Metabolomic Fingerprint Assay in Zebrafish Embryos

In order for new drugs to enter the market, extensive studies are needed to examine toxic effects. Among others, teratogenicity studies are of paramount importance. Of even higher importance is to gain knowledge on the biological responses that take place upon drug exposure, so as to have a better understanding of the molecular mechanisms that govern developmental changes. Metabolomics is the research field that studies the changes in the chemical composition of metabolites contained within cells. Conducting metabolomics studies results in valuable information. Zebrafish is a vertebrate model organism that bridges in vivo assays and in vivo studies. In this chapter, we propose a metabolomic fingerprint assay for the study of metabolic changes in zebrafish embryos upon exposure to various drugs. The metabolome of zebrafish is extracted, and the 1H-NMR spectrum is recorded. Using open-access metabolomic databases, a list of tentative metabolites is retrieved. The presence of the tentative metabolites is further confirmed by UHPLC-HRMS. Ultimately, after a metabolic pathway analysis, the metabolic network is revealed and useful conclusions can be drawn.

Two-Birds-with-One-Stone Synthesis of Hydrophilic and Hydrophobic Fluorescent Carbon Nanodots from Dunaliella salina Biomass as 4-Nitrophenol Nanoprobes Based on Inner Filter Effect and First Derivative Redshift of Emission Band

4-Nitrophenol (4-NP) has been listed as a priority pollutant and has also been reported as a human urinary metabolite used as a marker to evaluate exposure to certain pesticides. In the work herein, a solvothermal approach is applied to the one-pot synthesis of both hydrophilic and hydrophobic fluorescent carbon nanodots (CNDs), utilizing the halophilic microalgae Dunaliella salina as a biomass precursor. Both kinds of the produced CNDs showed appreciable optical properties and quantum yields, good photostability and they were capable of probing 4-NP by quenching their fluorescence through the inner filter effect. Interestingly, a prominent 4-NP concentration-dependent redshift of the corresponding emission band of the hydrophilic CNDs was noticed, which was further exploited, for the first time, as an analytical platform. Capitalizing on these properties, analytical methods were developed and applied to a variety of matrixes, such as tap water, treated municipal wastewater and human urine. The method based on the hydrophilic CNDs (λ_ex/λ_em: 330/420 nm) was linear in the range of 0.80-45.0 μM and showed acceptable recoveries (from 102.2 to 113.7%) with relative standard deviations of 2.1% (intra-day) and 2.8% (inter-day) for the quenching-based detection mode and 2.9% (intra-day) and 3.5% (inter-day) for the redshift one. The method based on the hydrophobic CNDs (λ_ex/λ_em: 380/465 nm) was linear in the range of 1.4-23.0 μM, with recoveries laying within the range of 98.2-104.5% and relative standard deviations of 3.3% and 4.0% for intra-day and inter-day assays, respectively.

Untargeted metabolomics of human keratinocytes reveals the impact of exposure to 2,6-dichloro-1,4-benzoquinone and 2,6-dichloro-3-hydroxy-1,4-benzoquinone as emerging disinfection by-products

INTRODUCTION

The 2,6-dichloro-1,4-benzoquinone (DCBQ) and its derivative 2,6-dichloro-3-hydroxy-1,4-benzoquinone (DCBQ-OH) are disinfection by-products (DBPs) and emerging pollutants in the environment. They are considered to be of particular importance as they have a high potential of toxicity and they are likely to be carcinogenic.

OBJECTIVES

In this study, human epidermal keratinocyte cells (HaCaT) were exposed to the DCBQ and its derivative DCBQ-OH, at concentrations equivalent to their IC₂₀ and IC₅₀, and a study of the metabolic phenotype of cells was performed.

METHODS

The perturbations induced in cellular metabolites and their relative content were screened and evaluated through a metabolomic study, using 1H-NMR and MS spectroscopy.

RESULTS

Changes in the metabolic pathways of HaCaT at concentrations corresponding to IC₂₀ and IC₅₀ of DCBQ-OH involved the activation of cell membrane α-linolenic acid, biotin, and glutathione and deactivation of glycolysis/gluconeogenesis at IC₅₀. The changes in metabolic pathways at IC₂₀ and IC₅₀ of DCBQ were associated with the activation of inositol phosphate, pertaining to the transfer of messages from the receptors of the membrane to the interior as well as with riboflavin. Deactivation of biotin metabolism was recorded, among others. The cells exposed to DCBQ exhibited a concentration-dependent decrease in saccharide concentrations. The concentration of steroids increased when cells were exposed to IC₂₀ and decreased at IC₅₀. Although both chemical factors stressed the cells, DCBQ led to the activation of transporting messages through phosphorylated derivatives of inositol.

CONCLUSION

Our findings provided insights into the impact of the two DBPs on human keratinocytes. Both chemical factors induced energy production perturbations, oxidative stress, and membrane damage.

Metabolomic Profiling Unveils the Impact of Non-Doped and Heteroatom-Doped Carbon Nanodots on Zebrafish (Danio rerio) Embryos

Recently, concern has been raised over the transport, transformation, and fate of carbon nanodots (CNDs) after their release into the environment. Their toxicity towards organisms and humans has recently been addressed as an important issue. In this study, a metabolomic approach was employed to obtain an insight into the effect of CNDs (either pristine or doped with nitrogen and nitrogen/sulfur) on zebrafish. Embryos were exposed to concentrations corresponding to lethal concentration (LC) LC₅₀ (550, 400, and 150 μg mL⁻¹), LC_50/2 (275, 200, and 75 μg mL⁻¹), and LC_50/4 (138, 100, and 38 μg mL⁻¹) of the three CNDs (non-doped, N-doped, and N,S-codoped, respectively) to scrutinize the interactions of the CNDs with the larvae. Numerous differences in the metabolic pathways were recorded in all cases. Seven metabolic pathways were detected in the control larvae. When the larvae were exposed to concentrations equal to LC₅₀, LC_50/2, and LC_50/4 of non-doped CNDs, 12, 12, and 3 metabolic pathways were detected, respectively. In the case of N-doped CNDs, 4, 7, and 4 pathways were detected, while in the case of N,S-codoped CNDs, 8, 5, and 5 pathways were detected when exposed to concentrations of LC₅₀, LC_50/2, and LC_50/4, respectively. In all cases, certain metabolic pathways were altered while others were either down-regulated or up-regulated. Some of these changes include the activation of alanine, aspartate, and glutamate metabolism, aminoacyl-tRNA biosynthesis, butanoate metabolism, D-glutamine, and D-glutamate metabolism, glutathione metabolism, selenoamino acid metabolism, valine, leucine, and isoleucine degradation pathways. Moreover, the deactivation of starch and sucrose metabolism, the glycine, serine, and threonine metabolism, among others, were recorded. Our findings underline the importance to further study the impact of CNDs on marine organisms. As zebrafish has been shown to share many similarities with humans in bioprocesses and genome, it can be assumed that CNDs may also pose a threat to human health.

Sponges and Sponge-Like Materials in Sample Preparation: A Journey from Past to Present and into the Future

Even though instrumental advancements are constantly being made in analytical chemistry, sample preparation is still considered the bottleneck of analytical methods. To this end, researchers are developing new sorbent materials to improve and replace existing ones, with the ultimate goal to improve current methods and make them more efficient and effective. A few years ago, an alternative trend was started toward sample preparation: the use of sponge or sponge-like materials. These materials possess favorable characteristics, such as negligible weight, open-hole structure, high surface area, and variable surface chemistry. Although their use seemed promising, this trend soon reversed, due to either the increasing use of nanomaterials in sample preparation or the limited scope of the first materials. Currently, with the development of new materials, such as melamine sponges, along with the advancement in nanotechnology, this topic was revived, and various functionalizations were carried out on such materials. The new materials are used as sorbents in sample preparation in analytical chemistry. This review explores the development of such materials, from the past to the present and into the future, as well as their use in analytical chemistry.

Metabolic Fingerprinting of Bacteria Exposed to Nanomaterials, Using Online Databases, NMR, and High-Resolution Mass Spectrometry

Nanomaterials are examined more and more for their antibacterial properties. Herein, we propose a method for assessing the bactericidal properties of nanomaterials against Escherichia coli and Staphylococcus aureus, as well as a method to investigate the metabolic alterations occurring to bacteria, induced by their exposure to nanomaterials. Bacterial metabolome is extracted and metabolic fingerprint is recorded by ¹H-NMR. Using metabolomic databases, the tentative metabolites in the samples are revealed, which are further confirmed by UHPLC-HRMS. Finally, conducting a pathway analysis, the metabolic network is revealed.

Matrix solid-phase dispersion based on magnetic ionic liquids: An alternative sample preparation approach for the extraction of pesticides from vegetables

In this study, we propose, for the first time, the direct use of a magnetic ionic liquid (MIL) in a matrix solid-phase extraction procedure. Because of the magnetic properties, the MIL can be harvested directly after the extraction step, using a magnet, while its hydrophobic nature makes feasible the extraction of analytes. Raw vegetables of high water content can be analyzed without any pretreatment. The viscous nature of the selected MIL assists in blending with the matrix, while its hydrophobicity facilitates easier separation and retrieval. Additionally, no solid dispersing materials or co-sorbents are needed. A simple, low-cost analytical method for the determination of multi-class pesticides residues in raw vegetables was developed, with satisfactory recoveries.

Enhanced magnetic ionic liquid-based dispersive liquid-liquid microextraction of triazines and sulfonamides through a one-pot, pH-modulated approach

In this study, an enhanced variant of magnetic ionic liquid (MIL)-based dispersive liquid-liquid microextraction is put forward. The procedure combines a water insoluble solid support and the [P₆₆₆₁₄⁺][Dy(III)(hfacac)₄^-] MIL, in a one-pot, pH-modulated procedure for microextraction of triazines (TZs) and sulfonamides (SAs). The solid supporting material was mixed with the MIL to overcome difficulties concerning the weighing of MIL and to control the uniform dispersion of the MIL, rendering the whole extraction procedure more reproducible. The pH-modulation during extraction step makes possible the one-pot extraction of SAs and TZs, from a single sample, in 15 min. Overall, the new analytical method developed enjoys the benefits of sensitivity (limits of quantification: 0.034-0.091 μg L^-1) and precision (relative standard deviation: 5.2-8.1%), while good recoveries (i.e., 89-101%) were achieved from lake water and effluent from a municipal wastewater treatment plant. Owing to all of the above, the new procedure can be used to determine the concentrations of SAs and TZs at levels below the maximum residue limits.

Carbonization of Human Fingernails: Toward the Sustainable Production of Multifunctional Nitrogen and Sulfur Codoped Carbon Nanodots with Highly Luminescent Probing and Cell Proliferative/Migration Properties

A simple yet effective method is employed to prepare multifunctional fluorescent carbon nanodots (CNDs) from human fingernails. The results demonstrate that the CNDs have excellent optical properties and a quantum yield of 81%, which is attributed to the intrinsic composition of the precursor material itself. The CNDs are used to develop an ultrasensitive fluorescent probe for the detection of hexavalent chromium (limit of detection: 0.3 nM) via a combined inner-filter and static mechanism. Moreover, the toxicity of the CNDs over four epithelial cell lines is assessed. A negligible toxicity is induced on the three of the cell lines, whereas an increase in HEK-293 cell viability is demonstrated, granting cell proliferation properties to the as-synthesized CNDs. According to cell cycle analysis, cell proliferation is achieved by enhancing the transition of cells from the S phase to the G2/M one. Interestingly, CNDs are found to significantly promote cell migration, maybe because of their free-radical scavenging ability, making the CNDs suitable for wound healing applications. In addition, relevant experiments have revealed the blood compatibility of the CNDs. Finally, the CNDs were found suitable for cell imaging applications, and all of the aforementioned merits make it possible for them to be used for extraordinary, more advanced biological applications.

Qualitative Alterations of Bacterial Metabolome after Exposure to Metal Nanoparticles with Bactericidal Properties: A Comprehensive Workflow Based on (1)H NMR, UHPLC-HRMS, and Metabolic Databases

Metal nanoparticles (NPs) have proven to be more toxic than bulk analogues of the same chemical composition due to their unique physical properties. The NPs, lately, have drawn the attention of researchers because of their antibacterial and biocidal properties. In an effort to shed light on the mechanism through which the bacteria elimination is achieved and the metabolic changes they undergo, an untargeted metabolomic fingerprint study was carried out on Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria species. The (1)H NMR spectroscopy, in conjunction with high resolution mass-spectrometry (HRMS) and an unsophisticated data processing workflow were implemented. The combined NMR/HRMS data, supported by an open-access metabolomic database, proved to be efficacious in the process of assigning a putative annotation to a wide range of metabolite signals and is a useful tool to appraise the metabolome alterations, as a consequence of bacterial response to NPs. Interestingly, not all the NPs diminished the intracellular metabolites; bacteria treated with iron NPs produced metabolites not present in the nonexposed bacteria sample, implying the activation of previously inactive metabolic pathways. In contrast, copper and iron-copper NPs reduced the annotated metabolites, alluding to the conclusion that the metabolic pathways (mainly alanine, aspartate, and glutamate metabolism, beta-alanine metabolism, glutathione metabolism, and arginine and proline metabolism) were hindered by the interactions of NPs with the intracellular metabolites.