A rapid method of DNA isolation using laundry detergent

Extraction of high-molecular-weight DNA from Streptococcus spp. for nanopore sequencing in resource-limited settings

The long-read sequencing platform MinION, developed by Oxford Nanopore Technologies, enables the sequencing of bacterial genomes in resource-limited settings, such as field conditions or low- and middle-income countries. For this purpose, protocols for extracting high-molecular-weight DNA using nonhazardous, inexpensive reagents and equipment are needed, and some methods have been developed for gram-negative bacteria. However, we found that without modification, these protocols are unsuitable for gram-positive Streptococcus spp., a major threat to fish farming and food security in low- and middle-income countries. Multiple approaches were evaluated, and the most effective was an extraction method using lysozyme, sodium dodecyl sulfate, and proteinase K for lysis of bacterial cells and magnetic beads for DNA recovery. We optimized the method to consistently achieve sufficient yields of pure high-molecular-weight DNA with minimal reagents and time and developed a version of the protocol which can be performed without a centrifuge or electrical power. The suitability of the method was verified by MinION sequencing and assembly of 12 genomes of epidemiologically diverse fish-pathogenic Streptococcus iniae and Streptococcus agalactiae isolates. The combination of effective high-molecular-weight DNA extraction and MinION sequencing enabled the discovery of a naturally occurring 15 kb low-copy number mobilizable plasmid in S. iniae, which we name pSI1. We expect that our resource-limited settings-adapted protocol for high-molecular-weight DNA extraction could be implemented successfully for similarly recalcitrant-to-lysis gram-positive bacteria, and it represents a method of choice for MinION-based disease diagnostics in low- and middle-income countries.

A handmade DNA extraction kit using laundry powder; insights on simplicity, cost-efficiency, rapidity, safety and the quality of purified DNA

Here we describe an in-house kit for high throughput DNA extraction using laundry detergent. A simplified lysis buffer made only from 0.08 M EDTA, 0.1 M Tris, and laundry powder is the core of our protocol. We extracted genomic DNA from 150 µL of whole blood collected from different farm animals and compared the performance to both the DNeasy Blood & Tissue Kit (Qiagen) and the widely used salting-out procedure. An evaluation of the concentration and quality of the extracted DNA was then assessed by the NanoDrop absorption spectra, agarose gel migration, amplification in PCR and the Sanger sequencing. The in-house kit successfully extracted clean DNA from all blood samples, and discernably outperformed the commercial kits and the original salting-out procedure in the sense of the simplicity, cost-efficiency, quantity, and the quality of purified DNA. Apart from replacing proteinase K and the sodium dodecyl sulfate treatment by the laundry detergent, our protocol instructs a lysis buffer that eliminates sucrose, Triton X-100, MgCl₂, NH₄Cl, and KCl. Our handmade kit might be of interest for laboratories in underdeveloped countries with a budget shortage or applications in difficult field conditions, for example, when fridge storage for proteinase K cannot be ensured.

‘Clean’ hydrolase reactions using commercial washing powder

We report the use of commercial laundry powder as a biocatalyst for a range of lipase-catalysed reactions including (trans)esterification, ester hydrolysis and chemoenzymatic epoxidation reactions. The enzymatic laundry powder exhibited excellent stability and recyclability, making it a readily available and cheap biocatalyst for chemical transformations.

We report the use of commercial laundry powder as a biocatalyst for a range of lipase-catalysed reactions including (trans)esterification, ester hydrolysis and chemoenzymatic epoxidation reactions.

Isolation of nematode DNA from 100 g of soil using Fe3O4 super paramagnetic nanoparticles

An economical method for extracting nematode DNA from 100 g of soil was developed to facilitate nematode detection and quantification, and tested using the Northern root-knot nematode,Meloidogyne hapla. The method utilised enzymatic laundry detergent lysis, Fe3O4super paramagnetic iron oxide nanoparticle (SPION) capture, and polyvinylpolypyrrolidone (PVPP) purification. Resultant DNA from this SPION capture method was approximately 100-fold less but of similar quality to DNA obtained from a standard phenol procedure and a commercial DNA extraction kit. An addition of 10 mg of nanoparticles to the extraction lysate was identified to maximise DNA yield while minimising co-capture of contaminants. The detection limit of the SPION capture method was approximately 100 nematodes (100 g soil)−1. The SPION capture method extracted nematode DNA from mineral soils but requires further optimisation for extraction from high organic matter (i.e., ‘muck’) soils. The benefits of this method compared to alternative techniques are discussed.

Laundry in a washing machine as a mediator of secondary and tertiary DNA transfer

The aim of this work was to investigate the possibility of secondary and tertiary DNA transfer during laundry. The modes of transfer tested were mixed and separate laundry of worn and unworn garments in household and public washing machines. In addition, the possibility of a background DNA carry-over from a washing machine's drum was investigated. In the mixed (worn and unworn garments washed together) laundry experiment, 22% of samples from new unworn socks with no traceable DNA prior to experiment produced DNA profiles post-laundry. In the tertiary DNA transfer experiment performed in a public washing machine (unworn garments only), no detectable DNA profiles were observed. Samples collected from the internal drum of 25 washing and drying machines did not produce detectable STR profiles. The implications of these results are discussed in the context of forensic DNA casework analysis. Graphical Abstract ᅟA real-life scenario of secondary DNA transfer between worn and unworn garments during machine washing has been evaluated. Experiments demonstrated this scenario is possible (22% of samples) and may in fact result in high quality DNA profiles. On the contrary, testing washing machine's interior for deposition of biological material between separate washing cycles to serve as a mediator of tertiary DNA transfer resulted in no DNA profiles.

Highly polymorphic microsatellite markers for Radix balthica (Linnaeus 1758)

We present data for eight polymorphic microsatellite markers isolated from a microsatellite-enriched DNA library for the freshwater snail Radix balthica. Three of them were specific for R. balthica while five also amplified polymorphic products in two congeneric species. Test application on populations from all over the species range has shown that these loci are highly informative for analysing population structure and estimating migration rates. Observed deviations from Hardy-Weinberg equilibrium are attributed to a mixed mating system.

Characterization of membrane vesicles in plant extracts

During the preparation of plant extracts by a press-slit technique, membranes of cell walls and cell organelles of the plant material form vesicles, which are colloidally dispersed. It was assumed that chlorophyll-containing green extracts enclose lipoidic structures. Vesicles in aqueous mistletoe extracts (extracts of Viscum album L.) were analyzed by cryo-transmission electron microscopy (cryo-TEM) without fixation. For the first time, it was possible to analyze unfixed vesicles in the mistletoe extract. Micrographs of cryo-TEM showed predominantly unilamellar vesicles of different sizes. The quantification of vesicles was established through the analysis of phospholipids, which are major components of membranes. The method was validated mainly according to ICH guidelines for the validation of analytical methods (Q2A and Q2B). For further characterization of the vesicle size, a method was developed which is based on the separation of the vesicles from low molecular weight substances by size exclusion chromatography. Fractions were collected and average sizes were determined by multi-angle laser light scattering (MALLS). Furthermore, the UV-vis absorbance and phospholipid concentration were analyzed. Phospholipid quantification was in agreement with photometrical data. Sizes determined by cryo-TEM and by light scattering showed consistent results.

Comparing the efficacy of morphologic and DNA-based taxonomy in the freshwater gastropod genus Radix (Basommatophora, Pulmonata)

Background

Reliable taxonomic identification at the species level is the basis for many biological disciplines. In order to distinguish species, it is necessary that taxonomic characters allow for the separation of individuals into recognisable, homogeneous groups that differ from other such groups in a consistent way. We compared here the suitability and efficacy of traditionally used shell morphology and DNA-based methods to distinguish among species of the freshwater snail genus Radix (Basommatophora, Pulmonata).

Results

Morphometric analysis showed that shell shape was unsuitable to define homogeneous, recognisable entities, because the variation was continuous. On the other hand, the Molecularly defined Operational Taxonomic Units (MOTU), inferred from mitochondrial COI sequence variation, proved to be congruent with biological species, inferred from geographic distribution patterns, congruence with nuclear markers and crossing experiments. Moreover, it could be shown that the phenotypically plastic shell variation is mostly determined by the environmental conditions experienced.

Conclusion

Contrary to DNA-taxonomy, shell morphology was not suitable for delimiting and recognising species in Radix. As the situation encountered here seems to be widespread in invertebrates, we propose DNA-taxonomy as a reliable, comparable, and objective means for species identification in biological research.

Modified salting-out method: high-yield, high-quality genomic DNA extraction from whole blood using laundry detergent

Different approaches have been used to extract DNA from whole blood. In most of these methods enzymes (such as proteinase K and RNAse A) or toxic organic solvents (such as phenol or guanidine isothiocyanate) are used. Since these enzymes are expensive, and most of the materials that are used routinely are toxic, it is desirable to apply an efficient DNA extraction procedure that does not require the use of such materials. In this study, genomic DNA was extracted by the salting-out method, but instead of using an analytical-grade enzyme and chemical detergents, as normally used for DNA isolation, a common laundry powder was used. Different concentrations of the powder were tested, and proteins were precipitated by NaCl-saturated distilled water. Finally, DNA precipitation was performed with the use of 96% ethanol. From the results, we conclude that the optimum concentration of laundry powder for the highest yield and purity of isolated DNA is 30 mg/mL. The procedure was optimized, and a final protocol is suggested. Following the same protocol, DNA was extracted from 100 blood samples, and their amounts were found to be >50 microg/mL of whole blood. The integrity of the DNA fragments was confirmed by agarose gel electrophoresis. Furthermore, the extracted DNA was used as a template for PCR reaction. The results obtained from PCR showed that the final solutions of extracted DNA did not contain any inhibitory material for the enzyme used in the PCR reaction, and indicated that the isolated DNA was of good quality. These results show that this method is simple, fast, safe, and cost-effective, and can be used in medical laboratories and research centers.

Why do snails have hairs? A Bayesian inference of character evolution

Background

Costly structures need to represent an adaptive advantage in order to be maintained over evolutionary times. Contrary to many other conspicuous shell ornamentations of gastropods, the haired shells of several Stylommatophoran land snails still lack a convincing adaptive explanation. In the present study, we analysed the correlation between the presence/absence of hairs and habitat conditions in the genus Trochulus in a Bayesian framework of character evolution.

Results

Haired shells appeared to be the ancestral character state, a feature most probably lost three times independently. These losses were correlated with a shift from humid to dry habitats, indicating an adaptive function of hairs in moist environments. It had been previously hypothesised that these costly protein structures of the outer shell layer facilitate the locomotion in moist habitats. Our experiments, on the contrary, showed an increased adherence of haired shells to wet surfaces.

Conclusion

We propose the hypothesis that the possession of hairs facilitates the adherence of the snails to their herbaceous food plants during foraging when humidity levels are high. The absence of hairs in some Trochulus species could thus be explained as a loss of the potential adaptive function linked to habitat shifts.

Molecular phylogeny and character evolution in the Western Palaearctic Helicidae s.l. (Gastropoda: Stylommatophora)

In this study, we present a molecular phylogeny for the west Palaearctic Helicidae sensu lato based on sequence data from two mitochondrial (COI, 16S rDNA) and two nuclear (ITS-1, 18S rDNA) genes. Maximum likelihood analysis and Bayesian inference revealed well supported monophyletic clades partly conflicting traditional classifications. Based on these results, we propose the following system. The Western Palaearctic Helicidae s.l. consist of two families, Helicidae and Hygromiidae. Within the Helicidae, three well supported subfamilies can be recognised: the Helicinae, Ariantinae, and Helicodontinae. The Hygromiidae consist of three clades: the Hygromiinae, the Helicellinae, and a yet unnamed clade comprising the genera Sphincterochila and Cochlicella. We then used the phylogeny to study the evolution of anatomical, and ecological characters traditionally used for systematic classification. In the Helicidae s.l., two independent evolutionary transitions to life in xeric environments occurred, which allowed the occupation of new niches with a subsequent radiation of the Helicellinae-Cochlicella/Sphincterochila clade and the Helicinae. Whereas, the multiplication of the Glandulae mucosae is a synapomorphy of the Hygromiidae, the lovedart sac apparatus is present in all groups and thus, the trait cannot provide a synapomorphy for either families or subfamilies. Additionally, we evaluated the use of structural molecular genetic characters for taxonomic assessment. The presence of an unique loop region of the 16S rDNA gene and a short tandem repeat in the ITS-1 region provide independent evidence for the monophyly of these major two groups, and can be used for preliminary classification.

Ecological and morphological differentiation among cryptic evolutionary lineages in freshwater limpets of the nominal form-group Ancylus fluviatilis (O.F. Müller, 1774)

The phylogeny and potential mode of speciation of the river limpet Ancylus fluviatilis (Basommatophora) was examined using mitochondrial DNA sequences from 16S ribosomal RNA, cytochrome c oxidase subunit I (COI) and nuclear DNA from internal transcribed spacer (ITS-1) regions from 103 populations across Europe. Four highly divergent lineages were observed within Ancylus. Clade 1, representing the nominal taxon Ancylus fluviatilis (O.F. Müller, 1774), is mainly found in central and northern Europe, Clade 2 is present in a single Portuguese population, Clade 3 is distributed on the Canary islands, North Africa and the eastern Mediterranean region, whereas Clade 4 inhabits the Northern Mediterranean coasts. Phylogenetic analyses revealed an overall consistent topology of nuclear and mitochondrial gene trees. Based on a molecular clock, we estimated that the basic radiation occurred in the late Pliocene. Although clades differ significantly in size independent shell shape, morphological differentiation of lineages is not feasible without genetic data. Environmental data related to climate (precipitation, temperature, etc.) showed a significant differentiation of clades. Clade 1 dwells in relatively colder and more stable habitats than Clades 3 and 4, whose habitats in turn differ in a low or high amount of precipitation during spring and autumn, respectively. Based on the combined data sets on mitochondrial DNA, nuclear DNA, morphological and ecological differentiation, we conclude that Ancylus represents a cryptic species complex of reproductively and genetically isolated lineages. In addition, the joint analysis suggests that ecological speciation is probable to explain current patterns.

Evidence for survival of Pleistocene climatic changes in Northern refugia by the land snail Trochoidea geyeri (Soós 1926) (Helicellinae, Stylommatophora)

BACKGROUND

The study of organisms with restricted dispersal abilities and presence in the fossil record is particularly adequate to understand the impact of climate changes on the distribution and genetic structure of species. Trochoidea geyeri (Soós 1926) is a land snail restricted to a patchy, insular distribution in Germany and France. Fossil evidence suggests that current populations of T. geyeri are relicts of a much more widespread distribution during more favourable climatic periods in the Pleistocene.

RESULTS

Phylogeographic analysis of the mitochondrial 16S rDNA and nuclear ITS-1 sequence variation was used to infer the history of the remnant populations of T. geyeri. Nested clade analysis for both loci suggested that the origin of the species is in the Provence from where it expanded its range first to Southwest France and subsequently from there to Germany. Estimated divergence times predating the last glacial maximum between 25-17 ka implied that the colonization of the northern part of the current species range occurred during the Pleistocene.

CONCLUSION

We conclude that T. geyeri could quite successfully persist in cryptic refugia during major climatic changes in the past, despite of a restricted capacity of individuals to actively avoid unfavourable conditions.

A sugar, laundry detergent, and salt method for extraction of deoxyribonucleic acid from blood

We present a method for DNA extraction from peripheral blood using sugar, commercial detergent, and sodium salt. Our method is simple, fast, and inexpensive; its qualitative parameters do not significantly differ from the standard salting-out procedure.

Phylogeographic history of the land snail Candidula unifasciata (Helicellinae, Stylommatophora): fragmentation, corridor migration, and secondary contact

We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.

Phenotypic evolution and hidden speciation in Candidula unifasciata ssp. (Helicellinae, Gastropoda) inferred by 16S variation and quantitative shell traits

In an effort to link quantitative morphometric information with molecular data on the population level, we have analysed 19 populations of the conchologically variable land snail Candidula unifasciata from across the species range for variation in quantitative shell traits and at the mitochondrial 16S ribosomal (r)DNA locus. In genetic analysis, including 21 additional populations, we observed two fundamental haplotype clades with an average pairwise sequence divergence of 0.209 +/- 0.009 between clades compared to 0.017 +/- 0.012 within clades, suggesting the presence of two different evolutionary lineages. Integrating additional shell material from the Senckenberg Malacological Collection, a highly significant discriminant analysis on the morphological shell traits with fundamental haplotype clades as grouping variable suggested that the less frequent haplotype corresponds to the described subspecies C. u. rugosiuscula, which we propose to regard as a distinct species. Both taxa were highly subdivided genetically (FST = 0.648 and 0.777 P < 0.001). This was contrasted by the partition of morphological variance, where only 29.6% and 21.9% of the variance were distributed among populations, respectively. In C. unifasciata, no significant association between population pairwise FST estimates and corresponding morphological fixation indices could be detected, indicating independent evolution of the two character sets. Partial least square analysis of environmental factors against shell trait variables in C. u. unifasciata revealed significant correlations between environmental factors and certain quantitative shell traits, whose potential adaptational values are discussed.