Effect of textile wastewaters on Saccharomyces cerevisiae using DNA microarray as a tool for genome-wide transcriptomics analysis

A Review on Molecular Mechanisms of Antifungal Resistance in Candida glabrata: Update and Recent Advances

Candida glabrata is the second frequent etiologic agent of mucosal and invasive candidiasis. Based on the recent developments in molecular methods, C. glabrata has been introduced as a complex composed of C. glabrata, Candida nivariensis, and Candida bracarensis. The four main classes of antifungal drugs effective against C. glabrata are pyrimidine analogs (flucytosine), azoles, echinocandins, and polyenes. Although the use of antifungal drugs is related to the predictable development of drug resistance, it is not clear why C. glabrata is able to rapidly resist against multiple antifungals in clinics. The enhanced incidence and antifungal resistance of C. glabrata and the high mortality and morbidity need more investigation regarding the resistance mechanisms and virulence associated with C. glabrata; additional progress concerning the drug resistance of C. glabrata has to be further prevented. The present review highlights the mechanism of resistance to antifungal drugs in C. glabrata.

Microbial bioassays in environmental toxicity testing

Accidental spills and the misuse of chemicals may lead to current and legacy environmental contamination and pose concerns over possible (eco)toxicological secondary effects and risks toward non-target microbes and higher eukaryotes, including humans, in ecosystems. In the last decades, scientists and regulators have faced requests to thoroughly screen, prioritize and predict the possible deleterious effects of the huge numbers of existing and emerging xenobiotics, wastewaters and environmental samples on biological systems. In this context, it has become necessary to develop and validate (eco)toxicity bioassays based on microorganisms (e.g., bacteria, microalga, yeast, filamentous fungi, protozoa) as test-organisms whose data should be meaningful for environmental (micro)organisms that may be exposed to contaminated environments. These generally simple, fast and cost-effective bioassays may be preliminary and complementary to the more complex and long-term whole-organism animal-based traditional ecotoxicity tests. With the goal of highlighting the potential offered by microbial-based bioassays as non-animal alternatives in (eco)toxicity testing, the present chapter provides an overview of the current state-of-the art in the development and use of microbial toxicity bioassays through the examination of relatively recent examples with a diverse range of toxicity endpoints. It goes into the (eco)toxicological relevance of these bioassays, ranging from the more traditional microalga- and bacterial-based assays already accepted at regulatory level and commercially available to the more innovative microbial transcriptional profiling and gene expression bioassays, including some examples of biosensors.

Transcriptomic analysis of HepG2 cells exposed to fractionated wastewater effluents suggested humic substances as potential inducer of whole effluent toxicity

We performed a transcriptome-based bioassay (TSB assay) using human hepatoma HepG2 cells to evaluate the potential toxicity of whole wastewater effluents from two membrane bioreactors (MBRs) and a conventional activated sludge process (AS). The biologically active agent(s) in the wastewater effluents were characterized based on expression of the marker genes (i.e., CYP1A1, AKR1B10, GCLM and GPX2) selected by DNA microarray analysis, after the wastewater effluent samples were concentrated by a reverse osmosis (RO) membrane and further fractionated by various manipulations. The qPCR assay of marker genes demonstrated that the induction of CYP1A1 and GPX2 was mitigated after passing through C18 and chelate columns. In addition, clear induction of CYP1A1 was observed in the smallest size fraction with 1 k Da or smaller organic molecules in all the tested effluents. These results together with the water quality data of the fractionated samples suggested that responsible constituents for potentially adverse and abnormal transcriptomic responses in HepG2 could have hydrophobic nature and act with metal-dissolved organic matter (DOM) complexes in 1 k Da or smaller size fraction. Although DOM is known to play two contradictory roles as a protector and an inducer of toxicants, our present study indicated the DOM in wastewater effluent, particularly humic substances with acidic nature, functioned as a toxicity inducer of residual chemicals in the effluents. This study provided a new insight into the nature of "toxic unknowns" in the wastewater effluents, which should be monitored whole through the reclamation process and prioritized for removal.

Comparative analysis of transcriptomic responses to sub-lethal levels of six environmentally relevant pesticides in Saccharomyces cerevisiae

Accidental spills and misuse of pesticides may lead to current and/or legacy environmental contamination and may pose concerns regarding possible risks towards non-target microbes and higher eukaryotes in ecosystems. The present study was aimed at comparing transcriptomic responses to effects of sub-lethal levels of six environmentally relevant pesticide active substances in the Saccharomyces cerevisiae eukaryotic model. The insecticide carbofuran, the fungicide pyrimethanil and the herbicides alachlor, S-metolachlor, diuron and methyl(4-chloro-2-methylphenoxy)acetate were studied. Some are currently used agricultural pesticides, while others are under restricted utilization or banned in Europe and/or North America albeit being used in other geographical locations. In the present work transcriptional profiles representing genome-wide responses in a standardized yeast population upon 2 h of exposure to concentrations of each compound exerting equivalent toxic effects, i.e., inhibition of growth by 20% relative to the untreated control cells, were examined. Hierarchical clustering and Venn analyses of the datasets of differentially expressed genes pointed out transcriptional patterns distinguishable between the six active substances. Functional enrichment analyses allowed predicting mechanisms of pesticide toxicity and response to pesticide stress in the yeast model. In general, variations in transcript numbers of selected genes assessed by Real-Time quantitative reverse transcription polymerase chain reaction confirmed microarray data and correlated well with growth inhibitory effects. A possible biological relevance of mechanistic predictions arising from these comparative transcriptomic analyses is discussed in the context of better understanding potential modes of action and adverse side-effects of pesticides.

Suitability of a Saccharomyces cerevisiae-based assay to assess the toxicity of pyrimethanil sprayed soils via surface runoff: comparison with standard aquatic and soil toxicity assays

The present study is aimed at evaluating whether a gene expression assay with the microbial eukaryotic model Saccharomyces cerevisiae could be used as a suitable warning tool for the rapid preliminary screening of potential toxic effects on organisms due to scenarios of soil and water contamination with pyrimethanil. The assay consisted of measuring changes in the expression of the selected pyrimethanil-responsive genes ARG3 and ARG5,6 in a standardized yeast population. Evaluation was held by assessing the toxicity of surface runoff, a major route of pesticide exposure in aquatic systems due to non-point-source pollution, which was simulated with a pyrimethanil formulation at a semifield scale mimicking worst-case scenarios of soil contamination (e.g. accident or improper disposal). Yeast cells 2-h exposure to the runoff samples led to a significant 2-fold increase in the expression of both indicator genes. These results were compared with those from assays with organisms relevant for the aquatic and soil compartments, namely the nematode Caenorhabditis elegans (reproduction), the freshwater cladoceran Daphnia magna (survival and reproduction), the benthic midge Chironomus riparius (growth), and the soil invertebrates Folsomia candida and Enchytraeus crypticus (survival and reproduction). Under the experimental conditions used to simulate accidental discharges into soil, runoff waters were highly toxic to the standard test organisms, except for C. elegans. Overall, results point out the usefulness of the yeast assay to provide a rapid preview of the toxicity level in preliminary screenings of environmental samples in situations of inadvertent high pesticide contamination. Advantages and limitations of this novel method are discussed.

Evaluation of whole wastewater effluent impacts on HepG2 using DNA microarray-based transcriptome analysis

DNA microarray-based transcriptome analysis with human hepatoma HepG2 cells was applied to evaluate the impacts of whole wastewater effluents from the membrane bioreactors (MBRs) and the activated sludge process (AS). In addition, the conventional bioassays (i.e., cytotoxicity tests and bioluminescence inhibition test), which were well-established for the evaluation of the overall effluent toxicity, were also performed for the same samples. Transcriptome analysis revealed that 2 to 926 genes, which were categorized to 0 to 225 biological processes, were differentially expressed after exposure to the effluents and the raw wastewater. Among the tested effluents, the effluent from a MBR operated at a relatively long solid retention time (i.e., 40 days) and small membrane pore size (i.e., 0.03 μm) showed the least impacts on the HepG2 even at the level comparable to tap water. The observed gene expression responses were in good agreement with the results of cytotoxicity tests, and provided additional molecular mechanistic information on adverse effects occurred in the sublethal region. Furthermore, the genes related to "lipid metabolism", "response to endogenous stimulus", and "response to inorganic substance" were selected as potential genetic markers, and their expression levels were quantified to evaluate the cellular impacts and treatability of wastewater effluents. Although the harmful impacts and innocuous impacts could not be distinguished at present, the results demonstrated that the DNA microarray-based transcriptome analysis with human HepG2 cells was a powerful tool to rapidly and comprehensively evaluate impacts of whole wastewater effluents.

Chronic exposure to contaminated drinking water stimulates PPAR expression in mice livers

Mice were fed with source water (SW) and tap water (TW) for 90 d to evaluate hepatotoxicity induced by the drinking water. Histopathologic observation showed no obvious damage to hepatic tissue in the SW and TW groups. However, microarray analysis indicated that the SW and TW exposures affected many metabolic pathways, among which PPAR (peroxisome proliferator-activated receptors) signaling was most susceptible. Immunohistochemical staining demonstrated that both PPAR-α and PPAR-γ were significantly increased in the exposure groups compared to control. Enzyme-linked immunosorbent assay revealed that PPAR-α expression level was increased from 23.37±0.53 ng g(-1) liver weight in control group to 26.60±1.43 ng g(-1) liver weight in SW group and 27.68±1.10 ng g(-1) liver weight in TW group (p<0.05). For PPAR-γ, the expression level was also significantly enhanced from 0.83±0.07 ng g(-1) liver weight in control group to 1.11±0.20 ng g(-1) liver weight in SW group and 1.16±0.07 ng g(-1) liver weight in TW group (p<0.05). The SW and DW posed no obvious hepatotoxicity on mice and PPAR-α/-γ could be used as a novel biomarker to assess public health risk induced by slightly contaminated drinking water.

Transcriptional profiling in Saccharomyces cerevisiae relevant for predicting alachlor mechanisms of toxicity

Alachlor has been a commonly applied herbicide and is a substance of ecotoxicological concern. The present study aims to identify molecular biomarkers in the eukaryotic model Saccharomyces cerevisiae that can be used to predict potential cytotoxic effects of alachlor, while providing new mechanistic clues with possible relevance for experimentally less accessible eukaryotes. It focuses on genome-wide expression profiling in a yeast population in response to two exposure scenarios exerting effects from slight to moderate magnitude at phenotypic level. In particular, 100 and 264 genes, respectively, were found as differentially expressed on a 2-h exposure of yeast cells to the lowest observed effect concentration (110 mg/L) and the 20% inhibitory concentration (200 mg/L) of alachlor, in comparison with cells not exposed to the herbicide. The datasets of alachlor-responsive genes showed functional enrichment in diverse metabolic, transmembrane transport, cell defense, and detoxification categories. In general, the modifications in transcript levels of selected candidate biomarkers, assessed by quantitative reverse transcriptase polymerase chain reaction, confirmed the microarray data and varied consistently with the growth inhibitory effects of alachlor. Approximately 16% of the proteins encoded by alachlor-differentially expressed genes were found to share significant homology with proteins from ecologically relevant eukaryotic species. The biological relevance of these results is discussed in relation to new insights into the potential adverse effects of alachlor in health of organisms from ecosystems, particularly in worst-case situations such as accidental spills or careless storage, usage, and disposal.

Mechanistic toxicity assessment of nanomaterials by whole-cell-array stress genes expression analysis

This study performed mechanistic toxicity assessment of nanosilver (nAg) and nanotitanium dioxide anatase (nTiO2_a) via toxicogenomic approach, employing a whole-cell-array library consisting of 91 recombinated Escherichia coli K12 strains with transcriptional GFP-fusions covering most known stress response genes. The results, for the first time, revealed more detailed transcriptional information on the toxic mechanism of nAg and nTiO2_a, and led to a better understanding of the mode of action (MOA) of metal and metal oxide nanomaterials (NMs). The detailed pathways network established for the oxidative stress system and for the SOS (DNA damage) repair system based on the temporal gene expression profiling data revealed the relationships and sequences of key genes involved in these toxin response systems. Both NMs were found to cause oxidative stress as well as cell membrane and transportation damage. Genotoxicity and DNA damage were also observed, although nTiO2_a induced SOS response via previously identified pathway and nAg seemed to induce DNA repair via a pathway different from SOS. We observed that the NMs at lower concentration tend to induce more chemical-specific toxicity response, while at higher concentrations, more general global stress response dominates. The information-rich real-time gene expression data allowed for identification of potential biomarkers that can be employed for specific toxin detection and biosensor developments. The concentration-dependent gene expression response led to the determination of the No Observed Transcriptional Effect Level (NOTEL) values, which can be potentially applied in the regulatory and risk assessment framework as an alternative toxicity assessment end point.

Recent developments in environmental metabolomics

Metabolomics is increasingly being used to characterise the interactions of organisms with their natural environment. This article describes the latest developments in this vibrant field. The first section highlights environmental studies that are exploiting recent technological advances in metabolomics, including developments in NMR spectroscopy and mass spectrometry, with a particular focus on toxicity testing in ecological risk assessment. Subsequently, recent laboratory studies of organism function and metabolic responses to stress are reviewed, including investigations of cold, heat and anoxic stress. The importance of model organisms and systems biology within environmental metabolomics is then highlighted. Finally, the first applications of metabolomics to actual field investigations are discussed, with a particular focus on environmental monitoring. During the past year, environmental metabolomics research has been conducted on more than 20 model and non-model species, including eight freshwater and marine fish, nine species of aquatic and terrestrial invertebrates, as well as plants and microbes, demonstrating the rapid growth of this field.

DNA microarray analyses reveal a post-irradiation differential time-dependent gene expression profile in yeast cells exposed to X-rays and γ-rays

Ionizing radiation (IR) is the most enigmatic of genotoxic stress inducers in our environment that has been around from the eons of time. IR is generally considered harmful, and has been the subject of numerous studies, mostly looking at the DNA damaging effects in cells and the repair mechanisms therein. Moreover, few studies have focused on large-scale identification of cellular responses to IR, and to this end, we describe here an initial study on the transcriptional responses of the unicellular genome model, yeast (Saccharomyces cerevisiae strain S288C), by cDNA microarray. The effect of two different IR, X-rays, and gamma (gamma)-rays, was investigated by irradiating the yeast cells cultured in YPD medium with 50 Gy doses of X- and gamma-rays, followed by resuspension of the cells in YPD for time-course experiments. The samples were collected for microarray analysis at 20, 40, and 80 min after irradiation. Microarray analysis revealed a time-course transcriptional profile of changed gene expressions. Up-regulated genes belonged to the functional categories mainly related to cell cycle and DNA processing, cell rescue defense and virulence, protein and cell fate, and metabolism (X- and gamma-rays). Similarly, for X- and gamma-rays, the down-regulated genes belonged to mostly transcription and protein synthesis, cell cycle and DNA processing, control of cellular organization, cell fate, and C-compound and carbohydrate metabolism categories, respectively. This study provides for the first time a snapshot of the genome-wide mRNA expression profiles in X- and gamma-ray post-irradiated yeast cells and comparatively interprets/discusses the changed gene functional categories as effects of these two radiations vis-à-vis their energy levels.