Adeno-associated virus genome quantification with amplification-free CRISPR-Cas12a.

Efficient manufacturing of recombinant Adeno-Associated Viral (rAAV) vectors to meet rising clinical demand remains a major hurdle. One of the most significant challenges is the generation of large amounts of empty capsids without the therapeutic genome. There is no standardized analytical method to accurately quantify the viral genes, and subsequently the empty-to-full ratio, making the manufacturing challenges even more complex. We propose the use of CRISPR diagnostics (CRISPR-Dx) as a robust and rapid approach to determine AAV genome titers. We designed and developed the CRISPR-AAV Evaluation (CRAAVE) assay to maximize sensitivity, minimize time-to-result, and provide a potentially universal design for quantifying multiple transgene constructs encapsidated within different AAV serotypes. We also demonstrate an on-chip CRAAVE assay with lyophilized reagents to minimize end user assay input. The CRAAVE assay was able to detect AAV titers as low as 7e7 vg/mL with high precision (<3% error) in quantifying unknown AAV titers when compared with conventional quantitative PCR (qPCR) method. The assay only requires 30 min of assay time, shortening the analytical workflow drastically. Our results suggest CRISPR-Dx could be a promising tool for efficient rAAV genome titer quantification and has the potential to revolutionize biomanufacturing process analytical technology (PAT).

In Vivo Effects of Silver Nanoparticles on Development, Behavior, and Mitochondrial Function are Altered by Genetic Defects in Mitochondrial Dynamics.

Silver nanoparticles (AgNPs) are extensively used in consumer products and biomedical applications, thus guaranteeing both environmental and human exposures. Despite extensive research addressing AgNP safety, there are still major knowledge gaps regarding AgNP toxicity mechanisms, particularly in whole organisms. Mitochondrial dysfunction is frequently described as an important cytotoxicity mechanism for AgNPs; however, it is still unclear if mitochondria are the direct targets of AgNPs. To test this, we exposed the nematodeCaenorhabditis elegans to sublethal concentrations of AgNPs and assessed specific mitochondrial parameters as well as organismal-level endpoints that are highly reliant on mitochondrial function, such as development and chemotaxis behavior. All AgNPs tested significantly delayed nematode development, disrupted mitochondrial bioenergetics, and blocked chemotaxis. However, silver was not preferentially accumulated in mitochondria, indicating that these effects are likely not due to direct mitochondria-AgNP interactions. Mutant nematodes with deficiencies in mitochondrial dynamics displayed both greater and decreased susceptibility to AgNPs compared to wild-type nematodes, which was dependent on the assay and AgNP type. Our study suggests that AgNPs indirectly promote mitochondrial dysfunction, leading to adverse outcomes at the organismal level, and reveals a role of gene-environment interactions in the susceptibility to AgNPs. Finally, we propose a novel hypothetical adverse outcome pathway for AgNP effects to guide future research.

Dosing, Not the Dose: Comparing Chronic and Pulsed Silver Nanoparticle Exposures.

The environmental impacts of manufactured nanoparticles are often studied using high-concentration pulse-additions of freshly synthesized nanoparticles, while predicted releases are characterized by chronic low-concentration additions of weathered particles. To test the effects in wetlands of addition rate and nanoparticle speciation on water column silver concentrations, ecosystem impacts, and silver accumulation by biota, we conducted a year-long mesocosm experiment. We compared a pulse addition of Ag0-NPs to chronic weekly additions of either Ag0-NPs or sulfidized silver nanoparticles. The initially high water column silver concentrations in the pulse treatment declined such that after 4 weeks it was lower on average than in the two chronic treatments. While the pulse caused a marked increase in dissolved methane in the first week of the experiment, the chronic treatments had smaller increases in methane concentration that were more prolonged between weeks 28-45. Much like water column silver, most organisms in chronic treatments had comparable silver concentrations to the pulse treatment after only 4 weeks, and all but one organism had similar or higher concentrations than the pulse treatment after one year. Pulse exposures thus both overestimate the intensity of short-term exposures and effects and underestimate the more realistic long-term exposure, ecosystem effects, and accumulation seen in chronic exposures.

Impacts of Pristine and Transformed Ag and Cu Engineered Nanomaterials on Surficial Sediment Microbial Communities Appear Short-Lived.

Laboratory-based studies have shown that many soluble metal and metal oxide engineered nanomaterials (ENM) exert strong toxic effects on microorganisms. However, laboratory-based studies lack the complexity of natural systems and often use "as manufactured" ENMs rather than more environmentally relevant transformed ENMs, leaving open the question of whether natural ligands and seasonal variation will mitigate ENM impacts. Because ENMs will accumulate in subaquatic sediments, we examined the effects of pristine and transformed Ag and Cu ENMs on surficial sediment microbial communities in simulated freshwater wetlands. Five identical mesocosms were dosed through the water column with either Ag(0), Ag2S, CuO or CuS ENMs (nominal sizes of 4.67 ± 1.4, 18.1 ± 3.2, 31.1 ± 12, and 12.4 ± 4.1, respectively) or Cu(2+). Microbial communities were examined at 0, 7, 30, 90, 180, and 300 d using qPCR and high-throughput 16S rRNA gene sequencing. Results suggest differential short-term impacts of Ag(0) and Ag2S, similarities between CuO and CuS, and differences between Cu ENMs and Cu(2+). PICRUSt-predicted metagenomes displayed differential effects of Ag treatments on photosynthesis and of Cu treatments on methane metabolism. By 300 d, all metrics pointed to reconvergence of ENM-dosed mesocosm microbial community structure and composition, suggesting that the long-term microbial community impacts from a pulse of Ag or Cu ENMs are limited.

Nanoparticle Surface Affinity as a Predictor of Trophic Transfer.

Nanoscale materials, whether natural, engineered, or incidental, are increasingly acknowledged as important components in large, environmental systems with potential implications for environmental impact and human health. Mathematical models are a useful tool for handling the rapidly increasing complexity and diversity of these materials and their exposure routes. Presented here is a mathematical model of trophic transfer driven by nanomaterial surface affinity for environmental and biological surfaces, developed in tandem with an experimental functional assay for determining these surface affinities. We found that nanoparticle surface affinity is a strong predictor of uptake through predation in a simple food web consisting of the algae Chlorella vulgaris and daphnid Daphnia magna. The mass of nanoparticles internalized by D. magna through consuming nanomaterial-contaminated algae varied linearly with surface-attachment efficiency. Internalized quantities of gold nanoparticles in D. magna ranged from 8.3 to 23.6 ng/mg for nanoparticle preparations with surface-attachment efficiencies ranging from 0.07 to 1. This model, coupled with the functional-assay approach, may provide a useful screening tool for existing materials as well as a predictive model for their development.

Cysteine-induced modifications of zero-valent silver nanomaterials: implications for particle surface chemistry, aggregation, dissolution, and silver speciation.

The persistence of silver nanoparticles in aquatic environments and their subsequent impact on organisms depends on key transformation processes, which include aggregation, dissolution, and surface modifications by metal-complexing ligands. Here, we studied how cysteine, an amino acid representative of thiol ligands that bind monovalent silver, can alter the surface chemistry, aggregation, and dissolution of zero-valent silver nanoparticles. We compared nanoparticles synthesized with two coatings, citrate and polyvinylpirrolidone (PVP), and prepared nanoparticle suspensions (approximately 8 µM total Ag) containing an excess of cysteine (400 µM). Within 48 h, up to 47% of the silver had dissolved, as indicated by filtration of the samples with a 0.025-µm filter. Initial dissolution rates were calculated from the increase of dissolved silver concentration when particles were exposed to cysteine and normalized to the available surface area of nanoparticles in solution. In general, the rates of dissolution were almost 3 times faster for citrate-coated nanoparticles relative to PVP-coated nanoparticles. Rates tended to be slower in solutions with higher ionic strength in which the nanoparticles were aggregating. X-ray absorption spectroscopy analysis of the particles suggested that cysteine adsorbed to silver nanoparticles surfaces through the formation of Ag(+I)--sulfhydryl bonds. Overall, the results of this study highlight the importance of modifications by sulfhydryl-containing ligands that can drastically influence the long-term reactivity of silver nanoparticles in the aquatic environment and their bioavailability to exposed organisms. Our findings demonstrate the need to consider multiple interlinked transformation processes when assessing the bioavailability, environmental risks, and safety of nanoparticles, particularly in the presence of metal-binding ligands.

Size-controlled dissolution of organic-coated silver nanoparticles.

The solubility of Ag NPs can affect their toxicity and persistence in the environment. We measured the solubility of organic-coated silver nanoparticles (Ag NPs) having particle diameters ranging from 5 to 80 nm that were synthesized using various methods, and with different organic polymer coatings including poly(vinylpyrrolidone) and gum arabic. The size and morphology of Ag NPs were characterized by transmission electron microscopy (TEM). X-ray absorption fine structure (XAFS) spectroscopy and synchrotron-based total X-ray scattering and pair distribution function (PDF) analysis were used to determine the local structure around Ag and evaluate changes in crystal lattice parameters and structure as a function of NP size. Ag NP solubility dispersed in 1 mM NaHCO(3) at pH 8 was found to be well correlated with particle size based on the distribution of measured TEM sizes as predicted by the modified Kelvin equation. Solubility of Ag NPs was not affected by the synthesis method and coating as much as by their size. Based on the modified Kelvin equation, the surface tension of Ag NPs was found to be ∼1 J/m(2), which is expected for bulk fcc (face centered cubic) silver. Analysis of XAFS, X-ray scattering, and PDFs confirm that the lattice parameter, a, of the fcc crystal structure of Ag NPs did not change with particle size for Ag NPs as small as 6 nm, indicating the absence of lattice strain. These results are consistent with the finding that Ag NP solubility can be estimated based on TEM-derived particle size using the modified Kelvin equation for particles in the size range of 5-40 nm in diameter.

Mechanism of silver nanoparticle toxicity is dependent on dissolved silver and surface coating in Caenorhabditis elegans.

The rapidly increasing use of silver nanoparticles (Ag NPs) in consumer products and medical applications has raised ecological and human health concerns. A key question for addressing these concerns is whether Ag NP toxicity is mechanistically unique to nanoparticulate silver, or if it is a result of the release of silver ions. Furthermore, since Ag NPs are produced in a large variety of monomer sizes and coatings, and since their physicochemical behavior depends on the media composition, it is important to understand how these variables modulate toxicity. We found that a lower ionic strength medium resulted in greater toxicity (measured as growth inhibition) of all tested Ag NPs to Caenorhabditis elegans and that both dissolved silver and coating influenced Ag NP toxicity. We found a linear correlation between Ag NP toxicity and dissolved silver, but no correlation between size and toxicity. We used three independent and complementary approaches to investigate the mechanisms of toxicity of differentially coated and sized Ag NPs: pharmacological (rescue with trolox and N-acetylcysteine), genetic (analysis of metal-sensitive and oxidative stress-sensitive mutants), and physicochemical (including analysis of dissolution of Ag NPs). Oxidative dissolution was limited in our experimental conditions (maximally 15% in 24 h) yet was key to the toxicity of most Ag NPs, highlighting a critical role for dissolved silver complexed with thiols in the toxicity of all tested Ag NPs. Some Ag NPs (typically less soluble due to size or coating) also acted via oxidative stress, an effect specific to nanoparticulate silver. However, in no case studied here was the toxicity of a Ag NP greater than would be predicted by complete dissolution of the same mass of silver as silver ions.

Plasmonic flow cytometry by immunolabeled nanorods.

Fluorescence-based flow cytometry measures multiple cellular characteristics, including levels of receptor expression, by assessing the fluorescence intensity from a population of cells whose cell surface receptors are bound by a fluorescently labeled antibody or ligand for that receptor. Functionalized noble metal nanoparticles provide a complementary method of receptor labeling based on plasmonics for population analysis by flow cytometry. The potential benefits of using plasmonic nanoparticles to label cell surface receptors in flow cytometry include scattering intensity from a single particle that is equivalent to fluorescence intensity of 105 fluorescein molecules, biocompatibility and low cytotoxicity, and nonquenching optical properties. The large spectral tunability of nanorods also provides convenient access to plasmonic markers with peak surface plasmon resonances ranging from 600 to 2,200 nm, unlike gold nanosphere markers that are limited to visible wavelengths. Gold nanorod-based plasmonic flow cytometry is demonstrated herein by comparing the scattering of cells bound to anti-epidermal growth factor receptor (EGFR)-conjugated nanorods to the emission of cells bound to anti-EGFR-conjugated fluorescent labels. EGFR-expressing cells exhibited a statistically significant six-fold increase in scattering when labeled with anti-EGFR-conjugated nanorods compared with labeling with IgG1-conjugated nanorods. Large scattering intensities were observed despite using a 1,000-fold lower concentration of nanorod-conjugated antibody relative to the fluorescently labeled antibody.

Spatially addressable chemoselective C-terminal ligation of an intein fusion protein from a complex mixture to a hydrazine-terminated surface.

Protein immobilization on surfaces is useful in many areas of research, including biological characterization, antibody purification, and clinical diagnostics. A critical limitation in the development of protein microarrays and heterogeneous protein-based assays is the enormous amount of work and associated costs in the purification of proteins prior to their immobilization onto a surface. Methods to address this problem would simplify the development of interfacial diagnostics that use a protein as the recognition element. Herein, we describe an approach for the facile, site-specific immobilization of proteins on a surface without any preprocessing or sample purification steps that ligates an intein fusion protein at its C-terminus by reaction with a hydrazine group presented by a surface. Furthermore, we demonstrate that this methodology can directly immobilize a protein directly from cell lysate onto a protein-resistant surface. This methodology is also compatible with soft lithography and inkjet printing so that one or more proteins can be patterned on a surface without the need for purification.

Dual-order snapshot spectral imaging of plasmonic nanoparticles.

The development of truly scalable, multiplexed optical microarrays requires a detection platform capable of simultaneous detection of multiple signals in real-time. We present a technique we term dual-order snapshot spectroscopic imaging (DOSSI) and demonstrate that it can be effectively used to collect spectrally resolved images of a full field of view of sparsely located spots in real time. Resonant peaks of plasmonic gold nanoparticles were tracked as a function of their surrounding refractive index. Measurement uncertainty analysis indicated that the spectral resolution of DOSSI in the described configuration is approximately 0.95 nm. Further, real-time measurements by DOSSI allowed discrimination between optically identical nanoparticles that were functionalized with two homologous small molecule ligands that bound to the same protein, albeit with different affinity, based purely on their different molecular interaction kinetics-a feat not possible with slower raster-type hyperspectral imaging systems, or other dark-field optical detection systems that solely rely on end point measurements. Kinetic measurements of plasmon bands by DOSSI can be performed with a relatively simple optical system, thereby opening up the possibility of developing low-cost detectors for arrayed plasmonic diagnostics.

Silver nanoparticle toxicity is related to coating materials and disruption of sodium concentration regulation.

Silver nanoparticles (AgNPs) have been increasingly commercialized and their release into the environment is imminent. Toxicity of AgNP has been studied with a wide spectrum of organisms, yet the mechanism of toxicity remains largely unknown. This study systematically compared toxicity of 10 AgNPs of different particle diameters and coatings to Japanese medaka (Oryzias latipes) larvae to understand how characteristics of AgNP relate to toxicity. Dissolution of AgNPs was largely dependent on particle size, but their aggregation behavior and toxicity were more dependent on coating materials. 96 h lethal concentration 50% (LC50) values correlated with AgNP aggregate size rather than size of individual nanoparticles. Of the AgNPs studied, the dissolved Ag concentration in the test suspensions did not account for all of the observed toxicity, indicating the role of NP-specific characteristics in resultant toxicity. Exposure to AgNP led to decrease of sodium concentration in the tissue and increased expression of Na(+)/K(+ )ATPase. Gene expression patterns also suggested that toxicity was related to disruption of sodium regulation and not to oxidative stress.

Decreased Uptake and Enhanced Mitochondrial Protection Underlie Reduced Toxicity of Nanoceria in Human Monocyte-Derived Macrophages.

Cerium dioxide nanoparticles (nanoceria), currently used as catalysts including additives to diesel fuel, also present potential as a novel therapeutic agent for disorders involving oxidative stress. However, little is known about the effects of nanoceria on primary human cells involved in the innate immune response. Here, we evaluate nanoceria effects on monocyte derived macrophages (MDMs) from healthy human subjects. Peripheral blood monocytes were isolated from healthy human volunteers. MDMs were obtained by maturing monocytes over a five-day period. MDMs were exposed to well-characterized nanoceria suspensions (0, 5, 10, 20 µg/mL) for 24 or 48 hours. We evaluated particle uptake, ultrastructural changes, cytotoxicity, and mitochondrial damage in MDMs through transmission electron microscopy (TEM), confocal imaging, flow cytometry, spectrometry, western blots, and immunofluorescence techniques. The role that intracellular concentration of nanoceria plays in the toxicity of MDMs was evaluated by 3D image analysis and compared to monocytes as a nanoceria sensitive cell model. Nanoceria failed to induce cytotoxicity in MDMs at the tested doses. Nanoceria-exposed MDMs showed no mitochondrial damage and displayed significant accumulation of anti-apoptotic proteins (Mcl-1 and Bcl-2) during the maturation process. TEM and confocal analyses revealed efficient uptake of nanoceria by MDMs, however 3D image analyses revealed lower nanoceria accumulation per unit cell volume in MDMs compared to monocytes. Taken together, our results suggest that mitochondrial protection and reduced volume-corrected intracellular nanoparticle concentration account for the lower sensitivity of human MDMs to nanoceria.

Characterization of physicochemical properties of nanomaterials and their immediate environments in high-throughput screening of nanomaterial biological activity.

Thousands of nanomaterials (NMs) are in commerce and few have toxicity data. To prioritize NMs for toxicity testing, high-throughput screening (HTS) of biological activity may be the only practical and timely approach to provide the necessary information. As in all nanotoxicologic studies, characterization of physicochemical properties of NMs and their immediate environments in HTS is critical to understanding how these properties affect NM bioactivity and to allow extrapolation to NMs not screened. The purpose of the study, the expert-groups-recommended minimal characterization, and NM physicochemical properties likely to affect measured bioactivity all help determine the scope of characterization. A major obstacle in reaping the full benefits of HTS for NMs is the low throughput of NM physicochemical characterization, which may require more sample quantity than HTS assays. Increasing the throughput and speed, and decreasing the amount of NMs needed for characterization are crucial. Finding characterization techniques and biological activity assays compatible with diverse classes of NMs is a challenge and multiple approaches for the same endpoints may be necessary. Use of computational tools and nanoinformatics for organizing and analyzing data are important to fully utilize the power of HTS. Other desired advances include the ability to more fully characterize: pristine NM without prior knowledge of NM physicochemical properties; non-pristine NMs (e.g., after use); NM in not-perfectly-dispersed suspension; and NM in biological samples at exposure-relevant conditions. Through combining HTS and physicochemical characterization results, we will better understand NM bioactivities, prioritize NMs for further testing, and build computational models to predict NM toxicity.

Uptake of silver nanoparticles and toxicity to early life stages of Japanese medaka (Oryzias latipes): effect of coating materials.

Silver nanoparticles (AgNPs) with antimicrobial properties are perhaps the most deployed engineered nanomaterials in consumer products. Almost all AgNPs are coated with organic materials to enhance their dispersion in water. Contributions of coatings to the toxicity of NPs have received little attention. Studies using AgNPs with one of three different coating materials (citrate (Cit), gum arabic (GA), and polyvinylpyrrolidone (PVP)) showed significantly different toxicity. GA AgNP proved to be the most toxic, while PVP and Cit AgNP exhibited similar and lower toxicity. However, all AgNPs were about three to ten times less toxic than AgNO(3) when their toxicities were compared on a mass-concentration basis. Evidence for NP-specific toxicity was observed with longer time for initiation of toxicity and increased incidence of resultant spinal flexure of medaka exposed to AgNPs, compared to AgNO(3). Hyperspectral imaging of 6 µm paraffin sections of fish exposed to AgNPs revealed AgNPs and their aggregates in tissues of fish. Gill distribution was ubiquitous, while small amounts were found in other organs, including the liver and brain. AgNPs were observed regularly in the gut lumen, but rarely in mural elements and mesentery. These results suggest that while ingestion was common, gills were the principal sites of AgNP uptake. In conclusion, AgNPs is a source of toxic Ag ions, while itself contribute partially to its toxicity to fish, and which interact with skin surface and were taken up via the gills.

Intracellular uptake and associated toxicity of silver nanoparticles in Caenorhabditis elegans.

Silver nanoparticles (AgNPs) are frequently used as antimicrobials. While the mechanism(s) by which AgNPs are toxic are unclear, their increasing use raises the concern that release into the environment could lead to environmental toxicity. We characterized the physicochemical behavior, uptake, toxicity (growth inhibition), and mechanism of toxicity of three AgNPs with different sizes and polyvinylpyrrolidone (PVP) or citrate coatings to the nematode Caenorhabditis elegans. We used wild-type (N2) C. elegans and strains expected to be sensitive to oxidative stress (nth-1, sod-2 and mev-1), genotoxins (xpa-1 and nth-1), and metals (mtl-2). Using traditional and novel analytical methods, we observed significant aggregation and extra-organismal dissolution of silver, organismal uptake and, in one case, transgenerational transfer of AgNPs. We also observed growth inhibition by all tested AgNPs at concentrations in the low mg/L levels. A metallothionein-deficient (mtl-2) strain was the only mutant tested that exhibited consistently greater AgNP sensitivity than wild-type. Although all tested AgNPs were internalized (passed cell membranes) in C. elegans, at least part of the toxicity observed was mediated by ionic silver. Finally, we describe a modified growth assay that permits differentiation between direct growth-inhibitory effects and indirect inhibition mediated by toxicity to the food source.

Rational selection of gold nanorod geometry for label-free plasmonic biosensors.

We present the development of an analytical model that can be used for the rational design of a biosensor based on shifts in the local surface plasmon resonance (LSPR) of individual gold nanoparticles. The model relates the peak wavelength of light scattered by an individual plasmonic nanoparticle to the number of bound analyte molecules and provides an analytical formulation that predicts relevant figures-of-merit of the sensor such as the molecular detection limit (MDL) and dynamic range as a function of nanoparticle geometry and detection system parameters. The model calculates LSPR shifts for individual molecules bound by a nanorod, so that the MDL is defined as the smallest number of bound molecules that is measurable by the system, and the dynamic range is defined as the maximum number of molecules that can be detected by a single nanorod. This model is useful because it will allow a priori design of an LSPR sensor with figures-of-merit that can be optimized for the target analyte. This model was used to design an LSPR sensor based on biotin-functionalized gold nanorods that offers the lowest MDL for this class of sensors. The model predicts a MDL of 18 streptavidin molecules for this sensor, which is in good agreement with experiments and estimates. Further, we discuss how the model can be utilized to guide the development of future generations of LSPR biosensors.

Label-free plasmonic detection of biomolecular binding by a single gold nanorod.

We report the use of individual gold nanorods as plasmonic transducers to detect the binding of streptavidin to individual biotin-conjugated nanorods in real time on a surface. Label-free detection at the single-nanorod level was performed by tracking the wavelength shift of the nanorod-localized surface plasmon resonant scattering spectrum using a dark-field microspectroscopy system. The lowest streptavidin concentration that was experimentally measured was 1 nM, which is a factor of 1000-fold lower than the previously reported detection limit for streptavidin binding by biotinylated single plasmonic nanostructures. We believe that the current optical setup is able to reliably measure wavelength shifts as small as 0.3 nm. Binding of streptavidin at 1 nM concentration induces a mean resonant wavelength shift of 0.59 nm suggesting that we are currently operating at close to the limit of detection of the system.

Plasmonic detection of a model analyte in serum by a gold nanorod sensor.

We describe the fabrication of a label-free, chip-based biosensor based on the localized surface plasmon resonance (LSPR) of gold nanorods. Gold nanorods were chemisorbed onto a mercaptosilane-modified glass substrate, followed by conjugation of biotin to the nanorods. Streptavidin binding to biotin was monitored by the wavelength shift of the LSPR peak in the UV-vis extinction spectrum of the immobilized gold nanorods due to the change in local refractive index at the gold nanorod surface induced by streptavidin binding. The limit of detection of the sensor is 0.005 microg/mL (94 pM) in PBS and 1 microg/mL (19 nM) in serum, and the dynamic range spans 94 pM to 0.19 microM. The advantages of the nanorod-based sensor over an LSPR sensor that we had previously fabricated from gold nanospheres (Nath, N.; Chilkoti, A. Anal. Chem. 2002, 74, 504-509; J. Fluoresc. 2004, 14, 377-389; Anal. Chem. 2004, 76, 5370-5378) are the significantly lower detection limit and the internal self-reference that the signal of the nanorod sensor provides based on the measurement of peak wavelength shift.