Ultrarapid detection of SARS-CoV-2 RNA using a reverse transcription-free exponential amplification reaction, RTF-EXPAR.

A rapid isothermal method for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, is reported. The procedure uses an unprecedented reverse transcription-free (RTF) approach for converting genomic RNA into DNA. This involves the formation of an RNA/DNA heteroduplex whose selective cleavage generates a short DNA trigger strand, which is then rapidly amplified using the exponential amplification reaction (EXPAR). Deploying the RNA-to-DNA conversion and amplification stages of the RTF-EXPAR assay in a single step results in the detection, via a fluorescence read-out, of single figure copy numbers per microliter of SARS-CoV-2 RNA in under 10 min. In direct three-way comparison studies, the assay has been found to be faster than both RT-qPCR and reverse transcription loop-mediated isothermal amplification (RT-LAMP), while being just as sensitive. The assay protocol involves the use of standard laboratory equipment and is readily adaptable for the detection of other RNA-based pathogens.

Rationalisation of a mechanism for sensing single point variants in target DNA using anthracene-tagged base discriminating probes.

The labelling of DNA oligonucleotides with signalling groups that give a unique response to duplex formation depending on the target sequence is a highly effective strategy in the design of DNA-based hybridisation sensors. A key challenge in the design of these so-called base discriminating probes (BDPs) is to understand how the local environment of the signalling group affects the sensing response. The work herein describes a comprehensive study involving a variety of photophysical techniques, NMR studies and molecular dynamics simulations, on anthracene-tagged oligonucleotide probes that can sense single base changes (point variants) in target DNA strands. A detailed analysis of the fluorescence sensing mechanism is provided, with a particular focus on rationalising the high dependence of this process on not only the linker stereochemistry but also the site of nucleobase variation within the target strand. The work highlights the various factors and techniques used to respectively underpin and rationalise the BDP approach to point variant sensing, which relies on different responses to duplex formation rather than different duplex binding strengths.

Linear dichroism of visible-region chromophores using M13 bacteriophage as an alignment scaffold.

It is a challenge within the field of biomimetics to recreate the properties of light-harvesting antennae found in plants and photosynthetic bacteria. Attempts to recreate these biological structures typically rely on the alignment of fluorescent moieties via attachment to an inert linear scaffold, e.g. DNA, RNA or amyloid fibrils, to enable Förster resonance energy transfer (FRET) between attached chromophores. While there has been some success in this approach, refinement of the alignment of the chromophores is often limited, which may limit the efficiency of energy transfer achieved. Here we demonstrate how linear dichroism spectroscopy may be used to ascertain the overall alignment of chromophores bound to the M13 bacteriophage, a model linear scaffold, and demonstrate how this may be used to distinguish between lack of FRET efficiency due to chromophore separation, and chromophore misalignment. This approach will allow the refinement of artificial light-harvesting antennae in a directed fashion.

Groundwater resource vulnerability and spatial variability of nitrate contamination: Insights from high density tubewell monitoring in a hard rock aquifer.

Agriculture has been increasingly relying on groundwater irrigation for the last decades, leading to severe groundwater depletion and/or nitrate contamination. Understanding the links between nitrate concentration and groundwater resource is a prerequisite for assessing the sustainability of irrigated systems. The Berambadi catchment (ORE-BVET/Kabini Critical Zone Observatory) in Southern India is a typical example of intensive irrigated agriculture and then an ideal site to study the relative influences of land use, management practices and aquifer properties on NO3 spatial distribution in groundwater. The monitoring of >200 tube wells revealed nitrate concentrations from 1 to 360mg/L. Three configurations of groundwater level and elevation gradient were identified: i) NO3 hot spots associated to deep groundwater levels (30-60m) and low groundwater elevation gradient suggest small groundwater reserve with absence of lateral flow, then degradation of groundwater quality due to recycling through pumping and return flow; ii) high groundwater elevation gradient, moderate NO3 concentrations suggest that significant lateral flow prevented NO3 enrichment; iii) low NO3 concentrations, low groundwater elevation gradient and shallow groundwater indicate a large reserve. We propose that mapping groundwater level and gradient could be used to delineate zones vulnerable to agriculture intensification in catchments where groundwater from low-yielding aquifers is the only source of irrigation. Then, wells located in low groundwater elevation gradient zones are likely to be suitable for assessing the impacts of local agricultural systems, while wells located in zones with high elevation gradient would reflect the average groundwater quality of the catchment, and hence should be used for regional mapping of groundwater quality. Irrigation with NO3 concentrated groundwater induces a "hidden" input of nitrogen to the crop which can reach 200kgN/ha/yr in hotspot areas, enhancing groundwater contamination. Such fluxes, once taken into account in fertilizer management, would allow optimizing fertilizer consumption and mitigate high nitrate concentrations in groundwater.

Metal concentration and bioaccessibility in different particle sizes of dust and aerosols to refine metal exposure assessment.

Refined exposure assessments were realized for children, 7-9yrs, in the mining/smelting city of Oruro, Bolivia. Aerosols (PM>2.5, PM1-2.5, PM0.4-1 and PM0.5) and dust (separated in different particle size fractions: 2000-200µm, 200-50µm, 50-20µm, 20-2µm and <2µm) were sampled on football fields highly frequented by children in both the mining and smelting areas. Trace element concentrations (Ag, As, Cd, Cu, Pb, Sb, Sn and Zn) in each size fraction of dust and aerosols, lung bioaccessibility of metals in aerosols, and gastric bioaccessibility of metals in dust were measured. Exposure was assessed considering actual external exposure (i.e. exposure pathways: metals inhaled and ingested) and simulated internal exposure (i.e., complex estimation using gastric and lung bioaccessibility, deposition and clearance of particles in lungs). Significant differences between external and simulated internal exposure were attributed to dissemblances in gastric and lung bioaccessibilities, as well as metal distribution within particle size range, revealing the importance of both parameters in exposure assessment.

Macrocyclic Metal Complex-DNA Conjugates for Electrochemical Sensing of Single Nucleobase Changes in DNA.

The direct incorporation of macrocyclic cyclidene complexes into DNA via automated synthesis results in a new family of metal-functionalized DNA derivatives that readily demonstrate their utility through the ability of one redox-active copper(II)-containing strand to distinguish electrochemically between all four canonical DNA nucleobases at a single site within a target sequence of DNA.

Single Site Discrimination of Cytosine, 5-Methylcytosine, and 5-Hydroxymethylcytosine in Target DNA Using Anthracene-Tagged Fluorescent Probes.

The ability to discriminate between epigenetic variants in DNA is a necessary tool if we are to increase our understanding of the roles that they play in various biological processes and medical conditions. Herein, it is demonstrated how a simple two-step fluorescent probe assay can be used to differentiate all three major epigenetic variants of cytosine at a single locus site in a target strand of DNA.

Toxic trace elements in maternal and cord blood and social determinants in a Bolivian mining city.

This study assessed lead, arsenic, and antimony in maternal and cord blood, and associations between maternal concentrations and social determinants in the Bolivian mining city of Oruro using the baseline assessment of the ToxBol/Mine-Niño birth cohort. We recruited 467 pregnant women, collecting venous blood and sociodemographic information as well as placental cord blood at birth. Metallic/semimetallic trace elements were measured using inductively coupled plasma mass spectrometry. Lead medians in maternal and cord blood were significantly correlated (Spearman coefficient = 0.59; p < 0.001; 19.35 and 13.50 µg/L, respectively). Arsenic concentrations were above detection limit (3.30 µg/L) in 17.9% of maternal and 34.6% of cord blood samples. They were not associated (Fischer's p = 0.72). Antimony medians in maternal and cord blood were weakly correlated (Spearman coefficient = 0.15; p < 0.03; 9.00 and 8.62 µg/L, respectively). Higher concentrations of toxic elements in maternal blood were associated with maternal smoking, low educational level, and partner involved in mining.

Metal-responsive structural transformation between artificial DNA duplexes and three-way junctions.

DNA three-way junctions (3WJs) are essential structural motifs for DNA nanoarchitectures and DNA-based materials. We report herein a metal-responsive structural transformation between DNA duplexes and 3WJs using artificial oligonucleotides modified with a 2,2'-bipyridine (bpy) ligand. A mixture of bpy-modified DNA strands and natural complementary strands were self-assembled exclusively into duplexes without any transition metal ions, while they formed 3WJs in the presence of NiII ions. This transformation was induced by the formation of an interstrand NiII(bpy)3 complex, which served as a template for the 3WJ assembly. Altering the amount and identity of the metal ion regulated the 3WJ induction efficiency. Removal of the metal using EDTA quantitatively regenerated the duplexes. The metal-dependent structural conversion shown here has many potential applications in the development of stimuli-responsive DNA materials.

Trophic structure and mercury biomagnification in tropical fish assemblages, Iténez River, Bolivia.

We examined mercury concentrations in three fish assemblages to estimate biomagnification rates in the Iténez main river, affected by anthropogenic activities, and two unperturbed rivers from the Iténez basin, Bolivian Amazon. Rivers presented low to moderate water mercury concentrations (from 1.25 ng L(-1) to 2.96 ng L(-1)) and natural differences in terms of sediment load. Mercury biomagnification rates were confronted to trophic structure depicted by carbon and nitrogen stable isotopes composition (δ(15)N; δ(13)C) of primary trophic sources, invertebrates and fishes. Results showed a slight fish contamination in the Iténez River compared to the unperturbed rivers, with higher mercury concentrations in piscivore species (0.15 µg g(-1) vs. 0.11 µg g(-1) in the unperturbed rivers) and a higher biomagnification rate. Trophic structure analysis showed that the higher biomagnification rate in the Iténez River could not be attributed to a longer food chain. Nevertheless, it revealed for the Iténez River a higher contribution of periphyton to the diet of the primary consumers fish species; and more negative δ(13)C values for primary trophic sources, invertebrates and fishes that could indicate a higher contribution of methanotrophic bacteria. These two factors may enhance methylation and methyl mercury transfer in the food web and thus, alternatively or complementarily to the impact of the anthropogenic activities, may explain mercury differences observed in fishes from the Iténez River in comparison to the two other rivers.

Photocontrolled binding and binding-controlled photochromism within anthracene-modified DNA.

Modified DNA strands undergo a reversible light-induced reaction involving the intramolecular photodimerization of two appended anthracene tags. The photodimers exhibit markedly different binding behavior toward a complementary strand that depends on the number of bases between the modified positions. By preforming the duplex, photochromism can be suppressed, illustrating dual-mode gated behavior.

Mercury bioaccumulation patterns in fish from the Iténez river basin, Bolivian Amazon.

The bioaccumulation mechanism expresses an increment of mercury concentration along the lifetime of each individual. It is generally investigated along the age or size range of organisms from a same population. Water chemistry and trophic position are important factors that may influence the emergence of bioaccumulation patterns. In order to detect the influence of these parameters on fish mercury bioaccumulation patterns, we explored the relations between mercury concentration, size and isotopic trophic position of fish populations of six species (three non piscivorous and three piscivorous) in three rivers of the Iténez basin (Bolivia) with different sediment load in water and anthropogenic impact. Fishes of the Iténez basin showed fairly lower mercury contamination in relation to the regional context. They presented lower total mercury concentrations in unperturbed clear water river (average of 0.051 µg g(-1) for non piscivores; 0.088 µg g(-1) for piscivores), intermediate values (average of 0.05 and 0.104 µg g(-1)) in unperturbed white water river, whereas the highest values (average of 0.062 and 0.194 µg g(-1)) were found in the perturbed clear water river. Piscivore and invertivore species showed significant positive bioaccumulation patterns in the perturbed river and in the unperturbed white water river. No positive pattern was detected in the unperturbed clear water river. Positive patterns could not be attributed to differences in trophic condition and mean fish mercury concentration between populations. Bioaccumulation seems not to be the main factor to explain increased mercury concentrations in fish from the perturbed river.

Detection of single nucleotide polymorphisms within a sequence of a gene associated with prostate cancer using a fluorophore-tagged DNA probe.

Single nucleotide polymorphisms within a sequence of a gene associated with prostate cancer were identified using oligodeoxynucleotide probe sequences bearing internal anthracene fluorophores proximal to the SNP site. Depending upon the nature of the synthesised target sequences, probe-target duplex formation could lead to enhanced or attenuated fluorescence emission from the anthracene, enabling detection of a proximal base-pair as either matching or mismatching.

Child neurodevelopment in a Bolivian mining city.

This study evaluates the neurodevelopment of children living near contaminated mining industries during their first year of life. Participants from the city of Oruro (Bolivia) were prospectively recruited during pregnancy. Follow-up occurred between May 2007 and November 2009. Information about the socioeconomic status and medical history of the pregnant women were collected using questionnaires. Neurodevelopment was evaluated for 246 children using the Bayley Scales of Infant Development (BSID) at 10.5-12.5 months of age. Exposure to trace elements (Pb, As, Cd, Sb, Cs, Zn, Fe, Cu, Se, Rb, and Sr) during prenatal life was evaluated by testing maternal blood concentrations before delivery. Almost all measured levels were lower than the control limits. The blood lead concentration of pregnant women was low, considering the contaminated environmental context. The geometric mean was 1.76 µg/dL (95% CI: 1.68-1.84), a level comparable with those observed in non-contaminated areas. The only element found to be relatively elevated was antimony, with a geometric mean of 1.03 µg/dL (95% CI: 0.96-1.11). Our results suggest that women from this mining area were not highly exposed. The Bayley Scales of Infant Development (BSID) did not reveal mental or psychomotor abnormalities. Surprisingly, at the observed low levels, lead was positively associated with the children's BSID performance.

Influence of source distribution and geochemical composition of aerosols on children exposure in the large polymetallic mining region of the Bolivian Altiplano.

The Bolivian Altiplano (Highlands) region is subject to intense mining, tailing and smelting activities since centuries because of the presence of large and unique polymetallic ore deposits (Ag, Au, Cu, Pb, Sn, Sb, Zn). A large scale PM(10), PM(2.5) aerosol monitoring survey was conducted during the dry season in one of the largest mining cities of this region (Oruro, 200,000 inhabitants). Aerosol fractions, source distribution and transport were investigated for 23 elements at approximately 1 km(2) scale resolution, and compared to children exposure data obtained within the same geographical space. As, Cd, Pb, Sb, W and Zn in aerosols are present at relatively high concentrations when compared to studies from other mining regions. Arsenic exceeds the European council PM(10) guide value (6 ng/m(3)) for 90% of the samples, topping 200 ng/m(3). Ag, As, Cd, Cu, Pb and Sb are present at significantly higher levels in the district located in the vicinity of the smelter zone. At the city level, principal component analysis combined with the mapping of factor scores allowed the identification and deconvolution of four individual sources: i) a natural magmatic source (Co, Cs, Fe, K, Mn, Na, Rb and U) originating from soil dust, resuspended by the traffic activity; ii) a natural sedimentary source (Mg, Ca, Sr, Ba and Th) resulting from the suspension of evaporative salt deposits located South; iii) an anthropogenic source specifically enriched in mined elements (As, Cd, Cu, Pb, Sb and Zn) mainly in the smelting district of the city; and iv) a Ni-Cr source homogenously distributed between the different city districts. Enrichment factors for As, Cd and Sb clearly show the impact of smelting activities, particularly in the finest PM(2.5) fraction. Comparison to children's hair metal contents collected in five schools from different districts shows a direct exposure to smelting activity fingerprinted by a unique trace elements pattern (Ag, As, Cu, Pb, Sb).

Detection of DNA base variation and cytosine methylation at a single nucleotide site using a highly sensitive fluorescent probe.

A fluorescent DNA probe containing an anthracene group attached via an anucleosidic linker can identify all four DNA bases at a single site as well as the epigenetic modification C/5-MeC via a hybridisation sensing assay.

Transfer of mercury and methylmercury along macroinvertebrate food chains in a floodplain lake of the Beni River, Bolivian Amazonia.

We have evaluated the mercury and methylmercury transfers to and within the macroinvertebrate communities of a floodplain lake of the Beni River basin, Bolivia, during three hydrological seasons and in two habitats (open water and vegetation belt). Using the stable isotopes delta(13)C and delta(15)N, six trophic chains were identified during a previous study. Four are based on only one source: seston, organic matter from the bottom sediment, periphyton and macrophytes. Two are based on mixed sources (seston and periphyton in one case, periphyton and macrophytes in the other). During sampling, we found only one taxon that had surface sediment organic matter as food source and very few taxa whose trophic source was constituted by macrophytes. The periphyton was the most important source during all seasons; it produced the longest chain, with three trophic positions. Whatever the season and trophic source, all collected macroinvertebrates contained methyl mercury and the latter was biomagnified in all trophic chains that we identified. The biomagnification of methylmercury through invertebrate trophic chains accurately reflected the existence and length of these chains. Biomagnification was virtually non-existent in the sediment-based chain, low and restricted to the dry season in the macrophyte-based chain. It was significant in the seston-based chain, but limited by the existence of only two trophic levels and restricted to the wet season. Finally, it was very effective in the periphyton-based chain, which offers the highest rate of contamination of the source but, above all, the largest number of trophic levels.