Nanoparticles inhibit DNA replication by binding to DNA: modeling and experimental validation

Beyond the promise: Exploring the complex interactions of nanoparticles within biological systems

The exploration of nanoparticle applications is filled with promise, but their impact on the environment and human health raises growing concerns. These tiny environmental particles can enter the human body through various routes, such as the respiratory system, digestive tract, skin absorption, intravenous injection, and implantation. Once inside, they can travel to distant organs via the bloodstream and lymphatic system. This journey often results in nanoparticles adhering to cell surfaces and being internalized. Upon entering cells, nanoparticles can provoke significant structural and functional changes. They can potentially disrupt critical cellular processes, including damaging cell membranes and cytoskeletons, impairing mitochondrial function, altering nuclear structures, and inhibiting ion channels. These disruptions can lead to widespread alterations by interfering with complex cellular signaling pathways, potentially causing cellular, organ, and systemic impairments. This article delves into the factors influencing how nanoparticles behave in biological systems. These factors include the nanoparticles' size, shape, charge, and chemical composition, as well as the characteristics of the cells and their surrounding environment. It also provides an overview of the impact of nanoparticles on cells, organs, and physiological systems and discusses possible mechanisms behind these adverse effects. Understanding the toxic effects of nanoparticles on physiological systems is crucial for developing safer, more effective nanoparticle-based technologies.

Gold Nanoparticles (AuNPs)-Toxicity, Safety and Green Synthesis: A Critical Review

In recent years, the extensive exploration of Gold Nanoparticles (AuNPs) has captivated the scientific community due to their versatile applications across various industries. With sizes typically ranging from 1 to 100 nm, AuNPs have emerged as promising entities for innovative technologies. This article comprehensively reviews recent advancements in AuNPs research, encompassing synthesis methodologies, diverse applications, and crucial insights into their toxicological profiles. Synthesis techniques for AuNPs span physical, chemical, and biological routes, focusing on eco-friendly "green synthesis" approaches. A critical examination of physical and chemical methods reveals their limitations, including high costs and the potential toxicity associated with using chemicals. Moreover, this article investigates the biosafety implications of AuNPs, shedding light on their potential toxic effects on cellular, tissue, and organ levels. By synthesizing key findings, this review underscores the pressing need for a thorough understanding of AuNPs toxicities, providing essential insights for safety assessment and advancing green toxicology principles.

Cellular Alterations Due to Direct and Indirect Interaction of Nanomaterials with Nucleic Acids

Deoxyribonucleic acid (DNA) represents the main reservoir of genetic information in the cells, which is why it is protected in the nucleus. Entry into the nucleus is, in general, difficult, as the nuclear membrane is a selective barrier to molecules longer than 40 kDa. However, in some cases, the size of certain nanoparticles (NPs) allows their internalization into the nucleus, thus causing a direct effect on the DNA structure. NPs can also induce indirect effects on DNA through reactive oxygen species (ROS) generation. In this context, nanomaterials are emerging as a disruptive tool for the development of novel therapies in a broad range of biomedical fields; although their effect on cell viability is commonly studied, further interactions with DNA or indirect alterations triggered by the internalization of these materials are not always clarified, since the small size of these materials makes them perfectly suitable for interaction with subcellular structures, such as the nucleus. In this context, and using as a reference the predicted interactions presented in a computational model, we describe and discuss the observed direct and indirect effects of the implicated nanomaterials on DNA.

Transport of double-stranded ribonucleic acids (dsRNA) and deoxyribonucleic acids (DNA) in sand and iron oxide-coated sand columns under varying solution chemistries

Assessing ecological risks associated with the use of genetically modified RNA interference crops demands an understanding of the fate of crop-released insecticidal double-stranded RNA (dsRNA) molecules in soils. We studied the adsorption of one dsRNA and two double-stranded DNA as model nucleic acids (NAs) during transport through sand- and iron oxide-coated sand (IOCS)-filled columns over a range of solution pH and ionic compositions. Consistent with NA-sand electrostatic repulsion, we observed only slight retention of NAs in sand columns. Conversely, pronounced NA retention in IOCS columns is consistent with strong and irreversible NA adsorption involving electrostatic attraction to and inner-sphere complex formation of NAs with iron oxide coatings. Adsorption of NAs to iron oxides revealed a fast and a slow kinetic adsorption regime, possibly caused by the excluded-area effect. Adsorption of NAs to sand and IOCS increased in the presence of dissolved Mg2+ and with increasing ionic strength, reflecting cation-bridging and screening of repulsive electrostatics, respectively. The co-solute phosphate and a pre-adsorbed dissolved organic matter isolate competitively suppressed dsRNA adsorption to IOCS. Similar adsorption characteristics of dsRNA and similarly sized DNA suggest that existing information on DNA adsorption to soil particles helps in predicting adsorption and fate of dsRNA molecules in soils.

Nanopesticide risk assessment based on microbiome profiling - Community structure and functional potential as biomarkers in captan@ZnO35-45 nm and captan@SiO220-30 nm treated orchard soil

Nanoformulation should minimise the usage of pesticides and limit their environmental footprint. The risk assessment of two nanopesticides with fungicide captan as an active organic substance and ZnO35-45 nm or SiO220-30 nm as nanocarriers was evaluated using the non-target soil microorganisms as biomarkers. The first time for that kind of nanopesticides next-generation sequencing (NGS) of bacterial 16 S rRNA and fungal ITS region and metagenomics functional predictions (PICRUST2) was made to study structural and functional biodiversity. During a 100-day microcosm study in soil with pesticide application history, the effect of nanopesticides was compared to pure captan and both nanocarriers. Nanoagrochemicals affected microbial composition, especially Acidobacteria-6 class, and alpha diversity, but the observed effect was generally more substantial for pure captan. As for beta diversity, the negative impact was detected only in response to captan and still observed on day 100. Fungal community in the orchard soil showed only a decrease in phylogenetic diversity in captan set-up since day 30. PICRUST2 analysis confirmed several times lower impact of nanopesticides considering the abundance of functional pathways and genes encoding enzymes. Furthermore, the overall data indicated that using SiO220-30 nm as a nanocarrier speeds up a recovery process compared to ZnO35-45 nm.

CeO2 Nanoparticles-Regulated Plasmid Uptake and Bioavailability for Reducing Transformation of Extracellular Antibiotic Resistance Genes

The direct uptake of extracellular DNA (eDNA) via transformation facilitates the dissemination of antibiotic resistance genes (ARGs) in the environment. CeO₂ nanoparticles (NPs) have potential in the regulation of conjugation-dominated ARGs propagation, whereas their effects on ARGs transformation remain largely unknown. Here, CeO₂ NPs at concentrations lower than 50 mg L^-1 have been applied to regulate the transformation of plasmid-borne ARGs to competent Escherichia coli (E. coli) cells. Three types of exposure systems were established to optimize the regulation efficiency. Pre-incubation of competent E. coli cells with CeO₂ NPs at 0.5 mg L^-1 inhibited the transformation (35.4%) by reducing the ROS content (0.9-fold) and cell membrane permeability (0.9-fold), thereby down-regulating the expression of genes related to DNA uptake and processing (bhsA, ybaV, and nfsB, 0.7-0.8 folds). Importantly, CeO₂ NPs exhibited an excellent binding capacity with the plasmids, decreasing the amounts of plasmids available for cellular uptake and down-regulating the gene expression of DNA uptake (bhsA, ybaV, and recJ, 0.6-0.7 folds). Altogether, pre-exposure of plasmids with CeO₂ NPs (10 and 25 mg L^-1) suppressed the transformation with an efficiency of 44.5-51.6%. This study provides a nano-strategy for controlling the transformation of ARGs, improving our understanding on the mechanisms of nanomaterial-mediated ARGs propagation.

Protein-Nanoparticle Interactions Govern the Interfacial Behavior of Polymeric Nanogels: Study of Protein Corona Formation at the Air/Water Interface

Biomedical applications of nanoparticles require a fundamental understanding of their interactions and behavior with biological interfaces. Protein corona formation can alter the morphology and properties of nanomaterials, and knowledge of the interfacial behavior of the complexes, using in situ analytical techniques, will impact the development of nanocarriers to maximize uptake and permeability at cellular interfaces. In this study we evaluate the interactions of acrylamide-based nanogels, with neutral, positive, and negative charges, with serum-abundant proteins albumin, fibrinogen, and immunoglobulin G. The formation of a protein corona complex between positively charged nanoparticles and albumin is characterized by dynamic light scattering, circular dichroism, and surface tensiometry; we use neutron reflectometry to resolve the complex structure at the air/water interface and demonstrate the effect of increased protein concentration on the interface. Surface tensiometry data suggest that the structure of the proteins can impact the interfacial properties of the complex formed. These results contribute to the understanding of the factors that influence the bio-nano interface, which will help to design nanomaterials with improved properties for applications in drug delivery.

Nano-bio interaction: An overview on the biochemical binding of DNA to inorganic nanoparticles for the development of anticancer and antibacterial nano-platforms

It has long been known that inorganic nanoparticles (NPs) can interact with biological macromolecules and show a wider range of biomedical characteristics, including antibacterial, anticancer and antioxidant effects, which cannot be mimicked by their bulky counterparts. It is of great importance in their biomedical applications to study DNA damage in bacterial and cancer cells to develop biocompatible therapeutic nano-platforms derived from inorganic NPs. Therefore, to determine how DNA interacts with inorganic NPs serving as therapeutic agents, thermodynamic and structural studies are essential for an understanding of those mechanisms, thereby allowing for their modulation and manipulation of nano-bio interface. In this paper, we aimed to overview the biophysical techniques typically employ to study DNA-NP interactions as well as the mechanistic aspects of the interaction between different inorganic NPs and calf thymus DNA (CT-DNA), a well-known laboratory model, followed by a survey of different parameters affecting the interaction of NPs and DNA. The molecular interactions between inorganic NPs and DNA were then discussed in relation to their anticancer and antibacterial properties. As a final point, we discussed challenges and future perspectives to put forward the possible applications of the field. In conclusion, the interaction between NPs and DNA needs to be studied more deeply in order to develop potential NP-based anticancer and antibacterial platforms for future clinical applications.

Comparison of In Vitro Approaches to Assess the Antibacterial Effects of Nanomaterials

The antibacterial properties of nanomaterials (NMs) can be exploited in a range of consumer products (e.g., wound dressings, food packaging, textiles, medicines). There is also interest in the exploitation of NMs as treatments for infectious diseases to help combat antibiotic resistance. Whilst the antibacterial activity of NMs has been assessed in vitro and in vivo in numerous studies, the methodology used is very varied. Indeed, while numerous approaches are available to assess the antibacterial effect of NMs in vitro, they have not yet been systematically assessed for their suitability and sensitivity for testing NMs. It is therefore timely to consider what assays should be prioritised to screen the antibacterial properties of NMs. The majority of existing in vitro studies have focused on investigating the antibacterial effects exhibited by silver (Ag) NMs and have employed a limited range of assays. We therefore compared the antibacterial effects of copper oxide (CuO) NMs to Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Bacillus subtilis at various concentrations (12.5-200 µg/mL) using a battery of tests (well and disc diffusion, plate counts-time-kill method, optical density measurement-OD, Alamar Blue and live/dead viability assays, and quantitative polymerase chain reaction). CuO NMs were most toxic to B. subtilis and E. coli, while P. aeruginosa was the least sensitive strain. All assays employed detected the antibacterial activity of CuO NMs; however, they varied in their sensitivity, time, cost, technical difficulty and requirement for specialized equipment. In the future, we suggest that a combination of approaches is used to provide a robust assessment of the antibacterial activity of NMs. In particular, we recommend that the time-kill and OD assays are prioritised due to their greater sensitivity. We also suggest that standard operating protocols are developed so that the antibacterial activity of NMs can be assessed using a harmonised approach.

Impact of Plastic Particles on the Horizontal Transfer of Antibiotic Resistance Genes to Bacterium: Dependent on Particle Sizes and Antibiotic Resistance Gene Vector Replication Capacities

Plastic particles impact the propagation of antibiotic resistance genes (ARGs) in environmental media, and their perturbation on the horizontal gene transfer (HGT) of ARGs is recognized as a critical influencing mechanism. However, studies concerning the influence and influencing mechanisms of plastic particles on the HGT of ARGs were limited, particularly for the effect of particle sizes and ARG vector-associated mechanisms. This study explored the impact of polystyrene (PS) particles with sizes of 75, 90, 100, 1000, and 10000 nm on the HGT (via transformation) of ARGs mediated by pUC19, pSTV29, and pBR322 plasmids into Escherichia coli cells. PS particles with sizes ≤100 nm impacted the transformation of ARGs, but large particles (1000 and 10000 nm) showed no obvious effects. Effects of PS particles on the transfer of three plasmids were vastly distinct. For pUC19 with high replication capacities, the transfer was monotonously promoted. However, for pSTV29 and pBR322 with low replication capacities, suppressing effects were observed. This was attributed to two competing mechanisms. The enhancing mechanism was that the direct interaction of PS particles with membrane lipids and the indirect effect associated with bacterial oxidative stress response induced pore formation on the cell membrane and increased membrane permeability, thus enhancing plasmid entrance. The inhibiting mechanism was that PS particles interfered with plasmid replication inside E. coli, thus decreasing the bacterial tranformation. This study deepened our understanding of the environmental dissemination of ARGs in plastic contamination.

Advanced sanitation products infused with silver nanoparticles for viral protection and their ecological and environmental consequences

The outbreak of coronavirus ailments (COVID-19) in 2019 resulted in public health crisis leading to global pandemonium. In response to the high prevalence of disease transmission, governments all around the globe implemented emergency measures in various routes (e.g., social distancing, personal hygiene, and disinfection of public/private places) to curb/contain COVID-19 infections. The social media infodemic, released as uncensored publishing and/or views/recommendations, also triggered large-scale behavior changes such as the overuse of advanced sanitation products (ASPs) containing nanomaterials. The majority of these ASPs contain silver nanoparticles (AgNPs) as an active ingredient to enhance their antimicrobial potential. Ecotoxicological concerns such as the transformation and degradation of these AgNP-infused products in terrestrial or aquatic environments are under the jurisdiction of the EPA. However, they are not considered in the FDA approval process. In light of excessive consumption of ASPs, it is time to consider their ecotoxicological screening prior to market approval jointly by the FDA and EPA, along with the implementation of post-market surveillance strategies. At the same time, efforts should be put into running awareness programs to prevent the overuse of ASPs.

Mechanism insights into bacterial sporulation at natural sphalerite interface with and without light irradiation: The suppressing role in bacterial sporulation by photocatalysis

Unveiling the mechanisms of bacterial sporulation at natural mineral interfaces is crucial to fully understand the interactions of mineral with microorganism in aquatic environment. In this study, the bacterial sporulation mechanisms of Bacillus subtilis (B. subtilis) at natural sphalerite (NS) interface with and without light irradiation were systematically investigated for the first time. Under dark condition, NS was found to inactivate vegetative cells of B. subtilis and promote their sporulation simultaneously. The released Zn2+ from NS was mainly responsible for the bacterial inactivation and sporulation. With light irradiation, the photocatalytic effect from NS could increase the bacterial inactivation efficiency, while the bacterial sporulation efficiency was decreased from 8.1 % to 4.5 %. The photo-generated H2O2 and O2- played the major roles in enhancing bacterial inactivation and suppressing bacterial sporulation process. The intracellular synthesis of dipicolinic acid (DPA) as biomarker for sporulation was promoted by NS in dark, which was suppressed by the photocatalytic effect of NS with light irradiation. The transformation process from vegetative cells to spores was monitored by both 3D-fluerecence EEM and SEM observations. Compared with the NS alone system, the NS/light combined system induced higher level of intracellular ROSs, up-regulated antioxidant enzyme activity and decreased cell metabolism activity, which eventually led to enhanced inactivation of vegetative cells and suppressed bacterial sporulation. These results not only provide in-depth understanding about bacterial sporulation as a new mode of sub-lethal stress response at NS interface, but also shed lights on putting forward suitable strategies for controlling spore-producing bacteria by suppressing their sporulation during water disinfection.

Application of α-Fe2O3 nanoparticles in controlling antibiotic resistance gene transport and interception in porous media

Metal oxide nanoparticles (MONPs) with a large specific surface area are expected to bind with antibiotic resistance genes (ARGs), thereby controlling ARGs' contamination by reducing their concentration and mobilization. Here, adsorption experiments were carried out and it was found that α-Fe₂O₃ NPs could chemically bind with ARGs (tetM-carrying plasmids) in water with an adsorption rate of 0.04 min^-1 and an adsorption capacity of 7.88 g/kg. Mixing α-Fe₂O₃ NPs into quartz sand column markedly increased the interceptive removal of ARGs from inflow water. The interception rate of 1.0 μg/mL ARGs in ultrapure water (25 mL, 5 pore volumes) through the sand column (plexiglass, length 8 cm, internal diameter 1.4 cm) with 1 g/kg α-Fe₂O₃ NPs was 1.73 times of that through the pure sand column; the interception rate overall increased with increasing addition of α-Fe₂O₃ NPs, reaching 68.8% with 20 g/kg α-Fe₂O₃ NPs. Coexisting Na⁺ (20 mM), Ca²⁺ (20 mM), and acidic condition (pH 4.0) could further increase the interception rate of ARGs by 1 g/kg α-Fe₂O₃ NPs from 21.1% to 86.2%, 90.7%, and 96.2%, respectively. The presence of PO₄^3- and humic acid at environmentally relevant concentrations would not significantly affect the interception of ARGs. In the treatment groups with PO₄^3- and humic acid, the removal rate decreased by only 1.8% and 0.1%, respectively. In addition, the interceptive removal of ARGs by α-Fe₂O₃ NPs-incorporated sand column was even better in actual surface water samples (87.2%) than that in the ultrapure water (21.1%). The findings provide a promising approach to treat ARGs-polluted water.

Influence of biosynthesized silver nanoparticles using red alga Corallina elongata on broiler chicks’ performance

Poultry meat is a great source of protein and provides lots of nutrients such as iodine, iron, zinc, vitamins, and essential fatty acids that humans require. The positive applications of metal nanoparticles (NPs) in the diets of various poultry species were studied, in relation to their metabolic, antibacterial effects on digestion and regulation of bowel function. This study was carried out to test the effects of fabrication green silver nanoparticles (AgNPs) of Corallina elongata extract and/or coating NPs with acetic acid on performance, immune response parameters and micro-flora population in Ross broiler. Chicks’ drinking water was mixed with bio-AgNPs (1 mM) and coating NPs with acetic acid for 35 days. Fourier-transform infrared spectroscopy, electron dispersive spectroscopy (EDS) analysis, scanning electron microscopy, and high resolution transmission electron microscope were used to determine the partial physiochemical characterizations of bio-AgNPs and coating ones. EDS analysis was used to determine the presence of AgNP in meat. Results confirmed that coating NPs with acetic acid reduced percentage of the micro-flora population, which were detected by VITEK® 2 system (BioMérieux, France) and identified as Pseudomonas orizihabitain 4211210040000210 and Sphinogomonas paucimobilis 5201210040000210. EDS analysis of meat chicks confirmed disappearance of Ag metals. Coating biogenic AgNPs with acetic acid on modulated intestinal microbial populations of the Ross broiler may be safe, and could be used as alternative antibiotics or antibacterial agents besides their physiological performance in small intestines of broiler chicken.

Binding Force and Site-Determined Desorption and Fragmentation of Antibiotic Resistance Genes from Metallic Nanomaterials

Interfacial interactions between antibiotic resistance genes (ARGs) and metallic nanomaterials (NMs) lead to adsorption and fragmentation of ARGs, which can provide new avenues for selecting NMs to control ARGs. This study compared the adsorptive interactions of ARGs (tetM-carrying plasmids) with two metallic NMs (ca. 20 nm), i.e., titanium dioxide (nTiO₂) and zero-valent iron (nZVI). nZVI had a higher adsorption rate (0.06 min^-1) and capacity (4.29 mg/g) for ARGs than nTiO₂ (0.05 min^-1 and 2.15 mg/g, respectively). No desorption of ARGs from either NMs was observed in the adsorptive background solution, isopropanol or urea solutions, but nZVI- and nTiO₂-adsorbed ARGs were effectively desorbed in NaOH and NaH₂PO₄ solutions, respectively. Molecular dynamics simulation revealed that nTiO₂ mainly bound with ARGs through electrostatic attraction, while nZVI bound with PO₄^3- of the ARG phosphate backbones through Fe-O-P coordination. The ARGs desorbed from nTiO₂ remained intact, while the desorbed ARGs from nZVI were splintered into small fragments irrelevant to DNA base composition or sequence location. The ARG removal by nZVI remained effective in the presence of PO₄^3-, natural organic matter, or protein at environmentally relevant concentrations and in surface water samples. These findings indicate that nZVI can be a promising nanomaterial to treat ARG pollution.

Toxicity of gold nanoparticles (AuNPs): A review

Gold nanoparticles are a kind of nanomaterials that have received great interest in field of biomedicine due to their electrical, mechanical, thermal, chemical and optical properties. With these great potentials came the consequence of their interaction with biological tissues and molecules which presents the possibility of toxicity. This paper aims to consolidate and bring forward the studies performed that evaluate the toxicological aspect of AuNPs which were categorized into in vivo and in vitro studies. Both indicate to some extent oxidative damage to tissues and cell lines used in vivo and in vitro respectively with the liver, spleen and kidney most affected. The outcome of these review showed small controversy but however, the primary toxicity and its extent is collectively determined by the characteristics, preparations and physicochemical properties of the NPs. Some studies have shown that AuNPs are not toxic, though many other studies contradict this statement. In order to have a holistic inference, more studies are required that will focus on characterization of NPs and changes of physical properties before and after treatment with biological media. So also, they should incorporate controlled experiment which includes supernatant control Since most studies dwell on citrate or CTAB-capped AuNPs, there is the need to evaluate the toxicity and pharmacokinetics of functionalized AuNPs with their surface composition which in turn affects their toxicity. Functionalizing the NPs surface with more peculiar ligands would however help regulate and detoxify the uptake of these NPs.

Multi-biomarker approach to assess the acute effects of cerium dioxide nanoparticles in gills, liver and kidney of Oncorhynchus mykiss

Cerium oxide nanoparticles (CeO₂-NP) have already been detected in the aquatic compartment, however, the evaluation of potential ecotoxicological effects on biota are scarce. The present study aimed to assess the toxic effects of CeO₂-NP in Oncorhynchus mykiss in different organs/tissues (gills, liver and kidney) after acute exposure (96 h) to three concentrations: 0.25, 2.5 and 25 mg/L. Oxidative stress response (catalase - CAT; glutathione S-transferases - GSTs), lipid peroxidation (thiobarbituric acid reactive substances - TBARS), Na⁺/K⁺-ATPase activity, genotoxicity (genetic damage index - GDI) and histopathology (organ's pathological indices) were evaluated. CAT activity was increased in gills and decreased in liver of fish exposed to the highest CeO₂-NPs concentration tested. However, GSTs and Na⁺/K⁺-ATPase activities and TBARS levels were not significantly altered in analysed organs. CeO₂-NP caused marked changes in the gills (aneurysms, blood capillary congestion, lamellar hypertrophy and hyperplasia, secondary lamella fusion and epithelial lifting), in liver (pyknotic nucleus, hyperemia, enlargement of sinusoids and leucocyte infiltration) and kidney (shrinkage of the glomeruli, enlargement of the Bowman space, tubular degeneration and nuclear hypertrophy). Moreover, a semi-quantitative histopathological scoring system (pathological index) confirmed significant alterations in the three organs of all exposed fish. Furthermore, a significant increase of GDI indices observed in gills and liver, for all tested concentrations, indicated a dose-dependent effect. The present study suggests that the release of CeO₂-NP into the aquatic environment promotes biochemical, genotoxic and histopathological damages in fish. However, the mechanisms underlying the occurrence of such effects require further investigation.

Multiparametric Profiling of Engineered Nanomaterials: Unmasking the Surface Coating Effect

Despite considerable efforts, the properties that drive the cytotoxicity of engineered nanomaterials (ENMs) remain poorly understood. Here, the authors inverstigate a panel of 31 ENMs with different core chemistries and a variety of surface modifications using conventional in vitro assays coupled with omics-based approaches. Cytotoxicity screening and multiplex-based cytokine profiling reveals a good concordance between primary human monocyte-derived macrophages and the human monocyte-like cell line THP-1. Proteomics analysis following a low-dose exposure of cells suggests a nonspecific stress response to ENMs, while microarray-based profiling reveals significant changes in gene expression as a function of both surface modification and core chemistry. Pathway analysis highlights that the ENMs with cationic surfaces that are shown to elicit cytotoxicity downregulated DNA replication and cell cycle responses, while inflammatory responses are upregulated. These findings are validated using cell-based assays. Notably, certain small, PEGylated ENMs are found to be noncytotoxic yet they induce transcriptional responses reminiscent of viruses. In sum, using a multiparametric approach, it is shown that surface chemistry is a key determinant of cellular responses to ENMs. The data also reveal that cytotoxicity, determined by conventional in vitro assays, does not necessarily correlate with transcriptional effects of ENMs.

Toxicological alterations induced by subacute exposure of silver nanoparticles in Wistar rats

Silver nanoparticles (AgNPs) have become crucial players in the field of medicine and various other industries. AgNPs have a wide array of applications, which includes production of electronic goods, cosmetics, synthesis of dyes, and printing inks, as well as targeted delivery of drugs to specialized cells inside the body. Even though humans readily come in contact with these particles, the organ-specific accumulation and resulting mechanisms of toxicity induced by inhaled AgNPs are still under investigation. The goal of this study was to determine the organ distribution of inhaled AgNPs and investigate the resulting systemic toxicity. To do this, male Wistar rats were exposed by inhalation to AgNPs for 4 hr/day (200 parts per billion/day) for five consecutive days. The nanoparticles were generated using a laser ablation technique using a soft-landing ion mobility (SLIM) instrument. Inductively coupled plasma mass spectrometric (ICP-MS) analysis showed organ-specific accumulation of the nanoparticles, with the highest concentration present in the lungs, followed by the liver and kidneys. Nanoparticle distribution was characterized in the organs using scanning electron microscopy (SEM) and matrix-assisted laser desorption/ionization mass spectrometric (MALDI-MS) imaging. Bone marrow cytotoxicity assay of the cells from the femur of rats showed micronuclei formation and signs of cellular cytotoxicity. Moreover, rats displayed increased levels of circulating lactate and glutathione disulphide (GSSG), as determined by liquid chromatography-mass spectrometry (LC-MS) analysis. Collectively, our observations suggest that inhaled subacute exposure to AgNP results in accumulation of AgNPs in the lungs, liver, and kidneys, preferentially, as well as mediates induced systemic toxicity.

Proteomics reveals surface electrical property-dependent toxic mechanisms of silver nanoparticles in Chlorella vulgaris

Silver nanoparticles (AgNPs) are known to exert adverse effects on both humans and aquatic organisms; however, the toxic mechanisms underlying these effects remain unclear. In this study, we investigated the toxic mechanisms of various AgNPs with different surface electrical properties in the freshwater algae Chlorella vulgaris using an advanced proteomics approach with Data-Independent Acquisition. Citrate-coated AgNPs (Cit-AgNPs) and polyethyleneimine-coated AgNPs (PEI-AgNPs) were selected as representatives of negatively and positively charged nanoparticles, respectively. Our results demonstrated that the AgNPs exhibited surface electrical property-dependent effects on the proteomic profile of C. vulgaris. In particular, the negatively charged Cit-AgNPs specifically regulated mitochondrial function-related proteins, resulting in the disruption of several associated metabolic pathways, such as those related to energy metabolism, oxidative phosphorylation, and amino acid synthesis. In contrast, the positively charged PEI-AgNPs primarily targeted ribosome function-related proteins and interrupted pathways of protein synthesis and DNA genetic information transmission. In addition, Ag⁺ ions released from the AgNPs had a significant influence on protein regulation and the induction of cellular stress. Collectively, our findings provide new insight into the surface electrical property-dependent proteomic effects of AgNPs on C. vulgaris and should improve our understanding of the toxic mechanisms of AgNPs in freshwater algae.

Effects of graphene oxide on PCR amplification for microbial community survey

BACKGROUND

Graphene oxide (GO) has been suggested as an efficient assistant additive to eliminate non-specific amplification of the polymerase chain reaction (PCR). Although many studies have focused on exploring its molecular mechanism, the practice of GO on the quantitation of microbial community has not been implemented yet. In this study, GO was added in PCR system to explore the changes on removing typical amplification errors, such as chimera and mismatches on two kinds of mock communities (an evenly mixed and a staggered mock communities) and environmental samples.

RESULTS

High-throughput sequencing of bacterial and fungal communities, based on 16S rRNA genes and internal transcribed spacers (ITS) respectively, showed that GO could significantly increase large segmental error (chimeric sequence) in PCR procedure while had no specific effect on point error (mismatched sequence). Besides, GO reduced the α-diversity of community, and changed the composition of fungal community more obviously than bacterial community.

CONCLUSIONS

Our study provides the first quantitative data on microbial community level to prove the negative effect of GO, and also indicates that there may be a more complex interaction between GO and comprehensive DNA fragments in PCR process.

Size Matters: Nano-Biochar Triggers Decomposition and Transformation Inhibition of Antibiotic Resistance Genes in Aqueous Environments

Antibiotic resistance genes (ARGs) are considered to be a type of emerging contaminant; their interaction with biochar (BC) could affect their dissemination and fate in the environment. Although adsorption of ARGs onto bulk-BC has been reported, the interaction with nanosized BC (nano-BC) is largely unknown. In this study, the interactions of a model extracellular DNA (eDNA, calf thymus DNA) and two typical ARGs (ampC and ermB) extracted from a natural river with bulk- and nano-BCs from two pyrolysis temperatures (400 and 700 °C) were investigated. Only adsorption was observed on bulk-BCs, while not only adsorption but also fragmentation of these eDNA molecules was found to occur on nano-BCs. Also, their replication was greatly inhibited by nano-BCs. The electron paramagnetic resonance results indicated that hydroxyl radicals produced from persistent free radicals (PFRs) on nano-BCs played a major role in the damage of eDNA. Moreover, the direct contact with nonradical reacting sites and PFRs on nano-BCs also contributed to the decay of eDNA. Comparatively, PFRs in bulk-BCs were difficult to be reached by eDNA because of steric hindrance and played a negligible role in destroying eDNA. These findings highlight the importance of the size effect in evaluating the reactivity and related environmental risks of PFRs on BC and improve our understanding on the interaction between ARGs and BC.

Studies on binding of single-stranded DNA with reduced graphene oxide-silver nanocomposites

The binding reaction of reduced graphene oxide-silver nanocomposites (rGO-AgNCs) with calf thymus single-stranded DNA (ssDNA) was studied by ultraviolet-visible absorption, fluorescence spectroscopy and circular dichroism (CD), using berberine hemisulphate (BR) dye as a fluorescence probe. The absorbance of ssDNA increases, but the fluorescence intensity is quenched with the addition of rGO-AgNCs. The binding of rGO-AgNCs with ssDNA was able to increase the quenching effects of BR and ssDNA, and induce the changes in CD spectra. All of the evidence indicated that there was a relatively strong interaction between ssDNA and rGO-AgNCs. The data obtained from fluorescence experiments revealed that the quenching process of ssDNA caused by rGO-AgNCs is primarily due to complex formation, i.e. static quenching. The increasing trend of the binding equilibrium constant (Ka) with rising temperature indicated that the binding process was an endothermic reaction. The calculated thermodynamic parameters showed that the binding process was thermodynamically spontaneous, and hydrophobic association played predominant roles in the binding of ssDNA to the surface of rGO-AgNCs.

Comparative study of toxicological assessment of yttrium oxide nano- and microparticles in Wistar rats after 28 days of repeated oral administration

Despite their enormous advantages, nanoparticles (NPs) have elicited disquiet over their safety. Among the numerous NPs, yttrium oxide (Y2O3) NPs are utilised in many applications. However, knowledge about their toxicity is limited, and it is imperative to investigate their potential adverse effects. Therefore, this study explored the effect of 28 days of repeated oral exposure of Wistar rats to 30, 120 and 480 mg/kg body weight (bw) per day of Y2O3 NPs and microparticles (MPs). Before initiation of the study, characterisation of the particles by transmission electron microscopy, dynamic light scattering, Brunauer-Emmett-Teller and laser Doppler velocimetry was undertaken. Genotoxicity was evaluated using the comet and micronucleus (MN) assays. Biochemical markers aspartate transaminase, alanine transaminase, alkaline phosphatase, malondialdehyde, superoxide dismutase, reduced glutathione, catalase and lactate dehydrogenase in serum, liver and kidney were determined. Bioaccumulation of the particles was analysed by inductively coupled plasma optical emission spectrometry. The results of the comet and MN assays showed significant differences between the control and groups treated with 120 and 480 mg/kg bw/day Y2O3 NPs. Significant biochemical alterations were also observed at 120 and 480 mg/kg bw/day. Haematological and histopathological changes were documented. Yttrium (Y) biodistribution was detected in liver, kidney, blood, intestine, lungs, spleen, heart and brain in a dose- and the organ-dependent manner in both the particles. Further, the highest levels of Y were found in the liver and the lowest in the brain of the treated rats. More of the Y from NPs was excreted in the urine than in the faeces. Furthermore, NP-treated rats exhibited much higher absorption and tissue accumulation. These interpretations furnish rudimentary data of the apparent genotoxicity of NPs and MPs of Y2O3 as well as the biodistribution of Y. A no-observed adverse effect level of 30 mg/kg bw/day was found after oral exposure of rats to Y2O3 NPs.

All Roads Lead to the Liver: Metal Nanoparticles and Their Implications for Liver Health

Metal nanoparticles (NPs) are frequently encountered in daily life, and concerns have been raised about their toxicity and safety. Among which, they naturally accumulate in the liver after introduction into the body, independent of the route of administration. Some NPs exhibit intrinsic pharmaceutical effects that are related to their physical parameters, and their inadvertent accumulation in the liver can exert strong effects on liver function and structure. Even as such physiological consequences are often categorically dismissed as toxic and deleterious, there are cell type-specific and NP-specific biological responses that elicit distinctive pharmacological consequences that can be harnessed for good. By limiting the scope of discussion to metallic NPs, this work attempts to provide a balanced perspective on their safety in the liver, and discusses both possible therapeutic benefits and potential accidental liver damage arising from their interaction with specific parenchymal and nonparenchymal cell types in the liver.

Adaptive changes induced by noble-metal nanostructures in vitro and in vivo

The unique features of noble-metal nanostructures (NMNs) are leading to unprecedented expansion of research and exploration of their application in therapeutics, diagnostics and bioimaging fields. With the ever-growing applications of NMNs, both therapeutic and environmental NMNs are likely to be exposed to tissues and organs, requiring careful studies towards their biological effects in vitro and in vivo. Upon NMNs exposure, tissues and cells may undergo a series of adaptive changes both in morphology and function. At the cellular level, the accumulation of NMNs in various subcellular organelles including lysosomes, endoplasmic reticulum, Golgi apparatus, mitochondria, and nucleus may interfere with their functions, causing changes in a variety of cellular functions, such as digestion, protein synthesis and secretion, energy metabolism, mitochondrial respiration, and proliferation. In animals, retention of NMNs in metabolic-, respiratory-, immune-related, and other organs can trigger significant physiological and pathological changes to these organs and influence their functions. Exploring how NMNs interact with tissues and cells and the underlying mechanisms are of vital importance for their future applications. Here, we illustrate the characteristics of NMNs-induced adaptive changes both in vitro and in vivo. Potential strategies in the design of NMNs are also discussed to take advantage of beneficial adaptive changes and avoid unfavorable changes for the proper implementation of these nanoplatforms.

Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects

The starting point of successful hazard assessment is the generation of unbiased and trustworthy data. Conventional toxicity testing deals with extensive observations of phenotypic endpoints in vivo and complementing in vitro models. The increasing development of novel materials and chemical compounds dictates the need for a better understanding of the molecular changes occurring in exposed biological systems. Transcriptomics enables the exploration of organisms' responses to environmental, chemical, and physical agents by observing the molecular alterations in more detail. Toxicogenomics integrates classical toxicology with omics assays, thus allowing the characterization of the mechanism of action (MOA) of chemical compounds, novel small molecules, and engineered nanomaterials (ENMs). Lack of standardization in data generation and analysis currently hampers the full exploitation of toxicogenomics-based evidence in risk assessment. To fill this gap, TGx methods need to take into account appropriate experimental design and possible pitfalls in the transcriptomic analyses as well as data generation and sharing that adhere to the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. In this review, we summarize the recent advancements in the design and analysis of DNA microarray, RNA sequencing (RNA-Seq), and single-cell RNA-Seq (scRNA-Seq) data. We provide guidelines on exposure time, dose and complex endpoint selection, sample quality considerations and sample randomization. Furthermore, we summarize publicly available data resources and highlight applications of TGx data to understand and predict chemical toxicity potential. Additionally, we discuss the efforts to implement TGx into regulatory decision making to promote alternative methods for risk assessment and to support the 3R (reduction, refinement, and replacement) concept. This review is the first part of a three-article series on Transcriptomics in Toxicogenomics. These initial considerations on Experimental Design, Technologies, Publicly Available Data, Regulatory Aspects, are the starting point for further rigorous and reliable data preprocessing and modeling, described in the second and third part of the review series.

Natural sphalerite nanoparticles can accelerate horizontal transfer of plasmid-mediated antibiotic-resistance genes

Minerals and microorganisms are integral parts of natural environments, and they inevitably interact. Antibiotic-resistance genes (ARGs) significantly threaten modern healthcare. However, the effects of natural minerals on ARG propagation in aquatic systems are not fully understood. The present work studied the effects of natural sphalerite (NS) nanoparticles on the horizontal transfer of ARGs from Escherichia coli DH5α (CTX) (donor) to E. coli C600 (Sm) (recipient), and from E. coli DH5α (MCR) (donor) to E. coli C600 (Sm), and their underlying mechanisms. NS particles (0.5-50 mg L^-1) induced an NS-concentration-dependent increase in conjugative transfer frequency. The underlying mechanisms associated with the facilitated ARG transfer included the production of intracellular reactive oxygen species, the SOS response, changes in bacterial cell morphology, and alteration of mRNA levels of bacterial cell membrane protein-related genes and genes associated with conjugative ARG transfer. The information herein offers new mechanistic understanding of risks of bacterial resistance resulting from NS.

Bimetallic gold-silver nanoparticles mediate bacterial killing by disrupting the actin cytoskeleton MreB

The actin cytoskeleton is required for the maintenance of the cell shape and viability of bacteria. It remains unknown to which extent nanoparticles (NPs) can orchestrate the mechanical instability by disrupting the cytoskeletal network in bacterial cells. Our work demonstrates that Au-Ag NPs disrupt the bacterial actin cytoskeleton specifically, fluidize the inner membrane and lead to killing of bacterial cells. In this study, we have tried to emphasize on the key parameters important for NP-cell interactions and found that the shape, specific elemental surface localization and enhanced electrostatic interaction developed due to the acquired partial positive charge by silver atoms in the aggregated NPs are some of the major factors contributing towards better NP interactions and subsequent cell death. In vivo studies in bacterial cells showed that the NPs exerted a mild perturbation of the membrane potential. However, its most striking effect was on the actin cytoskeleton MreB resulting in morphological changes in the bacterial cell shape from rods to predominantly spheres. Exposure to NPs resulted in the delocalization of MreB patches from the membrane but not the tubulin homologue FtsZ. Concomitant with the redistribution of MreB localization, a dramatic increase of membrane fluid regions was observed. Our studies reveal for the first time that Au-Ag NPs can mediate bacterial killing and disrupt the actin cytoskeletal functions in bacteria.

Recent Advances in Magnetite Nanoparticle Functionalization for Nanomedicine

Functionalization of nanomaterials can enhance and modulate their properties and behaviour, enabling characteristics suitable for medical applications. Magnetite (Fe3O4) nanoparticles are one of the most popular types of nanomaterials used in this field, and many technologies being already translated in clinical practice. This article makes a summary of the surface modification and functionalization approaches presented lately in the scientific literature for improving or modulating magnetite nanoparticles for their applications in nanomedicine.

Engineered nanomaterials: From their properties and applications, to their toxicity towards marine bivalves in a changing environment

As a consequence of their unique characteristics, the use of Engineered Nanomaterials (ENMs) is rapidly increasing in industrial, agricultural products, as well as in environmental technology. However, this fast expansion and use make likely their release into the environment with particular concerns for the aquatic ecosystems, which tend to be the ultimate sink for this type of contaminants. Considering the settling behaviour of particulates, benthic organisms are more likely to be exposed to these compounds. In this way, the present review aims to summarise the most recent data available from the literature on ENMs behaviour and fate in aquatic ecosystems, focusing on their ecotoxicological impacts towards marine and estuarine bivalves. The selection of ENMs presented here was based on the OECD's Working Party on Manufactured Nanomaterials (WPMN), which involves the safety testing and risk assessment of ENMs. Physical-chemical characteristics and properties, applications, environmental relevant concentrations and behaviour in aquatic environment, as well as their toxic impacts towards marine bivalves are discussed. Moreover, it is also identified the impacts derived from the simultaneous exposure of marine organisms to ENMs and climate changes as an ecologically relevant scenario.

Impact of metal oxide nanoparticles on in vitro DNA amplification

Polymerase chain reaction (PCR) is used as an in vitro model system of DNA replication to assess the genotoxicity of nanoparticles (NPs). Prior results showed that several types of NPs inhibited PCR efficiency and increased amplicon error frequency. In this study, we examined the effects of various metal oxide NPs on inhibiting PCR, using high- vs. low-fidelity DNA polymerases; we also examined NP-induced DNA mutation bias at the single nucleotide level. The effects of seven major types of metal oxide NPs (Fe₂O₃, ZnO, CeO₂, Fe₃O₄, Al₂O₃, CuO, and TiO₂) on PCR replication via a low-fidelity DNA polymerase (Ex Taq) and a high-fidelity DNA polymerase (Phusion) were tested. The successfully amplified PCR products were subsequently sequenced using high-throughput amplicon sequencing. Using consistent proportions of NPs and DNA, we found that the effects of NPs on PCR yield differed depending on the DNA polymerase. Specifically, the efficiency of the high-fidelity DNA polymerase (Phusion) was significantly inhibited by NPs during PCR; such inhibition was not evident in reactions with Ex Taq. Amplicon sequencing showed that the overall error rate of NP-amended PCR was not significantly different from that of PCR without NPs (p > 0.05), and NPs did not introduce single nucleotide polymorphisms during PCR. Thus, overall, NPs inhibited PCR amplification in a DNA polymerase-specific manner, but mutations were not introduced in the process.

3D hybrid structures based on biomimetic membranes and Caryophyllus aromaticus - "green" synthesized nano-silver with improved bioperformances

The paper describes an innovative bio-design of some hybrid nanoarchitectures containing bioartificial membranes and silver nanoparticles phytogenerated by using a natural extract Caryophyllus aromaticus (cloves) that contains many bioactive compounds. Two kinds of liposomes with and without chlorophyll a (Chla) obtained through thin film hydration method were used to achieve bio-green-generated hybrids by a simple, cost effective bottom-up approach. The characteristic peaks of CE-nAg monitored by UV-Vis absorption have firstly demonstrated the biohybrids formation. The slightly blue shift and fluorescence quenching observed by fluorescence emission spectra highlighted the formation of hybrid systems by biointeraction between lipid vesicles and silver nanoparticles. The incorporation of silver nanoparticles in lipid vesicles resulted in significant changes of FT-IR spectra of liposomes, indicating a reorganization of biomimetic membranes. All the microscopic methods (SEM, AFM and TEM) confirmed the biosynthesis of "green" AgNPs together with associated biohybrids, their spherical and quasi-spherical shapes with nano-scaled size. By TEM assay it was shown that CE-nAg are surrounded by petal like cloud structures that consist of biopolymers like proteins or polysaccharides and other phytochemicals arising from clove extract. EDS spectra confirmed the formation of phyto-nanoAg and also the presence of silver in the biohybrids. In addition, Selected Area Electron Diffraction showed characteristic polycrystalline ring patterns for a cubic structure of the clove-generated AgNPs. The hybrid materials showed efficient physical stability,i.e. ξ value of -28.0 mV (for biohybrids without Chla, BH) and of -31.7 mV (for biohybrids labelled with Chla, Chla-BH), assured by strong electrostatic repulsive forces between particles. The "green" nano-silver particles (CE-nAg) showed remarkable antioxidant activity (AA = 90.2%). The biohybrids loaded with clove-AgNPs proved to be more effective, scavenging about 98.8% of free radicals (in case of Chla-BH), and of 92.6% (in case of BH). The antibacterial effectiveness showed that green AgNPs combine in a synergistic manner the antibacterial properties of clove extract with those of silver, resulting in an enhancement of inhibition diameter, by 20%. Chla-BH proved to be more potent against Escherichia coli, than BH, exhibiting an inhibition diameter of 42 mm. Regarding the in vitro cytotoxicity against tumour cells, the CE-nAg concentration significantly influenced the cell viability, i.e. IC₅₀ was 3.6% (v/v) for HT-29 cells. Chla-BH was more effective against HT-29 cancer cells at the concentrations ranging from 0 to 18% (v/v), when the normal cells were not affected. Clove-generated AgNPs exhibited haemolytic activity against hRBCs, while the biohybrids were haemocompatible. The action mechanism on the two cell lines (mouse fibroblast L929 cells and human colorectal adenocarcinoma HT-29 cells) investigated by fluorescence microscopy demonstrated that CE-nAg killed almost all the cells (94%) through necrosis at a concentration of 33.4% (v/v). The treatment of HT-29 cells with BH resulted in: 71.5% viable cells, 19.5% apoptotic and only 9% necrotic cells, while in the case of Chla-BH treatment, only 77.5% cells were viable, 16% cells were apoptotic and 6.5% were necrotic. In this way, the developed silver-based nanoparticles can represent viable promoters to develop new biohybrids with improved features, e.g. antioxidant and antibacterial effectiveness, haemolytic activity and greater specificity towards tumour cells.

New Insights into Black Carbon Nanoparticle-Induced Dispersibility of Goethite Colloids and Configuration-Dependent Sorption for Phenanthrene

Black carbon nanoparticles (nano-BC) are one of the most active components in pyrogenic carbonaceous matter and involved in many biogeochemical processes. This study investigated heteroaggregation of nano-BC with goethite (a model of natural mineral colloids) and the configuration effect of heteroaggregates on phenanthrene (PHE) sorption. Nano-BC could significantly enhance the dispersion of goethite via heteroaggregation when its concentration was higher than the critical concentration ( C_c). The C_c was dependent on the surface potential of nano-BC, which was directly measured for the first time in this study. Configuration and stability of the heteroaggregates were regulated by BC-goethite mass ratio and solution pH. At pH 5.3, oppositely charged goethite and nano-BC interacted with each other through electrostatic attraction and the configuration of heteroaggregates was dependent on BC-goethite mass ratio. At pH 7.4, where both goethite and nano-BC were negatively charged, they heteroaggregated with each other mainly through H-bonding and Lewis acid-base mechanisms, and the configuration of heteroaggregates was independent of BC-goethite mass ratio. For PHE sorption, small-sized heteroaggregates were more favorable than large ones due to the higher content of active sorption sites. Interestingly, at a higher concentration of PHE, we found that the solute molecules could probably penetrate into and/or alter the configuration of heteroaggregates and enhance its sorption capacity for PHE. These findings are useful for understanding the effect of nano-BC on colloidal stability and organic compound sorption of minerals.

The effects of a human food additive, titanium dioxide nanoparticles E171, on Drosophila melanogaster - a 20 generation dietary exposure experiment

In this study, fruit flies (Drosophila melanogaster) were exposed to an estimated daily human E171 consumption concentration for 20 generations. Exposure to E171 resulted in: a change in normal developmental and reproductive dynamics, reduced fecundity after repetitive breeding, increased genotoxicity, the appearance of aberrant phenotypes and morphologic changes to the adult fat body. Marks of adaptive evolution and directional selection were also exhibited. The larval stages were at a higher risk of sustaining damage from E171 as they had a slower elimination rate of TiO2 compared to the adults. This is particularly worrisome, since among the human population, children tend to consume higher daily concentrations of E171 than do adults. The genotoxic effect of E171 was statistically higher in each subsequent generation compared to the previous one. Aberrant phenotypes were likely caused by developmental defects induced by E171, and were not mutations, since the phenotypic features were not transferred to any progeny even after 5 generations of consecutive crossbreeding. Therefore, exposure to E171 during the early developmental period carries a higher risk of toxicity. The fact that the daily human consumption concentration of E171 interferes with and influences fruit fly physiological, ontogenetic, genotoxic, and adaptive processes certainly raises safety concerns.

Atomic Force Microscopy Imaging Study of Aligning DNA by Dumbbell-like Au-Fe3O4 Magnetic Nanoparticles

Studies on nucleic acid structure and interactions between nucleic acid and its binding molecules are of great importance for understanding and controlling many important biological processes. Atomic force microscopy (AFM) imaging is one of the most efficient methods to disclose the DNA structure and binding modes between DNA and DNA-binding molecules. Long-chain DNA tends to form a random coiled structure, which prevents direct AFM imaging observation of the subtle structure formed by DNA itself or protein binding. Aligning DNA from the random coiled state into the extended state is not only important for applications in DNA nanotechnology but also for elucidating the interaction mechanism between DNA and other molecules. Here, we developed an efficient method based on the magnetic field to align long-chain DNA on a silicon surface. We used AFM imaging to study the alignment of DNA at the single-molecule level, showing that DNA can be stretched and highly aligned by the manipulation of magnetic nanoparticles tethered to one end of DNA and that the aligned DNA can be imaged clearly by AFM. In the absence of the magnetic field, the aligned DNA can relax back to a random coiled state upon rinsing. Such alignment and relaxation can be repeated many times, which provides an efficient method for the manipulation of individual DNA molecules and the investigation of DNA and DNA-binding molecule interactions.

Challenges facing nanotoxicology and nanomedicine due to cellular diversity

This review examines the interaction of nanomaterials (NMs) with cells from the perspective of major cellular differentiations. The structure and composition of cells reflect their role and function in a particular organ or environment. The normal differentiated-state and diseased cells may respond to NMs very differently. This review progresses with due care on nanotoxicology while emphasizing the potential of NMs in treating stress-associated disorders, including cancer and degeneration. The striking potential of NMs in inducing ROS, scavenging ROS, depleting cellular antioxidants, replenishing antioxidants, mimicking antioxidant enzyme activity, and modulating the immune system all show their considerable potential in treating cancer and other aging-associated disorders. It is now clear that NMs become more active and versatile when they come into contact with biological machinery, surprisingly in some cases, in a manner dependent on cell type. The mechanisms leading to the contrasting bioresponse of NMs ranging from toxicity to anticancer and from cell survival to carcinogenicity followed by their immuno-modulating potential show NMs to be a highly promising agent in biomedical therapy. This first-of-its-kind article seeks the challenges to be addressed that could provide a solid rationale in translating the promises of nanomedicine. A thorough understanding of normal and cancer biology could help to minimize the gap between basic and translational research in nanotechnology-based therapy.

Grouping of nanomaterials to read-across hazard endpoints: from data collection to assessment of the grouping hypothesis by application of chemoinformatic techniques

BACKGROUND

An increasing number of manufactured nanomaterials (NMs) are being used in industrial products and need to be registered under the REACH legislation. The hazard characterisation of all these forms is not only technically challenging but resource and time demanding. The use of non-testing strategies like read-across is deemed essential to assure the assessment of all NMs in due time and at lower cost. The fact that read-across is based on the structural similarity of substances represents an additional difficulty for NMs as in general their structure is not unequivocally defined. In such a scenario, the identification of physicochemical properties affecting the hazard potential of NMs is crucial to define a grouping hypothesis and predict the toxicological hazards of similar NMs. In order to promote the read-across of NMs, ECHA has recently published "Recommendations for nanomaterials applicable to the guidance on QSARs and Grouping", but no practical examples were provided in the document. Due to the lack of publicly available data and the inherent difficulties of reading-across NMs, only a few examples of read-across of NMs can be found in the literature. This manuscript presents the first case study of the practical process of grouping and read-across of NMs following the workflow proposed by ECHA.

METHODS

The workflow proposed by ECHA was used and slightly modified to present the read-across case study. The Read-Across Assessment Framework (RAAF) was used to evaluate the uncertainties of a read-across within NMs. Chemoinformatic techniques were used to support the grouping hypothesis and identify key physicochemical properties.

RESULTS

A dataset of 6 nanoforms of TiO₂ with more than 100 physicochemical properties each was collected. In vitro comet assay result was selected as the endpoint to read-across due to data availability. A correlation between the presence of coating or large amounts of impurities and negative comet assay results was observed.

CONCLUSION

The workflow proposed by ECHA to read-across NMs was applied successfully. Chemoinformatic techniques were shown to provide key evidence for the assessment of the grouping hypothesis and the definition of similar NMs. The RAAF was found to be applicable to NMs.

Methods of protein corona isolation for magnetic nanoparticles

Nanoparticles (NPs) in contact with a biological environment get covered by proteins and some are loosely bound and some are tightly bound. The latter form a hard protein corona (HPC) which is known to determine their biological behavior. Therefore, in order to study the biological behaviour of NPs one needs to start from the HPC. However, established methods and standards of HPC isolation are still not known. This is especially a challenge in the case of magnetic NPs which form a major branch of nanomedicine. Therefore, we developed a novel HPC isolation method, a multi-step centrifugation method (MSCM), for single-domain magnetic NPs. The MSCM was applied to iron oxide NPs in interaction with human blood and lymph serum with different dilutions in triplicate. The analysis of the composition of the obtained HPCs showed the reproducibility of the MSCM. This new method was also compared with the existing magnetic separation method (MagSep) and a study of the obtained HPC allowed us to establish the validity limits of MagSep and MSCM on only superparamagnetic NPs and on any single-domain magnetic NPs, respectively. Surprisingly, the HPCs obtained by these two isolation methods were quite different, up to 50%, suggesting that only these proteins, which are found in the HPCs of both isolation methods, are in fact real HPCs.

Development of nanoparticle-assisted PCR assay in the rapid detection of brain-eating amoebae

Brain-eating amoebae (Acanthamoeba spp., Balamuthia mandrillaris, Naegleria fowleri) have gained increasing attention owing to their capacity to produce severe human and animal infections involving the brain. Early detection is a pre-requisite in successful prognosis. Here, we developed a nanoPCR assay for the rapid detection of brain-eating amoebae using various nanoparticles. Graphene oxide, copper and alumina nanoparticles used in this study were characterized using Raman spectroscopy measurements through excitation with a He-Ne laser, while powder X-ray diffraction patterns were taken on a PANanalytical, X'Pert HighScore diffractometer and the morphology of the materials was confirmed using high-resolution transmission electron microscopy (HRTEM). Using nanoparticle-assisted PCR, the results revealed that graphene oxide, copper oxide and alumina nanoparticles significantly enhanced PCR efficiency in the detection of pathogenic free-living amoebae using genus-specific probes. The optimal concentration of graphene oxide, copper oxide and alumina nanoparticles for Acanthamoeba spp. was determined at 0.4, 0.04 and 0.4 μg per mL respectively. For B. mandrillaris, the optimal concentration was determined at 0.4 μg per mL for graphene oxide, copper oxide and alumina nanoparticles, and for Naegleria, the optimal concentration was 0.04, 4.0 and 0.04 μg per mL respectively. Moreover, combinations of these nanoparticles proved to further enhance PCR efficiency. The addition of metal oxide nanoparticles leads to excellent surface effect, while thermal conductivity property of the nanoparticles enhances PCR productivity. These findings suggest that nanoPCR assay has tremendous potential in the clinical diagnosis of parasitic infections as well as for studying epidemiology and pathology and environmental monitoring of other microbes.

A comparison of methods to assess the antimicrobial activity of nanoparticle combinations on bacterial cells

BACKGROUND

Bacterial cell quantification after exposure to antimicrobial compounds varies widely throughout industry and healthcare. Numerous methods are employed to quantify these antimicrobial effects. With increasing demand for new preventative methods for disease control, we aimed to compare and assess common analytical methods used to determine antimicrobial effects of novel nanoparticle combinations on two different pathogens.

METHODS

Plate counts of total viable cells, flow cytometry (LIVE/DEAD BacLight viability assay) and qPCR (viability qPCR) were used to assess the antimicrobial activity of engineered nanoparticle combinations (NPCs) on Gram-positive (Staphylococcus aureus) and Gram-negative (Pseudomonas aeruginosa) bacteria at different concentrations (0.05, 0.10 and 0.25 w/v%). Results were analysed using linear models to assess the effectiveness of different treatments.

RESULTS

Strong antimicrobial effects of the three NPCs (AMNP0-2) on both pathogens could be quantified using the plate count method and flow cytometry. The plate count method showed a high log reduction (>8-log) for bacteria exposed to high NPC concentrations. We found similar antimicrobial results using the flow cytometry live/dead assay. Viability qPCR analysis of antimicrobial activity could not be quantified due to interference of NPCs with qPCR amplification.

CONCLUSION

Flow cytometry was determined to be the best method to measure antimicrobial activity of the novel NPCs due to high-throughput, rapid and quantifiable results.

Elucidating the mechanism of the considerable mechanical stiffening of DNA induced by the couple Zn2+/Calix[4]arene-1,3-O-diphosphorous acid

The couple Calix[4]arene-1,3-O-diphosphorous acid (C4diP) and zinc ions (Zn²⁺) acts as a synergistic DNA binder. Silicon NanoTweezer (SNT) measurements show an increase in the mechanical stiffness of DNA bundles by a factor of >150, at Zn²⁺ to C4diP ratios above 8, as compared to Zinc alone whereas C4diP alone decreases the stiffness of DNA. Electroanalytical measurements using 3D printed devices demonstrate a progression of events in the assembly of C4diP on DNA promoted by zinc ions. A mechanism at the molecular level can be deduced in which C4diP initially coordinates to DNA by phosphate-phosphate hydrogen bonds or in the presence of Zn²⁺ by Zn²⁺ bridging coordination of the phosphate groups. Then, at high ratios of Zn²⁺ to C4diP, interdigitated dimerization of C4diP is followed by cross coordination of DNA strands through Zn²⁺/C4diP inter-strand interaction. The sum of these interactions leads to strong stiffening of the DNA bundles and increased inter-strand binding.

MiRNA extraction from cell-free biofluid using protein corona formed around carboxyl magnetic nanoparticles

MicroRNA (miRNA) in urine has been considered as a potential biomarker for early-stage diagnosis of multiple diseases like urinary system cancer, kidney injury and diabetes, owing to their many demonstrated advantages including long-term stability and noninvasiveness. However, the traditional enrichment and extraction processes of miRNAs from urine are cumbersome and tedious due to the low concentration and multiple carriers of miRNAs. Herein, we present a novel method to collect low concentrations of miRNAs from dilute solutions such as urine and cell culture medium. 10-nm core sized magnetic nanoparticles with carboxylic acid coating can adsorb low-concentration proteins, and form protein corona which makes them easy to aggregate and precipitate for subsequent isolation. In urine and cell culture medium, these nanoparticles can aggregate with proteins, including miRNAs-associated protein Argonaute 2 and microvesicle-related proteins, to form precipitates, so that miRNAs can be easily extracted from pellets by small amount of lysis buffer for subsequent analysis such as real-time PCR. Our method provides a facile way to enrich miRNAs from biofluids without the need of ultracentrifugation and immunoprecipitations, bringing remarkable convenience to miRNAs-based biomarker research.

Transformation of CuO Nanoparticles in the Aquatic Environment: Influence of pH, Electrolytes and Natural Organic Matter

Many studies have shown the effect of solution chemistry on the environmental behavior of metal-based nanoparticles (NPs), except CuO NPs. Here, we investigated the agglomeration, sedimentation, dissolution, and speciation of CuO NPs by varying pH, ionic strength, ionic valence, and natural organic matter (NOM). The results showed that as the pH moved away from 6, the size of CuO agglomerates decreased, along with the enhanced NP suspension stabilization, due to the increase of electrostatic repulsive force. Increasing ionic strength and valence intensified the agglomeration and sedimentation of CuO NPs because of the compression of electrical double layers. The presence of humic acid and citric acid enhanced the dispersion and stabilization of CuO NP suspension, but l-cysteine showed a different impact. Decreasing pH, increasing ionic strength and all NOM improved the dissolution of CuO NPs, but the divalent electrolyte (CaCl₂) inhibited the Cu²⁺ release from CuO NPs compared to the monovalent electrolyte (NaCl). In addition, X-ray absorption near edge structure (XANES) analysis demonstrated that the presence of l-cysteine transformed more than 30% of CuO NPs to Cu(I)-cysteine by coordinating with thiol group. This study can give us an in-depth understanding on the environmental behavior and fate of CuO NPs in the aquatic environment.