Simple, Robust Invertebrate DNA Barcoding: Chelex-Based DNA Extraction and Optimized COI Amplification

Chelex-based DNA extractions are well suited for student DNA barcoding research because they are simple, safe, and inexpensive and can be performed without specialized laboratory equipment, allowing them to be performed in classrooms or at home. Extracted DNA is stable in Chelex solution for at least a week at ambient temperature, allowing collection of DNA samples from remote students. These extractions provide quality DNA for many taxa and are optimal for barcoding invertebrates, especially in combination with novel cytochrome c oxidase I (COI) primer cocktails and PCR cycling conditions.

Measuring ZnO nanoparticles available concentrations in contaminated soils using the diffusive gradient in thin-films (DGT) technique

A major gap in understanding nanomaterials behaviour in the environment is a lack of reliable tools to measure their available concentrations. In this research we use diffusive gradients in thin films (DGT) for measuring concentrations of zinc oxide nanoparticles (ZNO NPs) in soils. Available nanoparticle concentrations were assessed by difference, using paired DGT devices with and without 1000 MWCO dialysis membranes to exclude NPs. We used ZnO because its toxic effects are accelerated through dissolution to Zn²⁺. Our test soils had different pH and organic matter (OM) contents, which both affect the dissolution rate of ZnO NPs. Woburn (pH ≈ 6.9, OM ≈ 1.8%) and Lufa (pH ≈ 5.9, OM ≈ 4.2%) soils were spiked to a single concentration of 500 mg of ZnO NPs per 1 kg of soil and the available concentrations of ZnO NPs and dissolved zinc were evaluated in 3, 7, 14, 21, 28, 60, 90, 120, 150 and 180 day intervals using DGT. The results showed that the dissolution of ZnO NPs, as well as the available concentrations of both dissolved and nanoparticulate Zn, was much higher in Lufa soil than in Woburn. This work demonstrates that DGT can be used as a simple yet reliable technique for determining concentrations of ZnO NPs in soils and probing its dissolution kinetics.

Assessing metal contaminants in Antarctic soils using diffusive gradients in thin-films

Metal contaminants in Antarctic soils are typically found around research stations which are concentrated in ice-free coastal areas. The risk of these contaminants to the Antarctic environment is not well understood, given Antarctica's unique organisms and climate. This study assessed the use of diffusive gradients in thin-films (DGT), a passive sampler that measures fluxes of labile metals from soils to porewaters, in Antarctic soils. DGT-labile measurements were compared to three chemical extractants of increasing strength including high-purity water, dilute acid (1 M HCl), and concentrated acids (3:1 v/v HNO₃:HCl), to understand differences in contaminant geochemistry that may affect environmental risk. One site had high lead concentrations measured with dilute (114 ± 4 mg kg^-1) and concentrated (150 ± 10 mg kg^-1) acids, while DGT-labile concentrations were below the method detection limit (0.5 μg L^-1), indicating that the lead species has low solubility or lability. Another site had low concentrations of zinc measured by dilute (36.2 ± 0.5 mg kg^-1) or concentrated (76 ± 6 mg kg^-1) acid extracts, but had high DGT-labile concentrations (350 ± 80 μg L^-1). This reflects an active source of zinc supplied from soil to pore water over time. Copper was found to be acid extractable, water-soluble, and DGT-labile, with DGT-labile concentrations of up to 12 μg L^-1. Despite the soil and metal-specific geochemical differences, any of the extracts could be used with statistical clustering techniques to identify differences in sites with elevated metal concentrations. This study shows that the DGT-method can identify contaminated sites comparably to chemical extracts but provides environmentally relevant measurements of metal contaminant lability in Antarctic soils.

MinION-Based DNA Barcoding of Preserved and Non-Invasively Collected Wildlife Samples

The ability to sequence a variety of wildlife samples with portable, field-friendly equipment will have significant impacts on wildlife conservation and health applications. However, the only currently available field-friendly DNA sequencer, the MinION by Oxford Nanopore Technologies, has a high error rate compared to standard laboratory-based sequencing platforms and has not been systematically validated for DNA barcoding accuracy for preserved and non-invasively collected tissue samples. We tested whether various wildlife sample types, field-friendly methods, and our clustering-based bioinformatics pipeline, SAIGA, can be used to generate consistent and accurate consensus sequences for species identification. Here, we systematically evaluate variation in cytochrome b sequences amplified from scat, hair, feather, fresh frozen liver, and formalin-fixed paraffin-embedded (FFPE) liver. Each sample was processed by three DNA extraction protocols. For all sample types tested, the MinION consensus sequences matched the Sanger references with 99.29%-100% sequence similarity, even for samples that were difficult to amplify, such as scat and FFPE tissue extracted with Chelex resin. Sequencing errors occurred primarily in homopolymer regions, as identified in previous MinION studies. We demonstrate that it is possible to generate accurate DNA barcode sequences from preserved and non-invasively collected wildlife samples using portable MinION sequencing, creating more opportunities to apply portable sequencing technology for species identification.

Evaluation of DNA Extraction Methods for Processing Fingerprint Powder-Coated Forensic Evidence

In unison, fingerprinting and DNA analysis have played a pivotal role in forensic investigations. Fingerprint powders that are available on the market can come in a range of colors and with specific properties. This study evaluated the efficiency of DNA extraction from samples coated with 3 brands of fingerprint powders: Lightning, Sirchie, and SupraNano, covering a range of colors and properties. A total of 23 fingerprint powders were tested using the Chelex, Promega DNA IQ™, and Applied Biosystems™ PrepFiler™ DNA extraction protocols. The DNA IQ™ and PrepFiler™ methods extracted higher yields of DNA in comparison to Chelex, which also accounted for better quality of PowerPlex x00AE; 21 DNA profiles recovered. There were no signs of degradation or inhibition in the quantification data, indicating that samples returning low DNA yield was due to interference during DNA extraction and not PCR inhibition. DNA profiles were recovered from the majority of fingerprint powders with only a single powder, Sirchie Magnetic Silver, failing to produce a profile using any of the methods tested. A link was observed between the DNA extraction chemistry, fingerprint powder property, that is, nonmagnetic, magnetic and aqueous, and the brand of fingerprint powder. Overall, the DNA IQ™ method was favorable for nonmagnetic fingerprint powders, while magnetic fingerprint powders produced more DNA profiles when extracted with the PrepFiler™ chemistry. This study highlights the importance of screening DNA extraction chemistries for the type of fingerprint powder used, as there is not a single DNA extraction method that suits all fingerprint powder brands and properties.

Comparison of two DNA extraction methods from larvae, pupae, and adults of Aedes aegypti

Mosquitoes are the most important arthropods from the point of view of public health, due to the fact that they can transmit a large number of pathogens which can cause diseases to humans and animals. Aedes aegypti (L.) is one of the most important vector species in the world, since it can transmit numerous pathogens such as dengue, Zika, and chikungunya. Therefore, studies involving the molecular aspects of this and other mosquitoes species are currently increasing. In this report, we describe the comparison between two DNA extraction techniques, Chelex and cetyltrimethylammonium bromide (CTAB), for carrying out DNA extraction in larvae, pupae and adult female of Ae. aegypti. The Chelex technique was superior in the amount and purity of DNA as compared to the CTAB technique in the three life stages we tested.

New insights into chelator recycling by a chelating resin: From molecular mechanisms to applicability

As part of the project of developing a "green" and highly feasible soil remediation process, recycling an eco-friendly chelating agent, glycine, using Chelex-100 chelating resin, was studied. Two model complexes, copper and nickel glycinates, were tested under various conditions, including equivalent viscosity but different temperature conditions. Two similar complexes demonstrated very different reactivity towards Chelex-100. An in-depth study led to the discovery of unusual metal-dependent mechanisms of the complex-to-resin metal transfer. Particularly, nickel transfer proceeds via a dissociative mechanism, whereas copper transfer does not require pre-dissociation of the complexes, and proceeds via the associative ligand-exchange mechanism. Both processes result in the recovery of the used chelator. The glycine solution was applied on the spiked soil, then recovered on Chelex-100 resin and successfully reused, thus demonstrating a proof of the concept. These findings contribute to the science, strategies, and methodology of both water purification and chelator recycling fields.

Assessing DNA recovery from chewing gum

The purpose of this study was to evaluate which DNA extraction method yields the highest quantity of DNA from chewing gum. In this study, several popular extraction methods were tested, including Chelex-100, phenol-chloroform-isoamyl alcohol (PCIA), DNA IQ, PrepFiler, and QIAamp Investigator, and the quantity of DNA recovered from chewing gum was determined using real-time polymerase chain reaction with Quantifiler. Chewed gum control samples were submitted by anonymous healthy adult donors, and discarded environmental chewing gum samples simulating forensic evidence were collected from outside public areas (e.g., campus bus stops, streets, and sidewalks). As expected, results indicate that all methods tested yielded sufficient amplifiable human DNA from chewing gum using the wet-swab method. The QIAamp performed best when DNA was extracted from whole pieces of control gum (142.7 ng on average), and the DNA IQ method performed best on the environmental whole gum samples (29.0 ng on average). On average, the QIAamp kit also recovered the most DNA from saliva swabs. The PCIA method demonstrated the highest yield with wet swabs of the environmental gum (26.4 ng of DNA on average). However, this method should be avoided with whole gum samples (no DNA yield) due to the action of the organic reagents in dissolving and softening the gum and inhibiting DNA recovery during the extraction.

Zinc enhances CDKN2A, pRb1 expression and regulates functional apoptosis via upregulation of p53 and p21 expression in human breast cancer MCF-7 cell

Zinc (Zn) is an essential trace elements, its deficiency is associated with increased incidence of human breast cancer. We aimed to study the effect of Zn on human breast cancer MCF-7 cells cultured in Zn depleted and Zn adequate medium. We found increased cancer cell growth in zinc depleted condition, further Zn supplementation inhibits the viability of breast cancer MCF-7 cell cultured in Zn deficient condition and the IC_25, IC₅₀ value for Zn is 6.2μM, 15μM, respectively after 48h. Zn markedly induced apoptosis through the characteristic apoptotic morphological changes and DNA fragmentation after 48h. In addition, Zn deficient cells significantly triggered intracellular ROS level and develop oxidative stress induced DNA damage; it was confirmed by elevated expression of CYP1A, GPX, GSK3β and TNF-α gene. Zinc depleted MCF-7 cells expressed significantly (p≤0.001) decreased levels of CDKN2A, pRb1, p53 and increased the level of mdm2 expression. Zn supplementation (IC₅₀=15μM), increased significantly CDKN2A, pRB1 & p53 and markedly reduced mdm2 expression; also protein expression levels of CDKN2A and pRb1 was significantly increased. In addition, intrinsic apoptotic pathway related genes such as Bax, caspase-3, 8, 9 & p21 expression was enhanced and finally induced cell apoptosis. In conclusion, physiological level of zinc is important to prevent DNA damage and MCF-7 cell proliferation via regulation of tumor suppressor gene.

Permanganate-assisted removal of PCR inhibitors during the DNA Chelex extraction from stained denim samples

In this study, it was demonstrated that the DNA Chelex extraction combined with the permanganate assisted-oxidation is highly efficient in removing the PCR inhibitors often found in clothing materials, such as phthalocyanine. The extraction assays were conducted in saliva, blood and epithelial cells samples mixed with three oxidation-resistant dye copper(II) α-phthalocyanine, copper(II) β-phthalocyanine and tetrasulfonated copper(II) β-phthalocyanine. After DNA amplification, all samples were able to provide full DNA profiles. The permanganate/Chelex system was tested further on denim-stained samples and displayed the same ability to remove the PCR inhibitors from the commercial textile materials.

DNA and bone structure preservation in medieval human skeletons

Morphological and ultrastructural data from archaeological human bones are scarce, particularly data that have been correlated with information on the preservation of molecules such as DNA. Here we examine the bone structure of macroscopically well-preserved medieval human skeletons by transmission electron microscopy and immunohistochemistry, and the quantity and quality of DNA extracted from these skeletons. DNA technology has been increasingly used for analyzing physical evidence in archaeological forensics; however, the isolation of ancient DNA is difficult since it is highly degraded, extraction yields are low and the co-extraction of PCR inhibitors is a problem. We adapted and optimised a method that is frequently used for isolating DNA from modern samples, Chelex(®) 100 (Bio-Rad) extraction, for isolating DNA from archaeological human bones and teeth. The isolated DNA was analysed by real-time PCR using primers targeting the sex determining region on the Y chromosome (SRY) and STR typing using the AmpFlSTR(®) Identifiler PCR Amplification kit. Our results clearly show the preservation of bone matrix in medieval bones and the presence of intact osteocytes with well preserved encapsulated nuclei. In addition, we show how effective Chelex(®) 100 is for isolating ancient DNA from archaeological bones and teeth. This optimised method is suitable for STR typing using kits aimed specifically at degraded and difficult DNA templates since amplicons of up to 250bp were successfully amplified.

Spectrophotometric determination and removal of unchelated europium ions from solutions containing Eu-diethylenetriaminepentaacetic acid chelate-peptide conjugates

Europium chelates conjugated with peptide ligands are routinely used as probes for conducting in vitro binding experiments. The presence of unchelated Eu ions in these formulations gives high background luminescence and can lead to poor results in binding assays. In our experience, the reported methods for purification of these probes do not achieve adequate removal of unchelated metal ions in a reliable manner. In this work, a xylenol orange-based assay for the quantification of unchelated metal ions was streamlined and used to determine levels of metal ion contamination as well as the success of metal ion removal on attempted purification. We compared the use of Empore chelating disks and Chelex 100 resin for the selective removal of unchelated Eu ions from several Eu-diethylenetriaminepentaacetic acid chelate-peptide conjugates. Both purification methods gave complete and selective removal of the contaminant metal ions. However, Empore chelating disks were found to give much higher recoveries of the probes under the conditions used. Related to the issue of probe recovery, we also describe a significantly more efficient method for the synthesis of one such probe using Rink amide AM resin in place of Tentagel S resin.

Comparison of four methods for extracting DNA from dried blood on filter paper for PCR targeting the mitochondrial Plasmodium genome

BACKGROUND

Few studies comparing multiple methods for DNA extraction from dried blood spots (DBS) on filter paper for PCR targeting the Plasmodium genome have been done.

METHODS

Frequently-used methods for DNA extraction from DBS using Chelex-100, InstaGene Matrix, QIAamp DNA Mini Kit and TE buffer were compared on a dilution series of a standardized Plasmodium falciparum positive sample. The two DNA extraction methods resulting in the lowest limits of detection were compared by testing both on 31 P. falciparum positive samples collected under field conditions and stored for 4 years.

RESULTS

The Chelex-100, InstaGene Matrix and QIAamp DNA Mini Kit methods performed similarly, resulting in the detection of 0.5 to 2 parasites per microliter (p/µl). The same 13 clinical samples (13/31; 42%) were positive using both DNA extraction methods with the lowest limits of detection.

CONCLUSIONS

Simple and low-cost methods can be sensitive and useful in extracting DNA from DBS. Poor results on stored clinical DBS indicate that further studies on the impact of storage duration and conditions, and choice of filter paper should be performed.