Applications of gold nanoparticles in ELISA, PCR, and immuno-PCR assays: A review.

Changes in the genetic material can lead to serious human health defects, as mutations in somatic cells may cause cancer and can contribute to other chronic diseases. Genotoxic events can appear at both the DNA, chromosomal or (during mitosis) whole genome level. The study of mechanisms leading to genotoxicity is crucially important, as well as the detection of potentially genotoxic compounds. We consider the current state of the art and describe here the main endpoints applied in standard human in vitro models as well as new advanced 3D models that are closer to the in vivo situation. We performed a literature review of in vitro studies published from 2000–2020 (August) dedicated to the genotoxicity of nanomaterials (NMs) in new models. Methods suitable for detection of genotoxicity of NMs will be presented with a focus on advances in miniaturization, organ-on-a-chip and high throughput methods.

https://www.mdpi.com/2079-4991/10/10/1911/pdf

Genotoxicity of Nanomaterials: Advanced In Vitro Models and High Throughput Methods for Human Hazard Assessment—A Review

Due to several gaps remaining in the toxicological evaluation of nanomaterials (NMs), consumers and public health agencies have shown increasing concern for human health protection. In addition to aluminum (Al) microparticles, Al-containing nanomaterials (Al NMs) have been applied by food industry as additives and contact materials. Due to the limited amount of literature on the toxicity of Al NMs, this study aimed to evaluate the in vivo genotoxic potential of Al0 and Al2O3 NMs after acute oral exposure. Male Sprague-Dawley rats were administered three successive gavages at 6, 12.5 and 25 mg/kg bw. A comparison with AlCl3 was done in order to assess the potential effect of dissolution into Al ions. Both DNA strand breaks and oxidative DNA damage were investigated in six organs/tissues (duodenum, liver, kidney, spleen, blood and bone marrow) with the alkaline and the Fpg-modified comet assays. Concomitantly, chromosomal damage was investigated in bone marrow and colon with the micronucleus assay. The comet assay only showed DNA damage with Al2O3 NMs in bone marrow (BM), while AlCl3 induced slight but non-significant oxidative DNA damage in blood. No increase of chromosomal mutations was observed after treatment with the two Al MNs either in the BM or in the colons of rats.

https://hal-anses.archives-ouvertes.fr/anses-02870263/document

Genotoxicity of Aluminum and Aluminum Oxide Nanomaterials in Rats Following Oral Exposure.

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.

/pdf/transcriptomics-in-toxicogenomics-part-i-experimental-design-3uv65mut29.pdf

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

Bacterial antibiotic resistance in water environments is becoming increasingly severe, and new antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) have also attracted the attention of researchers. The horizontal transfer of ARGs in water environments is considered one of the main sources of bacterial resistance in the natural environment. Horizontal gene transfer (HGT) mainly includes conjugation, natural transformation, and transduction, and conjugation has been investigated most. Several studies have shown that there are a large number of environmental factors that might affect the horizontal transfer of ARGs in water environments, such as nanomaterials, various oxidants, and light; however, there is still a lack of systematic and comprehensive reviews on the detection and the effects of the influence factors of on ARG horizontal transfer. Therefore, this study introduced three HGT modes, analysed the advantages and disadvantages of current methods for monitoring HGT, and then summarized the influence and mechanism of various factors on ARG horizontal transfer, and the possible reasons for the different effects caused by similar factors were mainly critically discussed. Finally, existing research deficiencies and future research directions of ARG horizontal transfer in water environments were discussed. 

Detection and various environmental factors of antibiotic resistance gene horizontal transfer.

Widespread antibiotic resistance genes (ARGs) have caused critical threats to public health on a global scale. Soil, composed mainly of minerals, acts as a source of resistance determinants, playing a considerable role in the development and dissemination of ARGs. The great abundance of ARGs in the soil environment raises concern about the effect of minerals on the spread of ARGs. Herein, the horizontal transfer of a model plasmid pMP2463 containing ARGs from Escherichia coli S17‐1 to Pseudomonas putida KT2440 was monitored following exposure to four common soil minerals, namely, kaolinite, montmorillonite, goethite and birnessite. Birnessite resulted in concentration‐dependent increases in conjugative transfer of plasmid pMP2463 by 1.3–4.3 fold, compared with that in the control group. However, no obvious laws were found in the change of conjugative transfer rate at different concentrations of kaolinite and montmorillonite. As for goethite, the conjugative transfer rate increased firstly and then decreased as the concentration increased. The possible mechanisms underlying birnessite‐induced conjugative transfer of plasmid were explored; birnessite is capable of initiating intracellular reactive oxygen species (ROS) formation, inducing the oxidative stress response. Additionally, birnessite notably facilitated the mRNA expression of the outer membrane protein genes, which contributed to cellular membrane pore formation and horizontal gene transfer, and altered the mRNA expression of conjugative‐related genes that are responsible for conjugative transfer of mobile genetic elements between bacteria. This study triggers questions regarding the potential role of soil minerals in the global dissemination of antimicrobial resistance and provides insights into the interactions between bacteria and minerals in the natural soil environment. HIGHLIGHTS: The effect of soil minerals on conjugative transfer of ARGs was explored. Birnessite induced the concentration‐dependent increase of conjugative transfer. Mechanisms underlying ROS formation, membrane permeability increase, gene expression alteration were revealed. Our results provide evidence for the effect of birnessite on antibiotic resistance dissemination.

Insights into conjugative transfer of antibiotic resistance genes affected by soil minerals

Soil, a potential reservoir of antibiotic resistance genes (ARGs), is inhabited by numerous microorganisms. Many microorganisms in soil are embedded within a self-produced matrix of extracellular p...

An invisible workforce in soil: The neglected role of soil biofilms in conjugative transfer of antibiotic resistance genes

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.

/pdf/impact-of-metal-oxide-nanoparticles-on-in-vitro-dna-1x5s6iseno.pdf

Impact of metal oxide nanoparticles on in vitro DNA amplification

Microfluidics confers unique advantages in microbiological studies as these devices can accurately replicate the micro- and even nano-scale structures of soil to simulate the habitats of bacteria. It not only helps us understand the spatial distribution of bacterial communities (such as biofilms), but also provides mechanistic insights into microbial behaviors including chemotaxis and horizontal gene transfer (HGT). Microfluidics provides a feasible means for real-time, in situ studies and enables in-depth exploration of the mechanisms of interactions in the soil microbiome. This review aims to introduce the basic principles of microfluidic technology and summarize the recent progress in microfluidic devices to study bacterial spatial distribution and functions, as well as biological processes, such bacterial chemotaxis, biofilm streamers (BS), quorum sensing (QS), and HGT. The challenges in and future development of microfluidics for soil microbiological studies are also discussed.

/pdf/zooming-in-to-acquire-micro-reaction-application-of-1sblgrxrnr.pdf

Shan Wu

Papers

Insights into conjugative transfer of antibiotic resistance genes affected by soil minerals

An invisible workforce in soil: The neglected role of soil biofilms in conjugative transfer of antibiotic resistance genes

Impact of metal oxide nanoparticles on in vitro DNA amplification

Zooming in to acquire micro-reaction: Application of microfluidics on soil microbiome

Effects of hematite on the dissemination of antibiotic resistance in pathogens and underlying mechanisms.