Standards for Quantitative Measurement of DNA Damage in Mammalian Cells.

As the potential applications of DNA diagnostics continue to expand, there is a need for improved methods and standards for DNA analysis. This report describes several methods that could be considered for the production of reference materials for the quantitative measurement of DNA damage in mammalian cells. With the focus on DNA strand breaks, potentially useful methods for assessing DNA damage in mammalian cells are reviewed. The advantages and limitations of each method, as well as additional concerns with respect to reference material development, are also discussed. In conclusion, we outline strategies for developing candidate DNA damage reference materials that could be adopted by research laboratories in a wide variety of applications.

Agglomeration of Escherichia coli with Positively Charged Nanoparticles Can Lead to Artifacts in a Standard Caenorhabditis elegans Toxicity Assay.

The increased use and incorporation of engineered nanoparticles (ENPs) in consumer products requires a robust assessment of their potential environmental implications. However, a lack of standardized methods for nanotoxicity testing has yielded results that are sometimes contradictory. Standard ecotoxicity assays may work appropriately for some ENPs with minimal modification but produce artifactual results for others. Therefore, understanding the robustness of assays for a range of ENPs is critical. In this study, we evaluated the performance of a standard Caenorhabditis elegans ( C. elegans) toxicity assay containing an Escherichia coli ( E. coli) food supply with silicon, polystyrene, and gold ENPs with different charged coatings and sizes. Of all the ENPs tested, only those with a positively charged coating caused growth inhibition. However, the positively charged ENPs were observed to heteroagglomerate with E. coli cells, suggesting that the ENPs impacted the ability of nematodes to feed, leading to a false positive toxic effect on C. elegans growth and reproduction. When the ENPs were tested in two alternate C. elegans assays that did not contain E. coli, we found greatly reduced toxicity of ENPs. This study illustrates a key unexpected artifact that may occur during nanotoxicity assays.

Quantification of Carbon Nanotubes in Environmental Matrices: Current Capabilities, Case Studies, and Future Prospects.

Carbon nanotubes (CNTs) have numerous exciting potential applications and some that have reached commercialization. As such, quantitative measurements of CNTs in key environmental matrices (water, soil, sediment, and biological tissues) are needed to address concerns about their potential environmental and human health risks and to inform application development. However, standard methods for CNT quantification are not yet available. We systematically and critically review each component of the current methods for CNT quantification including CNT extraction approaches, potential biases, limits of detection, and potential for standardization. This review reveals that many of the techniques with the lowest detection limits require uncommon equipment or expertise, and thus, they are not frequently accessible. Additionally, changes to the CNTs (e.g., agglomeration) after environmental release and matrix effects can cause biases for many of the techniques, and biasing factors vary among the techniques. Five case studies are provided to illustrate how to use this information to inform responses to real-world scenarios such as monitoring potential CNT discharge into a river or ecotoxicity testing by a testing laboratory. Overall, substantial progress has been made in improving CNT quantification during the past ten years, but additional work is needed for standardization, development of extraction techniques from complex matrices, and multimethod comparisons of standard samples to reveal the comparability of techniques.

DNA damaging potential of photoactivated p25 titanium dioxide nanoparticles.

Titanium dioxide nanoparticles (TiO2 NPs) are found in numerous commercial and personal care products. Thus, it is necessary to understand and characterize their potential environmental health and safety risks. It is well-known that photoactivated TiO2 NPs in aerated aqueous solutions can generate highly reactive hydroxyl radicals ((•)OH), which can damage DNA. Surprisingly, recent in vitro studies utilizing the comet assay have shown that nonphotoactivated TiO2 NPs kept in the dark can also induce DNA damage. In this work, we utilize stable isotope-dilution gas chromatography/tandem mass spectrometry to quantitatively characterize the levels and types of oxidatively generated base lesions in genomic DNA exposed to NIST Standard Reference Material TiO2 NPs (Degussa P25) under precisely controlled illumination conditions. We show that DNA samples incubated in the dark for 24 h with TiO2 NPs (0.5-50 µg/mL) do not lead to the formation of base lesions. However, when the same DNA is exposed to either visible light from 400 to 800 nm (energy dose of ∼14.5 kJ/m(2)) for 24 h or UVA light at 370 nm for 30 min (energy dose of ∼10 kJ/m(2)), there is a significant formation of lesions at the 50 µg/mL dose for the visible light exposure and a significant formation of lesions at the 5 and 50 µg/mL doses for the UVA light exposure. These findings suggest that commercial P25 TiO2 NPs do not have an inherent capacity to oxidatively damage DNA bases in the absence of sufficient photoactivation; however, TiO2 NPs exposed to electromagnetic radiation within the visible portion of the light spectrum can induce the formation of DNA lesions. On the basis of these findings, comet assay processing of cells exposed to TiO2 should be performed in the dark to minimize potential artifacts from laboratory light.

Probing the intracellular glutathione redox potential by in-cell NMR spectroscopy.

Non-invasive and real-time analysis of cellular redox processes has been greatly hampered by lack of suitable measurement techniques. Here we describe an in-cell nuclear magnetic resonance (NMR) based method for measuring the intracellular glutathione redox potential by direct and quantitative measurement of isotopically labeled glutathione introduced exogenously into living yeast. By using this approach, perturbations in the cellular glutathione redox homeostasis were also monitored as yeast cells were subjected to oxidative stress.

Stability-Enhanced Cisplatin Gold Nanoparticles As Therapeutic Anticancer Agents.

Using dendron chemistry, we developed stability enhanced, carboxylate surface modified (negatively charged dendron) AuNPs (Au-NCD). Since the carboxylate surface of Au-NCD is optimal for complexation with cisplatin (Pt) moieties, we further synthesized Pt loaded Au-NCD (Au-NCD/Pt) to serve as potential therapeutic anticancer agents. The size distribution, zeta potential and surface plasmon resonance of both Au-NCDs and Au-NCD/Pt were characterized via dynamic light scattering, scanning transmission electron microscopy and ultraviolet-visible spectrophotometry. Surface chemistry, Pt uptake, and Pt release were evaluated using inductively coupled plasma-mass spectrometry and X-ray photoelectron spectroscopy. Colloidal stability in physiological media over a wide pH range (1 to 13) and shelf-life stability (up to 6 months) were also assessed. Finally, the cytotoxicity of both Au-NCD and Au-NCD/Pt to Chinese hamster ovary cells (CHO K1; as a normal cell line) and to human lung epithelial cells (A549; as a cancer cell line) were evaluated. The results of these physicochemical and functional cytotoxicity studies with Au-NCD/Pt demonstrated that the particles exhibited superlative colloidal stability, cisplatin uptake and in vitro anticancer activity despite low amounts of Pt release from the conjugate.

Size and density measurement of core-shell Si nanoparticles by analytical ultracentrifugation.

Si nanocrystals, terminated with cyclohexane and allylamine, were analyzed using analytical ultracentrifugation (AUC), dynamic light scattering (DLS) and transmission electron microscopy. We found that AUC yielded equivalent particle size distribution data to other nanoparticle characterization techniques, while also providing important information not probed by techniques such as DLS regarding the relative size of the particle core and shell components and the overall effective particle density. Estimates of particle core and shell dimensions are consistent with the particle's optical properties within the quantum confinement representation and available theoretical Si nanocrystal models. Measurement of sedimentation velocity in several solvents with different densities presents a way to circumvent the ambiguity of simultaneous fitting of particle density and sedimentation coefficient and allows us to significantly reduce the uncertainty in the estimates of particle hydrodynamic diameter by finding the effective particle density value.

Quantitative measurements of glutathione in yeast cell lysate using 1H NMR.

Methods for quantifying the level of glutathione (GSH) in yeast cell lysate are described using (1)H NMR analysis. For quantification purposes, the (1)H resonances corresponding to the Cys ßCH2 of GSH were identified as having the fewest overlapping spectral interferences from lysate matrix components using GSH spiked yeast lysate samples. Two methods, standard addition based on peak integration and a spectral subtraction approach, were evaluated for quantifying GSH in lysate samples. The peak integration procedure required baseline estimation and a peak fitting step to correct for background interferences while the spectral subtraction procedure was comparatively straightforward. The level of GSH measured by (1)H NMR was in good agreement with the concentration measured by the DTNB-GSSG reductase recycling assay. The proposed NMR method can lead to a reliable quantitation of GSH and could be applicable to a variety of other analytes of interest in complex biological matrices.

Polyethyleneimine/polyethylene glycol-conjugated gold nanoparticles as nanoscale positive/negative controls in nanotoxicology: testing in frog embryo teratogenesis assay-Xenopus and mammalian tissue culture system.

Despite the great potential of using positively charged gold nanoparticles (AuNPs) in nanomedicine, no systematic studies have been reported on their synthesis optimization or colloidal stability under physiological conditions until a group at the National Institute of Standards and Technology recently succeeded in producing remarkably stable polyethyleneimine (PEI)-coated AuNPs (Au-PEI). This improved version of Au-PEI (Au-PEI25kB) has increased the demand for toxicity and teratogenicity information for applications in nanomedicine and nanotoxicology. In vitro assays for Au-PEI25kB in various cell lines showed substantial active cytotoxicity. For advanced toxicity research, the frog embryo teratogenesis assay-Xenopus (FETAX) method was employed in this study. We observed that positively-charged Au-PEI25kB exhibited significant toxicity and teratogenicity, whereas polyethylene glycol conjugated AuNPs (Au-PEG) used as comparable negative controls did not. There is a characteristic avidity of Au-PEI25kB for the jelly coat, the chorionic envelope (also known as vitelline membrane) and the cytoplasmic membrane, as well as a barrier effect of the chorionic envelope observed with Au-PEG. To circumvent these characteristics, an injection-mediated FETAX approach was utilized. Like treatment with the FETAX method, the injection of Au-PEI25kB severely impaired embryo development. Notably, the survival/concentration curve that was steep when the standard FETAX approach was employed became gradual in the injection-mediated FETAX. These results suggest that Au-PEI25kB may be a good candidate as a nanoscale positive control material for nanoparticle analysis in toxicology and teratology.

Development of a Reference Method and Materials for Quantitative Measurement of UV-Induced DNA Damage in Mammalian Cells: Comparison of Comet Assay and Cell Viability.

Application of DNA damage diagnostic tests is rapidly growing, in particular for ovarian, prostate, and skin cancers; environmental monitoring; chronic and degenerative diseases; and male infertility. Such tests suffer from significant variability among different laboratories due the lack of standardization, experimental validation, and differences in data interpretation. Reference methods and materials for quantitative measurement of UVA-induced DNA damage in mammalian cells are frequently needed. In this study, we examined the use of the single-cell gel electrophoresis (comet) assay to assess the UVA-induced DNA damage in surface-attached Chinese hamster ovary (CHO) cells treated with a photosensitizer as a candidate cellular oxidative damage reference material. We found that the comet images became diffused and the viability of the cells decreased substantially (>20%) as the UVA dose and benzo [a] pyrene (BaP) concentration exceeded 6.3 J/cm2 and 10-6 mol/L BaP. Maintaining the conditions of exposure within this range can improve DNA damage measurement fidelity, particularly if used as a quantitative reference method and to produce materials considered as an in vitro standard for the comet assay.

Photocatalytic activity of nanoparticles: the development of the standardized measurement for physiological conditions.

Recently a new International Standard for testing nanomaterial photocatalytic activity under physiological conditions was issued by Technical Committee 229 (Nanotechnologies) of the International Organization for Standardization (ISO 20814:2019 Nanotechnologies-Testing the photocatalytic activity of nanoparticles for NADH oxidation). The document offers a robust, high throughput photocatalytic assay using a bio-compatible indicator nicotinamide amide dinucleotide (NAD) and provides a screening tool to gauge nanomaterial potency for phototoxicity. This paper describes the measurement principles behind this assay, the scope of the standard and its validation through an interlaboratory comparison study using a traceable standard reference material (SRM 1898).

Titanium Dioxide Induces Apoptosis under UVA Irradiation via the Generation of Lysosomal Membrane Permeabilization-Dependent Reactive Oxygen Species in HaCat Cells.

Titanium dioxide nanoparticles (TiO2 NPs) have wide commercial applications, owing to their small size; however, the biosafety of TiO2 NPs should be evaluated further. In this study, we aimed to investigate the cytotoxicity of TiO2 NPs in the presence and absence of ultraviolet A (UVA) irradiation in human keratinocyte HaCaT cells. TiO2 NPs did not significantly affect cell viability in the absence of UVA irradiation. Nonetheless, UVA-irradiated TiO2 NPs induced caspase-dependent apoptosis of HaCaT cells. Exposure of HaCaT cells to TiO2 NPs and UVA resulted in reactive oxygen species (ROS) generation and lysosomal membrane permeabilization (LMP); both effects were not observed in the absence of UVA irradiation. An analysis of the relationship between LMP and ROS, using CA-074 as a cathepsin inhibitor or NAC as an antioxidant, showed that LMP stimulates ROS generation under these conditions. These results imply that LMP-dependent oxidative stress plays a critical role in the UVA phototoxicity of TiO2 NPs in HaCaT cells.

Genotoxic Effects of Etoposide, Bleomycin, and Ethyl Methanesulfonate on Cultured CHO Cells: Analysis by GC-MS/MS and Comet Assay.

To evaluate methods for analysis of genotoxic effects on mammalian cell lines, we tested the effect of three common genotoxic agents on Chinese hamster ovary (CHO) cells by single-cell gel electrophoresis (comet assay) and gas chromatography-tandem mass spectrometry (GC-MS/MS). Suspension-grown CHO cells were separately incubated with etoposide, bleomycin, and ethyl methanesulfonate and analyzed by an alkaline comet assay and GC-MS/MS. Although DNA strand breaks were detected by the comet assay after treatment with all three agents, GC-MS/MS could only detect DNA nucleobase lesions oxidatively induced by bleomycin. This demonstrates that although GC-MS/MS has limitations in detection of genotoxic effects, it can be used for selected chemical genotoxins that contribute to oxidizing processes. The comet assay, used in combination with GC-MS/MS, can be a more useful approach to screen a wide range of chemical genotoxins as well as to monitor other DNA-damaging factors.

Cellular Reference Materials for DNA Damage Using Electrochemical Oxidation.

Reference materials are needed to quantify the level of DNA damage in cells, to assess sources of measurement variability and to compare results from different laboratories. The comet assay (single cell gel electrophoresis) is a widely used method to determine DNA damage in the form of strand breaks. Here we examine the use of electrochemical oxidation to produce DNA damage in cultured mammalian cells and quantify its percentage using the comet assay. Chinese hamster ovary (CHO) cells were grown on an indium tin oxide electrode surface and exposed 12 h to electrochemical potentials ranging from 0.5 V to 1.5 V (vs Ag/AgCl). The resulting cells were harvested and analyzed by comet and a cell viability assay. We observed a linear increase in the percentage (DNA in tail) of strand breaks along with a loss of cell viability with increasing oxidation potential value. The results indicate that electrochemically induced DNA damage can be produced in mammalian cells under well-controlled conditions and could be considered in making a cellular reference material for the comet assay.

The Impacts of Moisture and Ultraviolet Light on the Degradation of Graphene Oxide/Polymer Nanocomposites.

The extent to which hydrophilic GO nanofillers regulate polymer degradation during exposure to a combination of ultraviolet (UV) radiation and moisture is presently unknown. Accordingly, this study systematically evaluated the effect of GO on polymer degradability under both humid UV and dry UV conditions. Both GO accumulation at the polymer nanocomposite (PNC) surface and GO release following degradation were also investigated. Different mass loadings of GO were incorporated into waterborne polyurethane (WBPU), a commonly used exterior coating, and the resulting GO/WBPU nanocomposites were exposed to precisely controlled accelerated weathering conditions using the NIST Simulated Photodegradation via High Energy Radiant Exposure (SPHERE) device. Thickness loss and infrared spectroscopy measurements indicated GO slightly improved the durability of WBPU under dry UV conditions but not under humid UV conditions. Raman spectroscopy, scanning electron microscopy, and atomic force microscopy modulus measurements indicated that GO accumulation occurred at and near the PNC surface under both conditions but to a more rapid extent under humid UV conditions. Minimal GO release occurred under dry UV conditions as measured with Raman spectroscopy of aqueous run-off from a simulated rain spray applied to degraded PNCs. In contrast, PNC surface transformations under humid UV conditions suggested that GO release occurred.

Toxicity and photosensitizing assessment of gelatin methacryloyl-based hydrogels photoinitiated with lithium phenyl-2,4,6-trimethylbenzoylphosphinate in human primary renal proximal tubule epithelial cells.

Gelatin methacryloyl (GelMA) and lithium phenyl-2,4,6-trimethylbenzoylphosphinate (LAP) photoinitiator are commonly used in combination to produce a photosensitive polymer but there are concerns that must be addressed: the presence of unreacted monomer is well known to be cytotoxic, and lithium salts are known to cause acute kidney injury. In this study, acellular 10% GelMA hydrogels cross-linked with different LAP concentrations and cross-linking illumination times were evaluated for their cytotoxicity, photosensitizing potential, and elastic moduli. Alamar Blue and CyQuant Direct Cell viability assays were performed on human primary renal proximal tubule epithelial cells (hRPTECs) exposed to extracts of each formulation. UV exposure during cross-linking was not found to affect extract cytotoxicity in either assay. LAP concentration did not affect extract cytotoxicity as determined by the Alamar Blue assay but reduced hRPTEC viability in the CyQuant Direct cell assay. Photocatalytic activity of formulation extracts toward NADH oxidation was used as a screening method for photosensitizing potential; longer UV exposure durations yielded extracts with less photocatalytic activity. Finally, elastic moduli determined using nanoindentation was found to plateau to approximately 20-25 kPa after exposure to 342 mJ/cm2 at 2.87 mW of UV-A exposure regardless of LAP concentration. LAP at concentrations commonly used in bioprinting (<0.5% w/w) was not found to be cytotoxic although the differences in cytotoxicity evaluation determined from the two viability assays imply cell membrane damage and should be investigated further. Complete cross-linking of all formulations decreased photocatalytic activity while maintaining predictable final elastic moduli.

Efficient electrochemical degradation of multiwall carbon nanotubes.

As the production mass of multiwall carbon nanotubes (MWCNT) increases, the potential for human and environmental exposure to MWCNTs may also increase. We have shown that exposing an aqueous suspension of pristine MWCNTs to an intense oxidative treatment in an electrochemical reactor, equipped with an efficient hydroxyl radical generating Boron Doped Diamond (BDD) anode, leads to their almost complete mineralization. Thermal optical transmittance analysis showed a total carbon mass loss of over two orders of magnitude due to the electrochemical treatment, a result consistent with measurements of the degraded MWCNT suspensions using UV-vis absorbance. Liquid chromatography data excludes substantial accumulation of the low molecular weight reaction products. Therefore, up to 99% of the initially suspended MWCNT mass is completely mineralized into gaseous products such as CO2 and volatile organic carbon. Scanning electron microscopy (SEM) images show sporadic opaque carbon clusters suggesting the remaining nanotubes are transformed into structure-less carbon during their electrochemical mineralization. Environmental toxicity of pristine and degraded MWCNTs was assessed using Caenorhabditis elegans nematodes and revealed a major reduction in the MWCNT toxicity after treatment in the electrochemical flow-by reactor.

Controlled potential electro-oxidation of genomic DNA.

Exposure of mammalian cells to oxidative stress can result in DNA damage that adversely affects many cell processes. Lack of dependable DNA damage reference materials and standardized measurement methods, despite many case-control studies hampers the wider recognition of the link between oxidatively degraded DNA and disease risk. We used bulk electrolysis in an electrochemical system and gas chromatographic mass spectrometric analysis (GC/MS/MS) to control and measure, respectively, the effect of electrochemically produced reactive oxygen species on calf thymus DNA (ct-DNA). DNA was electro-oxidized for 1 h at four fixed oxidizing potentials (E = 0.5 V, 1.0 V, 1.5 V and 2 V (vs Ag/AgCl)) using a high surface area boron-doped diamond (BDD) working electrode (WE) and the resulting DNA damage in the form of oxidatively-modified DNA lesions was measured using GC/MS/MS. We have shown that there are two distinct base lesion formation modes in the explored electrode potential range, corresponding to 0.5 V < E < 1.5 V and E > 1.5 V. Amounts of all four purine lesions were close to a negative control levels up to E = 1.5 V with evidence suggesting higher levels at the lowest potential of this range (E = 0.5 V). A rapid increase in all base lesion yields was measured when ct-DNA was exposed at E = 2 V, the potential at which hydroxyl radicals were efficiently produced by the BDD electrode. The present results demonstrate that controlled potential preparative electrooxidation of double-stranded DNA can be used to purposely increase the levels of oxidatively modified DNA lesions in discrete samples. It is envisioned that these DNA samples may potentially serve as analytical control or quality assurance reference materials for the determination of oxidatively induced DNA damage.

pH-Sensitive Compounds for Selective Inhibition of Acid-Producing Bacteria.

Stimuli-responsive compounds that provide on-site, controlled antimicrobial activity promise an effective approach to prevent infections, reducing the need for systemic antibiotics. We present a novel pH-sensitive quaternary pyridinium salt (QPS), whose antibacterial activity is boosted by low pH and controlled by adjusting the pH between 4 and 8. Particularly, this compound selectively inhibits growth of acid-producing bacteria within a multispecies community. The successful antibacterial action of this QPS maintains the environmental pH above 5.5, a threshold pH, below which demineralization/erosion takes place. The design, synthesis, and characterization of this QPS and its short-chain analogue are discussed. In addition, their pH-sensitive physicochemical properties in aqueous and organic solutions are evaluated by UV-vis spectroscopy, dynamic light scattering, and NMR spectroscopy. Furthermore, the mechanism of action reveals a switchable assembly that is triggered by acid-base interaction and formed by tightly stacked π-conjugated systems and base moieties. Finally, a model is proposed to recognize the correlated but different mechanisms of pH sensitivity and acid-induced, pH-controlled antibacterial efficacy. We anticipate that successful application of these QPSs and their derivatives will provide protections against infection and erosion through targeted treatments to acid-producing bacteria and modulation of environmental pH.

Porous silicon biosensor for detection of viruses.

There is a growing need for virus sensors with improved sensitivity and dynamic range, for applications including disease diagnosis, pharmaceutical research, agriculture and homeland security. We report here a new method for improving the sensitivity for detection of the bacteriophage virus MS2 using thin films of nanoporous silicon. Porous silicon is an easily fabricated material that has extremely high surface area to volume ratio, making it an ideal platform for surface based sensors. We have developed and evaluated two different methods for covalent bioconjugation of antibodies inside of porous silicon films, and we show that the pore penetration and binding efficiency depend on the wettability of the porous surface. The resulting films were used to selectively capture dye-labeled MS2 viruses from solution, and a viral concentration as low as 2 x 10(7) plaque-forming units per mL (pfu/mL) was detectable by measuring the fluorescence from the exposed porous silicon film. The system exhibits sensitivity and dynamic range similar to the Luminex liquid array-based assay while outperforming protein micro-array methods.