Screening Of Environmental Samples Research Articles

Electrochemical biosensor strategy combining DNA entropy-driven technology to activate CRISPR-Cas13a activity and triple-stranded nucleic acids to detect SARS-CoV-2 RdRp gene.

By merging DNA entropy-driven technology with triple-stranded nucleic acids in an electrochemical biosensor to detect the SARS-CoV-2 RdRp gene, we tackled the challenges of false negatives and the high cost of SARS-CoV-2 detection. The approach generates a CRISPR-Cas 13a-activated RNA activator, which then stimulates CRISPR-Cas 13a activity using an entropy-driven mechanism. The activated CRISPR-Cas 13a can cleave Hoogsteen DNA due to the insertion of two uracil (-U-U-) in Hoogsteen DNA. The DNA tetrahedra changed on the electrode surface andcanthereforenot construct a three-stranded structure after cleaving Hoogsteen DNA. Significantly, this DNA tetrahedron/Hoogsteen DNA-based biosensor can regenerate at pH = 10.0, which keeps Hoogsteen DNA away from the electrode surface, allowing the biosensor to function at pH = 7.0. We could use this technique to detect the SARS-CoV-2 RdRp gene with a detection limit of 89.86 aM. Furthermore, the detection method is very stable and repeatable. This technique offers the prospect of detecting SARS-CoV-2 at a reasonable cost. This work has potential applications in the dynamic assessment of the diagnostic and therapeutic efficacy of SARS-CoV-2 infection and in the screening of environmental samples.

Novel Assay for Detection of Progesterone Receptor-Interacting Endocrine Disruptors

The presence of progesterone receptor (PR)-interacting compounds in the environment may have serious health consequences for humans and wildlife, but the methods for their detection and monitoring are limited. Here we report the development and testing of a cell line expressing a chimeric construct containing ligand-binding domain of progesterone receptor and green fluorescent protein-tagged domain of the glucocorticoid receptor (GFP-GR-PR) under tetracycline regulation. Unlike the constitutively nuclear PR, this chimera is cytoplasmic in the absence of the ligand and translocates to the nucleus in response to the hormone or its analogues. The GFP-GR-PR chimera maintains specificity for binding to progesterone and does not cross-react with GR-activating hormones. A concentration- and time-dependent translocation in response to progesterone confirmed picomolar sensitivity for detecting PR ligands. Importantly, the assay can detect both agonist and antagonist activities and thus can be used for screening environmental samples for contamination with endocrine disruptors and for drug development. Using this approach, we screened water samples collected at 23 sites along 2 major rivers in Virginia: Mattaponi and Rappahannock Rivers. We detected a low, but reproducible PR-binding activity in 34.8 % of the sites tested. The calculated progesterone equivalent concentration (EQ) in some of these sites reached ~ 0.8 ng/L. The assay provides an effect-based approach for screening PR-interacting endocrine disrupting chemicals regardless of whether they exert agonist or antagonist activities. Either one could be seriously disruptive for the health of humans and wildlife.

Testing of Eluates from Waterproof Building Materials for Potential Environmental Effects Due to the Behavior of Enchytraeus albidus.

In order to determine the potential environmental impact of construction products, it is necessary to evaluate their influence on organisms exposed to them or their eluates under environmental conditions. The behavior of the white worm Enchytraeus albidus is a useful tool for assessing the potential environmental impact of construction products in contact with water and soil. This study investigates the environmental effects of eluates from two construction products, a reactive waterproofing product, and an injection resin, on the reproduction and avoidance behavior of E. albidus. The eluates were prepared according to existing guidelines. The soil used for the tests was moistened with the eluates of the construction products. The reproduction results of the worms were collected after six weeks of exposure. Offsprings were counted under the microscope and statistically analyzed. Results from the avoidance behavior were collected after 48 h of exposure, and results were compared with the reproduction results. The eluates from both construction products induced significant changes in the reproduction behavior of E. albidus. Undiluted or only slightly diluted eluates of the injection resin drastically reduced the reproduction of the worms, whereas the leaches of the reactive waterproofing product only had a minor effect. The avoidance results for the injection resin indicates that its presence in the habitat is clearly detrimental to the survival of E. albidus, while the avoidance results for the waterproofing resin showed an initial avoidance of the eluates, but no harmful effects were observed. The avoidance test is a way of rapid toxicity screening of environmental samples when time is a critical parameter to measure possible environmental effects. This study shows that ecotoxicological tests using Enchytraeids are a valuable and important tool for understanding the mode of action of eluates from construction products in the environment.

Validation of droplet digital Polymerase Chain Reaction for the detection and absolute quantification of Taenia solium eggs in spiked soil samples

To enable the detection of taeniid eggs in environmental samples, a sensitive technology is required. In this study, we validated the effectiveness of a digital droplet Polymerase Chain Reaction (ddPCR) assay for detection, identification and absolute quantification of taeniid DNA from artificially contaminated soils with varying numbers of taeniid eggs using a set of universal primers, JB3 & JB4.5. The results showed that the number of cox1 copies detected increased gradually for both species with the number of taeniid eggs added to the different soil types. The highest cox1 DNA copies recovery for Taenia solium and T. lynciscapreoli was from the sand soil with lowest recovery being observed in clay soils. Therefore, ddPCR is a promising technology for screening of taeniid eggs from soil samples collected in the environment irrespective of the soil type and the number of eggs. The potential of the ddPCR protocol to detect taeniid egg DNA in spiked soil samples has great practical application for taeniid egg screening in soils from endemic areas. However, when universal primers are used in screening environmental samples, the identity of ddPCR positive samples must be confirmed by sequencing. In addition, more validation studies using species-specific primers and field soil samples is recommended.

Laccase multigene families in Agaricomycetes.

Here we present the results of the exploration of laccase multigene families (MGFs) in basidiomycetous fungi from different taxonomic groups using a next generation sequencing (NGS) technology. In our study, multiple laccase genes were identified in all of the investigated fungi (13 species) from Polyporaceae, Phanerochaetaceae, Meruliaceae, Pleurotaceae, Physalacriaceae, and Peniophoraceae families. It was shown that phylogenetic positioning of the newly identified sequences exhibit patterns of clusterization with respect to enzyme properties. This can be a potentially useful tool for selecting naturally existing laccases with different physicochemical characteristics relevant to different biotechnological applications. Moreover, the method developed in this study can be used in the screening of environmental samples and fast characterization of laccase MGFs in newly identified fungal species.

DNA microarray-based detection of Coxiella burnetii, the causative agent of Q fever.

BackgroundAn easy-to-handle microarray assay based on the cost-effective ArrayTube™ platform has been designed for the rapid and unequivocal identification of Coxiella burnetii, the causative agent of Q fever. The gene targets include the chromosomally coded markers icd, omp/com1, and IS1111 as well as the plasmid coded markers cbbE and cbhE.ResultsA representative panel comprising 50 German C. burnetii isolates and 10 clinical samples was examined to validate the test. All tested isolates harboured plasmid QpH1 and were correctly identified, corresponding to 100% sensitivity. The assay’s limit of detection was 100 genome equivalents (GE) for icd, omp/com1, cbbE and cbhE and 10 GE for IS1111. Assay specificity was 100% as determined by analysing a panel of 37 non-Coxiella strains.ConclusionsThe present array is a rational assembly of established and evaluated targets for the rapid and unequivocal detection of C. burnetii. This array could be applied to the screening of vaginal swabs from small ruminants; screening of environmental samples e.g. on farms or screening of human samples.

Detection of coccidioidal antibodies in serum of a small rodent community in Baja California, Mexico

Coccidioidomycosis (Valley Fever) represents a serious threat to inhabitants of endemic areas of North America. Despite successful clinical isolations of the fungal etiological agent, Coccidioides spp., the screening of environmental samples has had low effectiveness, mainly because of the poor characterization of Coccidioides ecological niche. We explored Valle de las Palmas, Baja California, Mexico, a highly endemic area near the U.S.–Mexico border, where we previously detected Coccidioides via culture-independent molecular methods. By testing the serum from 40-trapped rodents with ELISA, we detected antibodies against Coccidioides in two species: Peromyscus maniculatus and Neotoma lepida. This study comprises the first report of wild rodent serum tested for coccidioidal antibodies, and sets the basis to analyze this pathogen in its natural environment and explore its potential ecological niche.

Isolation of bacterial strains able to metabolize lignin from screening of environmental samples

To develop a method to detect bacteria from environmental samples that are able to metabolize lignin. A previously developed UV-vis assay method for lignin degradation activity has been developed for use as a spray assay on agar plates. Nine mesophilic strains were isolated using this method from woodland soil incubated in enrichment cultures containing wheat straw lignocellulose: four Microbacterium isolates, two Micrococcus isolates, Rhodococcus erythropolis (all Actinobacteria) and two Ochrobactrum isolates (Alphaproteobacteria). Three thermotolerant isolates were isolated from the same screening method applied at 45°C to samples of composted wheat straw from solid-state fermentation: Thermobifida fusca and two isolates related to uncharacterized species of Rhizobiales and Sphingobacterium (Bacteroidetes), the latter strain showing tenfold higher lignin degradation activity than other isolates. The isolated strains were able to depolymerize samples of size-fractionated high molecular weight and low molecular weight Kraft lignin, and produced low molecular weight metabolites oxalic acid and protocatechuic acid from incubations containing wheat straw lignocellulose. A new method for the isolation of bacteria able to metabolize lignin has been developed, which has been used to identify 12 bacterial isolates from environmental sources. The majority of isolates cluster into the Actinobacteria and the Alphaproteobacteria. Lignin-degrading bacterial strains could be used to convert lignin-containing feedstocks into renewable chemicals and to identify new bacterial lignin-degrading enzymes.

Application of Resequencing Microarrays in Microbial Detection and Characterization

Microarrays are powerful, highly parallel assays that are transforming microbiological diagnostics and research. The adaptation of microarray-based resequencing technology for microbial detection and characterization resulted in the development of a number assays that have unique advantages over other existing technologies. This technological platform seems to be especially useful for sensitive and high-resolution multiplexed diagnostics for clinical syndromes with similar symptoms, screening environmental samples for biothreat agents, as well as genotyping and whole-genome analysis of single pathogens.

Rapid resonance Raman microspectroscopy to probe carbon dioxide fixation by single cells in microbial communities

Photosynthetic microorganisms play crucial roles in aquatic ecosystems and are the major primary producers in global marine ecosystems. The discovery of new bacteria and microalgae that play key roles in CO(2) fixation is hampered by the lack of methods to identify hitherto-unculturable microorganisms. To overcome this problem we studied single microbial cells using stable-isotope probing (SIP) together with resonance Raman (RR) microspectroscopy of carotenoids, the light-absorbing pigments present in most photosynthetic microorganisms. We show that fixation of (13)CO(2) into carotenoids produces a red shift in single-cell RR (SCRR) spectra and that this SCRR-SIP technique is sufficiently sensitive to detect as little as 10% of (13)C incorporation. Mass spectrometry (MS) analysis of labelled cellular proteins verifies that the red shift in carotenoid SCRR spectra acts as a reporter of the (13)C content of single cells. Millisecond Raman imaging of cells in mixed cultures and natural seawater samples was used to identify cells actively fixing CO(2), demonstrating that the SCRR-SIP is a noninvasive method for the rapid and quantitative detection of CO(2) fixation at the single cell level in a microbial community. The SCRR-SIP technique may provide a direct method for screening environmental samples, and could help to reveal the ecophysiology of hitherto-unculturable microorganisms, linking microbial species to their ecological function in the natural environment.

Development of the DNAA System for Screening Environmental Samples to Measure fissile Material

The DNAA system made up of pneumatic transport system, neutron detector assembly, and signal processing equipment was installed in the High-flux Advanced Neutron Application Reactor (HANARO). The optimized position of the detector in the delayed neutron counting (DNC) system was evaluated at a distance 15.1 cm from center of the DNC system with 18 He-3 detectors using MCNP simulation. The system shows excellent linearity from 0.67 ng to 713 ng U-235, and reproducibility of 1.26% standard deviation for the various mass groups of U-235 samples. The DNAA system shows detection efficiency of ~30 % and U-235 detection limit of 1ng. This system can be used on a screening method to assist the environmental sample analysis and to protect the clean room from elevated levels of fissile material that might be in routine samples.

The development of a rapid screening technique to measure antibiotic activity in effluents and surface water samples

Use of antibiotics in medicine, farming and aquaculture results in a continual supply of these pharmaceuticals and their breakdown products reaching the environment. A method has been developed to use for screening environmental samples to establish whether they contain antibiotics. The assay is based on a commercially available test kit and uses some modifications of the test procedure and SPE techniques to deliver a fast, semi-quantifiable result. Development of the assay and results from spiked and environmental samples are discussed.

High-performance liquid chromatography with fluorescence detection for aqueous analysis of nanogram-level N-nitrosodimethylamine

High-performance liquid chromatography (HPLC) and fluorescence derivatization were applied for a nanogram-level N-nitrosodimethylamine (NDMA) analysis of water samples. For the analysis of N-nitrosodimethylamine, samples were first denitrosated by a mixed solution of hydrobromic acid and acetic acid to produce dimethylamine, which was derivatized with dansyl chloride for HPLC fluorescence detection. Fluorescence detection was optimized with excitation and emission wavelengths of 340 and 530 nm, respectively. pH adjustment after denitrosation was necessary to maximize fluorescence intensity with pHs in the range of 9–12. A dansyl chloride concentration of 500 mg l −1 was found to be optimal for measuring a fluorescence signal. An instrumental detection limit of 0.1 ng of NDMA was possible with fluorescence derivatization. The NDMA in water samples was extracted by continuous solid-phase extraction using Ambersorb 572. Although the determination of NDMA was variable at lower concentrations (less than 200 ng l −1), it was observed that the NDMA detection limit with this method could be lowered to a concentration of 10 ng l −1. Another benefit of this method can be found in its selectivity for NDMA. Unlike gas chromatographic (GC) methods, this method generates a distinct peak for NDMA without interference even in the complex matrix of wastewater effluents. The HPLC with fluorescence derivatization method may be applicable for determining NDMA in water and wastewater samples for various research purposes and for screening environmental samples.

A teleost in vitro reporter gene assay to screen for agonists of the peroxisome proliferator‐activated receptors

Several contaminants detected in aquatic ecosystems are agonists of peroxisome proliferator-activated receptors (PPARs). Peroxisome proliferator-activated receptors interact with the retinoid X receptor (RXR) to activate the transcription of genes that control a variety of physiological functions. We cloned and sequenced partial cDNA fragments of rainbow trout (Oncorhynchus mykiss) PPARalpha and PPARbeta from rainbow trout (rt) gill-W1 cells, a cell line derived from rainbow trout gills; predicted amino acid identities are 77% and 82% compared with their respective human homologs and 83 to 88% and 91 to 98% identical to fish homologs. A reporter gene assay was developed by transfecting rt-gill-W1 cells with a reporter gene construct containing the peroxisome proliferator response element (PPRE) of the rat liver 3-ketoacyl-CoA thiolase B (TB) gene, which drives luciferase expression. Agonists of both PPARalpha (WY14,643 and gemfibrozil) and PPARbeta (bezafibrate) induced luciferase activity, while rosiglitazone, a PPARgamma agonist, was not effective. The fibrate drug, bezafibrate increased luciferase activity in a dose-dependent manner, but addition of 50 nM 9-cis-retinoic acid to the transfected rt-gill-W1 cell culture maximized the sensitivity of the assay so that bezafibrate could be detected at concentrations as low as 6 nM. Extracts from treated domestic wastewater containing fibrate drugs induced luciferase activity in the transfected gill cells. This in vitro reporter gene assay shows promise as a rapid and sensitive technique for screening environmental samples for PPAR-active substances.

Metabolic primers for detection of (Per)chlorate-reducing bacteria in the environment and phylogenetic analysis of cld gene sequences.

Natural attenuation of the environmental contaminant perchlorate is a cost-effective alternative to current removal methods. The success of natural perchlorate remediation is dependent on the presence and activity of dissimilatory (per)chlorate-reducing bacteria (DPRB) within a target site. To detect DPRB in the environment, two degenerate primer sets targeting the chlorite dismutase (cld) gene were developed and optimized. A nested PCR approach was used in conjunction with these primer sets to increase the sensitivity of the molecular detection method. Screening of environmental samples indicated that all products amplified by this method were cld gene sequences. These sequences were obtained from pristine sites as well as contaminated sites from which DPRB were isolated. More than one cld phylotype was also identified from some samples, indicating the presence of more than one DPRB strain at those sites. The use of these primer sets represents a direct and sensitive molecular method for the qualitative detection of (per)chlorate-reducing bacteria in the environment, thus offering another tool for monitoring natural attenuation. Sequences of cld genes isolated in the course of this project were also generated from various DPRB and provided the first opportunity for a phylogenetic treatment of this metabolic gene. Comparisons of the cld and 16S ribosomal DNA (rDNA) gene trees indicated that the cld gene does not track 16S rDNA phylogeny, further implicating the possible role of horizontal transfer in the evolution of (per)chlorate respiration.

Toxicological profiling of sediments using in vitro bioassays, with emphasis on endocrine disruption.

In vitro bioassays are valuable tools for screening environmental samples for the presence of bioactive (e.g., endocrine-disrupting) compounds. They can be used to direct chemical analysis of active compounds in toxicity identification and evaluation (TIE) approaches. In the present study, five in vitro bioassays were used to profile toxic potencies in sediments, with emphasis on endocrine disruption. Nonpolar total and acid-treated stable extracts of sediments from 15 locations in the Rhine Meuse estuary area in The Netherlands were assessed. Dioxin-like and estrogenic activities (using dioxin-responsive chemical-activated luciferase gene expression [DR-CALUX] and estrogen-responsive chemical-activated luciferase gene expression [ER-CALUX] assays) as well as genotoxicity (UMU test) and nonspecific toxic potency (Vibrio fischeri assay) were observed in sediment extracts. For the first time, to our knowledge, in vitro displacement of thyroid hormone thyroxine (T4) from the thyroid hormone transport protein thransthyretin by sediment extracts was observed, indicating the presence of compounds potentially able to disrupt T4 plasma transport processes. Antiestrogenic activity was also observed in sediment. The present study showed the occurrence of endocrine-disrupting potencies in sediments from the Dutch delta and the suitability of the ER- and DR-CALUX bioassays to direct endocrine-disruption TIE studies.

Fidelity of select restriction endonucleases in determining microbial diversity by terminal-restriction fragment length polymorphism.

An evaluation of 18 DNA restriction endonucleases for use in terminal-restriction fragment length polymorphism (T-RFLP) analysis was performed by using richness and density indices in conjunction with computer simulations for 4,603 bacterial small-subunit rRNA gene sequences. T-RFLP analysis has become a commonly used method for screening environmental samples for precursory identification and community comparison studies due to its precision and high-throughput capability. The accuracy of T-RFLP analysis for describing a community has not yet been thoroughly evaluated. In this study, we attempted to classify restriction endonucleases based upon the ability to resolve unique terminal-restriction fragments (T-RFs) or operational taxonomic units (OTUs) from a database of gene sequences. Furthermore, we assessed the predictive accuracy of T-RFLP at fixed values of community richness (n = 1, 5, 10, 50, and 100). Classification of restriction endonuclease fidelity was performed by measuring richness and density for the entire database of T-RFs. Further analysis of T-RFLP accuracy for determining richness was performed by iterative, random sampling from the derived database of T-RFs. It became apparent that two constraints were influential for measuring the fidelity of a given restriction endonuclease: (i) the ability to resolve unique sequence variants and (ii) the number of unique T-RFs that fell within a measurable size range. The latter constraint was found to be more significant for estimating restriction endonuclease fidelity. Of the 18 restriction endonucleases examined, BstUI, DdeI, Sau96I, and MspI had the highest frequency of resolving single populations in model communities. All restriction endonucleases used in this study detected < or =70% of the OTUs at richness values greater than 50 OTUs per modeled community. Based on the results of our in silico experiments, the most efficacious uses of T-RFLP for microbial diversity studies are those that address situations where there is low to intermediate species richness (e.g., colonization, early successional stages, biofilm formation).

Development of clade- (Roseobacter and Alteromonas) and taxon-specific oligonucleotide probes to study interactions between toxic dinoflagellates and their associated bacteria

Bacteria associated with toxic algae in culture have been implicated in the enhancement of algal toxin production and auto-toxigenesis. Toxigenic and non-toxigenic bacterial isolates from Alexandrium spp. have been determined to belong predominantly to the α- and γ-subclasses of the class Proteobacteria. Within these subclasses, the isolates were further classified into two clades that were phylogenetically affiliated with (1) the genus Roseobacter, a newly identified group that is of major significance within the α-Proteobacteria and (2) the genus Alteromonas. Specific 16S rRNA sequence signatures were identified for these clades as well as for three pairs of isolates and for one subcluster within the Roseobacter clade and for three clusters representing eight isolates in the Alteromonas clade. Oligonucleotide probes complementary to these regions were designed and their specificities were tested using dot-blot and whole-cell in situ hybridizations of target and non-target strains. The empirically determined dissociation temperatures of the probes ranged between 55 and 65 making them applicable as a set for screening environmental samples. In situ hybridization of bacteria in cultures of Alexandrium spp. with the clade-specific probes showed a loose association of these bacteria within the phycosphere. In addition, the fluorescent signal of the probes was bright and easily distinguishable from autofluorescent bacteria and the dinoflagellates.

Screening environmental samples for source-specific bacteriophage hosts using a method for the simultaneous pouring of 12 petri plates

A simple apparatus was developed to allow 12 petri plates to be poured simultaneously by hand. It was used when screening bacterial isolates from sewage and dog feces for their ability to detect phages from these sources. This was done to assess the ease with which source-specific phage hosts can be isolated from these sources of fecal pollution. Host bacteria that consistently detected phages from sewage were easily isolated from sewage. These bacterial isolates did not detect phages from dog feces. Host bacteria were not isolated from dog feces even after screening hundreds of colonies from fecal samples from six dogs. Journal of Industrial Microbiology & Biotechnology (2000) 24, 124–126.

Evaluation of a Reporter Gene System Biomarker for Detecting Contamination in Tropical Marine Sediments.

A major challenge in conducting field assessments of potential ecological impacts is optimizing the number of samples and the costs. This is especially important in light of the growing concern over the presence of persistent organic contaminants, such as PCBs, dioxins, furans, and PAHs in sediments. A reporter gene system (RGS) assay that measures induction of the CYP1A1 gene and transcription of P450 enzyme systems is often used to assess potential toxicity of these compounds in environmental samples (1, 2, 3). RGS has gained acceptance as an inexpensive, rapid method for screening environmental samples for contaminants (4, 5). The RGS approach has been validated in the laboratory with pure compounds, known chemical mixtures, and from field-collected sediments by comparing RGS system response and chemical concentrations (1, 2, 3, 6). Our study differed from other validation studies in two respects: we used field-collected sediments over a wide range of contaminant concentrations and evaluated RGS response to sediment samples containing a mixture of dioxins, furans, and PAHs. With few exceptions, the previous validation studies using field-collected samples used fairly small sample sizes and generally evaluated one chemical group (3, 6). Few studies have compared large numbers of samples containing both PAHs and 2,3,7,8 tetrachlorodibenzo-p-dioxin (TCDD) over the range reported here. The purpose of this study was to determine if there is a high correlation between RGS response and chemistry results from the same samples. If this proves to be the case, the assay could be used to screen large areas at a relatively low cost. Samples exhibiting high responses could be targeted for further characterization using more precise, but costly, GC/MS methods. Matched sediment samples (n = 31) were collected off the northwestern shore of Johnston Island, adjacent to potential sources of PAHs and 2,3,7,8 tetrachlorodibenzo-p-dioxin (TCDD) (Site 1), and at sites farther removed from the potential contaminant sources (Sites 3, 4). To ensure blind analysis of the samples, P450 RGS assays were conducted by MEC Analytical Systems (Carlsbad, California) and Columbia Analytical Services (Vista, California) while chemical analyses were completed by the Toxic Contaminant Research Laboratory at Wright State University (Dayton, Ohio). The RGS assay used in this study was developed by Anderson et al. (1) and detailed methods have been described (1, 7). Induction in the assay is dependent upon the aryl hydrocarbon receptor (AhR) activation pathway. AhR ligands, including planar PCBs, PAHs, and TCDD, bind to AhR, activating it and resulting in its translocation to the nucleus of the cell. In the nucleus, the activated