition of GTP. This system can sensitively detect GTP with a detection limit of 0.13 μM. Moreover, based on the varying binding affinities of these CoZn-ZIFs towards different nucleoside triphosphates (NTPs), a ZIF fluorescent sensor array was also designed for the discrimination of the four types of NTPs.
Stabilization of Gold Nanoparticles by Hairpin DNA and Implications for Label-Free Colorimetric Biosensors
(2022-04-21) Liu, Xun; Zhao, Yu; Ding, Yuzhe; Wang, Jianhua; Liu, Juewen
With extremely high extinction coefficients and other unique optical properties, gold nanoparticles (AuNPs) have received growing interest in developing biosensors. DNA hairpin structures are very popular probes for the detection of not only complementary DNA or RNA but also aptamer targets. This work aims to understand the effect of the structure and sequence of hairpin DNA for the stabilization of AuNPs and its implications in AuNP-based label-free colorimetric biosensors. A series of hairpin DNA with various loop sizes from 4 to 26 bases and sequences (random sequences, poly-A and poly-T) were tested, but they showed similar abilities to protect AuNPs from aggregation. Using hairpin DNA with a tail under the same conditions, optimal protection was achieved with a six-base or longer tail. DNA hairpins are likely adsorbed via their tail regions or with their terminal bases if no tail is present. Molecular dynamics simulations showed that the rigidity of the hairpin loop region disfavored its adsorption to AuNPs, while the flexible tail region is favored. Finally, a DNA sensing assay was conducted using different structured DNA, where hairpin DNA with a tail doubled the sensitivity compared to the tail-free hairpin.
2-Aminopurine Fluorescence Spectroscopy for Probing a Glucose Binding Aptamer
(Chemistry Europe: European Chemical Societies Publishing, 2022-04-25) Lu, Chang; Huang, Po-Jung Jimmy; Zheng, Jingkai; Liu, Juewen
Glucose is the most important analyte for biosensors. Recently a DNA aptamer was reported allowing binding-based detection. However, due to a relatively weak binding affinity, it is difficult to perform binding assays to understand the property of this aptamer. In this work, we replaced the only adenine base in the aptamer binding pocket with a 2-aminopurine (2AP) and used fluorescence spectroscopy to study glucose binding. In the selection buffer, glucose increased the 2AP fluorescence with a Kd of 15.0 mM glucose, which was comparable with the 10 mM Kd previously reported using the strand displacement assay. The binding required two Na+ ions or one Mg2+ that cannot be replaced by Li+ or K+. The binding was weaker at higher temperature and its van't Hoff plot indicated enthalpy-driven binding. While other monosaccharides failed to achieve saturated binding even at high concentrations, two glucose-containing disaccharides, namely trehalose and sucrose, reached a similar fluorescence level as glucose although with over 10-fold higher Kd values. Detection limits in both the selection buffer (0.9 mM) and in artificial interstitial fluids (6.0 mM) were measured.
DNA-Directed Seeded Synthesis of Gold Nanoparticles without Changing DNA Sequence
(Asian Chemical Editorial Society (ACES), 2022-05-06) Lu, Chang; Zandieh, Mohamad; Zheng, Jinkai; Liu, Juewen
DNA has been used for directing the growth of noble metal nanoparticles into different morphologies. Most previous studies focused on the effect of DNA sequence, while the effect of DNA adsorption was not thoroughly explored. In this work, we controlled the seeded growth of AuNPs by using the same DNA sequence but under different initial adsorption conditions: room temperature and heating. DNA adsorbed by heating induced more anisotropic nanoparticle growth, and the most effect was observed with 100 nM C30 DNA, where nanoflowers were obtained for the heated sample. By measuring DNA adsorption and desorption, heating did not increase DNA adsorption density but increased the adsorption affinity. The percentage of adsorbed DNA before the growth was only about 10%, regardless of heating, while after the growth, the associated DNA reached 75% or more, indicating that the free DNA also influenced the growth. This study offers fundamental insights into the effect of DNA adsorption on seeded AuNP growth, providing a method to tune the morphology of nanoparticles without changing DNA sequence.
Capping Gold Nanoparticles to Achieve a Protein-like Surface for Loop-Mediated Isothermal Amplification Acceleration and Ultrasensitive DNA Detection
(Americal Chemical Society, 2022-06-10) Jiang, Xingxing; Yang, Minghui; Liu, Juewen
Loop-mediated isothermal amplification (LAMP) is a popular DNA amplification method. Gold nanoparticles (AuNPs) were reported to enhance the efficiency of LAMP, although the underlying mechanism remained elusive. Since AuNPs strongly adsorb a range of ligands, preadsorbed ligands cannot be easily displaced. In this work, we systematically investigated the effect of surface-modified AuNPs on LAMP by varying the order of mixing of AuNPs with each reagent in the LAMP system (Mg2+, template DNA, dNTPs, primers, and polymerase). Mixing the AuNPs with the primers delayed the LAMP based on SYBR green I fluorescence. While other orders of mixing had little effect, all accelerated the reaction. We then tested other common ligands including polymers (polyethylene glycol and polyvinylpyrrolidone), inorganic ions (Br–), proteins, glutathione (GSH), and DNA (A15) on AuNP-LAMP. The boosted AuNP performance on LAMP was most obvious when the AuNPs formed a protein-like surface. Finally, using GSH-capped AuNPs, a detection limit of around 100 copies/μL–1 of target DNA was achieved. This work has identified a ligand-capped AuNP strategy to boost LAMP and yielded a higher sensitivity in DNA sensing, which also deepens our understanding of AuNP-assisted LAMP.
Binding Studies of Cationic Conjugated Polymers and DNA for Label-Free Fluorescent Biosensors
(American Chemical Society, 2022-07-19) Zhang, Pengbo; Lu, Chang; Niu, Chenqi; Wang, Xiaoyu; Li, Zhengping; Liu, Juewen
Cationic conjugated polymers (CCPs), especially polythiophene, have been extensively used as probes for developing DNA and aptamer-based biosensors. Although many interesting applications have been achieved, a fundamental understanding of this system remains quite limited. In this work, we performed systematic binding assays to understand the interactions between poly(3-(3′-N,N,N-triethylamino-1′-propyloxy)-4-methyl-2,5-thiophene) (PMNT) and DNA. The fluorescence of PMNT at 530 nm initially decreased and then a peak at 580 nm emerged after binding with single-stranded DNA (ssDNA). The binding force between PMNT and DNA was dominated by electrostatic interactions at first and then DNA base-mediated interactions also became important. Since the bases in double-stranded DNA (dsDNA) were shielded, their fluorescence changes were quite different. To best differentiate ssDNA and dsDNA, the optimal pH was between 6 and 8, and the optimal NaCl concentration was around 0.3 M. Moreover, by changing the sequence and length of ssDNA, poly-T had the largest fluorescence shift and poly-A had the smallest change. Under the optimized conditions, the PMNT-based biosensor had a detection limit of 1 nM DNA, which was similar to the SYBR Green I-based assay.
Label-free and Dye-free Fluorescent Sensing of Tetracyclines Using a Capture-Selected DNA Aptamer
(American Chemical Society, 2022-07-01) Zhao, Yichen; Ong, Steven; Chen, Yijing; Huang, Po-Jung Jimmy; Liu, Juewen
Tetracyclines are a group of important antibiotics with a common four-ring scaffold. While most tetracyclines are currently used only in animals, their leaching into the environment and residues in food have caused health concerns. Aptamers are an attractive way to detect tetracyclines, and all previously reported aptamers for tetracyclines were obtained by immobilizing target molecules. In this work, we selected a few DNA aptamers by immobilizing the DNA library using oxytetracycline as the target. We obtained new aptamers with no overlapping sequences compared to the previously reported ones, and a representative sequence named OTC5 had a dissociation constant of 147 nM measured by isothermal titration calorimetry. Similar binding affinities were also observed with tetracycline and doxycycline. Because tetracyclines are fluorescent and their fluorescence intensity was enhanced by binding to the aptamers, a label-free and dye-free fluorescent biosensor was developed with a detection limit of 25 nM oxytetracycline. The sensor was able to detect targets in milk after extraction. Fluorescence polarization measurement showed that this aptamer is insensitive to sodium concentration but requires magnesium. Finally, a strand-displacement biosensor was designed, and it has a detection limit of 1.2 μM oxytetracycline.

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