Solid-state reference electrodes based on carbon nanotubes and polyacrylate membranes

A novel potentiometric solid-state reference electrode containing single-walled carbon nanotubes as the transducer layer between a polyacrylate membrane and the conductor is reported here. Single-walled carbon nanotubes act as an efficient transducer of the constant potentiometric signal originating from the reference membrane containing the Ag/AgCl/Cl− ions system, and they are needed to obtain a stable reference potentiometric signal. Furthermore, we have taken advantage of the light insensitivity of single-walled carbon nanotubes to improve the analytical performance characteristics of previously reported solid-state reference electrodes. Four different polyacrylate polymers have been selected in order to identify the most efficient reservoir for the Ag/AgCl system. Finally, two different arrangements have been assessed: (1) a solid-state reference electrode using photo-polymerised n-butyl acrylate polymer and (2) a thermo-polymerised methyl methacrylate:n-butyl acrylate (1:10) polymer. The sensitivity to various salts, pH and light, as well as time of response and stability, has been tested: the best results were obtained using single-walled carbon nanotubes and photo-polymerised n-butyl acrylate polymer. Water transport plays an important role in the potentiometric performance of acrylate membranes, so a new screening test method has been developed to qualitatively assess the difference in water percolation between the polyacrylic membranes studied. The results presented here open the way for the true miniaturisation of potentiometric systems using the excellent properties of single-walled carbon nanotubes

Multivariate analysis of mineral constituents of edible Parasol Mushroom (Macrolepiota procera) and soils beneath fruiting bodies collected from Northern Poland

Caps and stipes of 141 fruiting bodies of Parasol Mushroom (Macrolepiota procera) and surface layer of soils collected from 11 spatially distant and background (pristine) areas in Northern Poland were analyzed for Ag, Al, Ba, Ca, Cd, Co, Cr, Cu, Fe, Hg, K, Mg, Mn, Na, Ni, P, Pb, Rb, Sr, and Zn by inductively coupled plasma optical emission spectroscopy and cold vapor atomic absorption spectroscopy. In terms of bioconcentration and bioexclusion concept, K, Ag, Cu, Rb, and P were highly bioconcentrated in caps, and their bioconcentration factor values varied for the 11 sites between 120 and 500—67–420, 70–220, 10–170, and 45–100, respectively. Cd, Zn, Mg, and Na showed bioconcentration factors (BCFs) between 3.3 and 36, 3.7–15, 0.92–6.3, and 1.4–44 while Al, Ba, Ca, Co, Cr, Mn, Ni, Pb, and Sr were excluded (BCF < 1). The Parasol Mushroom is a species harvested in the wild, and its caps are of unique taste and can contain a spectrum of essential and hazardous mineral compounds accumulated at elevated concentrations, even if collected at the background (pristine) areas. These elevated mineral concentrations of the caps are due to the efficient bioconcentration potential of the species (K, Ag, Cu, Rb, P, Cd, Zn, Mg, and Na) and abundance in the soil substrates (Al, Ca, Fe, Mn). The estimated intake rates of Cd, Hg, and Pb contained in Parasol Mushroom’s caps show a cause for concern associated with these metals resulting from the consumption of between 300- and 500-g caps daily, on a frequent basis in the mushrooming season

Familial hypercholesterolaemia in children and adolescents from 48 countries: a cross-sectional study

Background: Approximately 450 000 children are born with familial hypercholesterolaemia worldwide every year, yet only 2·1% of adults with familial hypercholesterolaemia were diagnosed before age 18 years via current diagnostic approaches, which are derived from observations in adults. We aimed to characterise children and adolescents with heterozygous familial hypercholesterolaemia (HeFH) and understand current approaches to the identification and management of familial hypercholesterolaemia to inform future public health strategies. Methods: For this cross-sectional study, we assessed children and adolescents younger than 18 years with a clinical or genetic diagnosis of HeFH at the time of entry into the Familial Hypercholesterolaemia Studies Collaboration (FHSC) registry between Oct 1, 2015, and Jan 31, 2021. Data in the registry were collected from 55 regional or national registries in 48 countries. Diagnoses relying on self-reported history of familial hypercholesterolaemia and suspected secondary hypercholesterolaemia were excluded from the registry; people with untreated LDL cholesterol (LDL-C) of at least 13·0 mmol/L were excluded from this study. Data were assessed overall and by WHO region, World Bank country income status, age, diagnostic criteria, and index-case status. The main outcome of this study was to assess current identification and management of children and adolescents with familial hypercholesterolaemia. Findings: Of 63 093 individuals in the FHSC registry, 11 848 (18·8%) were children or adolescents younger than 18 years with HeFH and were included in this study; 5756 (50·2%) of 11 476 included individuals were female and 5720 (49·8%) were male. Sex data were missing for 372 (3·1%) of 11 848 individuals. Median age at registry entry was 9·6 years (IQR 5·8-13·2). 10 099 (89·9%) of 11 235 included individuals had a final genetically confirmed diagnosis of familial hypercholesterolaemia and 1136 (10·1%) had a clinical diagnosis. Genetically confirmed diagnosis data or clinical diagnosis data were missing for 613 (5·2%) of 11 848 individuals. Genetic diagnosis was more common in children and adolescents from high-income countries (9427 [92·4%] of 10 202) than in children and adolescents from non-high-income countries (199 [48·0%] of 415). 3414 (31·6%) of 10 804 children or adolescents were index cases. Familial-hypercholesterolaemia-related physical signs, cardiovascular risk factors, and cardiovascular disease were uncommon, but were more common in non-high-income countries. 7557 (72·4%) of 10 428 included children or adolescents were not taking lipid-lowering medication (LLM) and had a median LDL-C of 5·00 mmol/L (IQR 4·05-6·08). Compared with genetic diagnosis, the use of unadapted clinical criteria intended for use in adults and reliant on more extreme phenotypes could result in 50-75% of children and adolescents with familial hypercholesterolaemia not being identified. Interpretation: Clinical characteristics observed in adults with familial hypercholesterolaemia are uncommon in children and adolescents with familial hypercholesterolaemia, hence detection in this age group relies on measurement of LDL-C and genetic confirmation. Where genetic testing is unavailable, increased availability and use of LDL-C measurements in the first few years of life could help reduce the current gap between prevalence and detection, enabling increased use of combination LLM to reach recommended LDL-C targets early in life

Cross-linking methods to identify the mRNA targets of microRNAs

microRNAs (miRNAs, miRs) constitute a class of small, endogenous, non-coding RNAs (ncRNAs) and have a great influence on various processes within the cell. By base‐pairing selectively to partially‐complementary sites located predominantly in the 3′-untranslated region (3′‐UTR) of target messenger RNAs (mRNAs), miRNAs participate in the post-transcriptional regulation of gene expression. miRNAs are responsible for controlling the expression of the majority of human protein‐coding genes and their dysregulation has been related to many pathological processes and diseases, including cancer. Thus, an in-depth understanding of the miRNA mechanisms of action is of great importance. One of the key challenges is the elucidation of the exact sites of the canonical and non-canonical interactions in a cell-specific context. An imperfect pairing between miRNAs and their target RNAs in animals, as well as high false-positive and false-negative rates for current prediction algorithms, generate a need for the experimental validation of the predicted binding sites. For this purpose, various cross-linking-based methods for target identification have been established. The microRNA cross‐linking and immunoprecipitation (miR‐CLIP) approach developed previously in our group allows capturing predicted and unpredicted miRNA targets in cells. The miR-CLIP technique employs the pre-miR-CLIP probes site-specifically modified with trioxsalen and biotin moieties introduced pre- or post-synthetically at the 2′-O-position of the nucleoside by the copper(I)-catalysed azide-alkyne cycloaddition (CuAAC/’CLICK’) reaction. It was shown that a miR‐106a-5p pre-miR-CLIP probe was able to cross‐link to the complementary regions present in the RNA targets. However, further tests suggested that the cross-linking with this probe design is more sequence-dependent than initially expected and therefore the outcome of the reaction is more difficult to predict. The overall objective of this research was to design miR-CLIP probes for all miRNAs of a cell, for which an understanding of the cross-linking chemistry with respect to sequence preferences, linker composition and sites of conjugation was required. The first project described in this thesis focused on exploring the nature of the cross-linking with the original miR‐106a-5p miR-CLIP probe. In vitro cross-linking assays performed with a set of trioxsalen-labelled miR-106a-5p analogues and probes for other miRNAs allowed us to establish a working hypothesis about the sequence preferences of cross-linking. The results suggested that inter-strand cross-linking most likely took place with a uridine positioned 2-3 base pairs upstream from the desired (juxtaposed) cross-linking site. This allowed proposing an alternative strategy for the positioning of the trioxsalen modification within these probes. In the second project, diazirine-based probes were synthesized and tested. The results showed that the attachment of the cross-linker at the 2′-O-position of the ribose or C5-position of the pyrimidine was ineffective and resulted in quenching of reactive species by the solvent molecules. Finally, a different approach aiming to achieve a versatile (sequence-independent) cross-linking was developed and tested. The new strategy was based on the utilization of probes in which the trioxsalen molecule was introduced at the N4-position of cytidine through short poly(ethylene glycol) (PEG)-based linkers. Probes for miR-124-3p were functionalized post-synthetically by the application of the convertible nucleoside approach and showed more efficient cross-linking than analogous probes prepared with the use of the CLICK chemistry

Design and Application of Mini‐libraries of the miRNA Probes for an Efficient and Versatile miRNA‐mRNA Cross‐linking

MicroRNAs constitute a class of endogenous, non-coding RNAs that influence various processes within the cell. By base-pairing to partially-complementary sites located in the 3’ untranslated region of target messenger RNAs, microRNAs participate in post-transcriptional regulation of the majority of human protein-coding genes. Their dysregulation has been related to many pathological processes and diseases. Thus, an in-depth understanding of the microRNA mechanisms of action is crucial. Here, we present a new concept of probe design to achieve an efficient and sequence-independent miRNA-mRNA cross-linking. The new strategy is based on the utilization of a controlled mixture of probes for a chosen miRNA, in which a trioxsalen moiety is introduced at the N4-position of a selected cytidine through short oligoethylene glycol-based linkers. In vitro photo-cross-linking experiments with mini-libraries of probes for microRNAs of interest showed variable cross-linking efficiencies, demonstrating a general applicability of the presented approach.ISSN:0947-6539ISSN:1521-376

Site-Specific Fluorophore Labeling of Guanosines in RNA G‑Quadruplexes

RNA G-quadruplexes are RNA secondary structures that are implicated in many cellular processes. Although conventional biophysical techniques are widely used for their in vitro characterization, more advanced methods are needed to study complex equilibria and the kinetics of their folding. We have developed a new Förster resonance energy-transfer-based method to detect the folding of RNA G-quadruplexes, which is enabled by labeling the 2′-positions of participating guanosines with fluorophores. Importantly, this does not interfere with the required anti conformation of the nucleobase in a quadruplex with parallel topology. Sequential click reactions on the solid phase and in solution using a stop-and-go strategy circumvented the issue of unselective cross-labeling. We exemplified the method on a series of sequences under different assay conditions. In contrast to the commonly used end-labeling approach, our internal labeling strategy would also allow the study of G-quadruplex formation in long functional RNAs

MiR-CLIP reveals iso-miR selective regulation in the miR-124 targetome

Many microRNAs regulate gene expression via atypical mechanisms, which are difficult to discern using native cross-linking methods. To ascertain the scope of non-canonical miRNA targeting, methods are needed that identify all targets of a given miRNA. We designed a new class of miR-CLIP probe, whereby psoralen is conjugated to the 3p arm of a pre-microRNA to capture targetomes of miR-124 and miR-132 in HEK293T cells. Processing of pre-miR-124 yields miR-124 and a 5′-extended isoform, iso-miR-124. Using miR-CLIP, we identified overlapping targetomes from both isoforms. From a set of 16 targets, 13 were differently inhibited at mRNA/protein levels by the isoforms. Moreover, delivery of pre-miR-124 into cells repressed these targets more strongly than individual treatments with miR-124 and iso-miR-124, suggesting that isomirs from one pre-miRNA may function synergistically. By mining the miR-CLIP targetome, we identified nine G-bulged target-sites that are regulated at the protein level by miR-124 but not isomiR-124. Using structural data, we propose a model involving AGO2 helix-7 that suggests why only miR-124 can engage these sites. In summary, access to the miR-124 targetome via miR-CLIP revealed for the first time how heterogeneous processing of miRNAs combined with non-canonical targeting mechanisms expand the regulatory range of a miRNA

Towards Improved Oligonucleotide Therapeutics Through Faster Target Binding Kinetics

ISSN:0947-6539ISSN:1521-376

Structural basis of siRNA recognition by TRBP double-stranded RNA binding domains

The accurate cleavage of pre-micro(mi)RNAs by Dicer and mi/siRNA guide strand selection are important steps in forming the RNA-induced silencing complex (RISC). The role of Dicer binding partner TRBP in these processes remains poorly understood. Here, we solved the solution structure of the two N-terminal dsRNA binding domains (dsRBDs) of TRBP in complex with a functionally asymmetric siRNA using NMR, EPR, and single-molecule spectroscopy. We find that siRNA recognition by the dsRBDs is not sequence-specific but rather depends on the RNA shape. The two dsRBDs can swap their binding sites, giving rise to two equally populated, pseudo-symmetrical complexes, showing that TRBP is not a primary sensor of siRNA asymmetry. Using our structure to model a Dicer-TRBP-siRNA ternary complex, we show that TRBP's dsRBDs and Dicer's RNase III domains bind a canonical 19 base pair siRNA on opposite sides, supporting a mechanism whereby TRBP influences Dicer-mediated cleavage accuracy by binding the dsRNA region of the pre-miRNA during Dicer cleavage

Cellular and Gene Expression Response to the Combination of Genistein and Kaempferol in the Treatment of Mucopolysaccharidosis Type I

Flavonoids are investigated as therapeutics for mucopolysaccharidosis, a metabolic disorder with impaired glycosaminoglycan degradation. Here we determined the effects of genistein and kaempferol, used alone or in combination, on cellular response and gene expression in a mucopolysaccharidosis type I model. We assessed the cell cycle, viability, proliferation, subcellular localization of the translocation factor EB (TFEB), number and distribution of lysosomes, and glycosaminoglycan synthesis after exposure to flavonoids. Global gene expression was analysed using DNA microarray and quantitative PCR. The type and degree of flavonoid interaction were determined based on the combination and dose reduction indexes. The combination of both flavonoids synergistically inhibits glycosaminoglycan synthesis, modulates TFEB localization, lysosomal number, and distribution. Genistein and kaempferol in a 1:1 ratio regulate the expression of 52% of glycosaminoglycan metabolism genes. Flavonoids show synergy, additivity, or slight antagonism in all analysed parameters, and the type of interaction depends on the concentration and component ratios. With the simultaneous use of genistein and kaempferol in a ratio of 4:1, even a 10-fold reduction in the concentration of kaempferol is possible. Flavonoid mixtures, used as the treatment of mucopolysaccharidosis, are effective in reducing glycosaminoglycan production and storage and show a slight cytotoxic effect compared to single-flavonoid usage