Revealing Differential RNA Editing Specificity of Human ADAR1 and ADAR2 in Schizosaccharomyces pombe.

Adenosine-to-inosine (A-to-I) RNA editing is an important post-transcriptional modification mediated by the adenosine deaminases acting on RNA (ADAR) family of enzymes, expanding the transcriptome by altering selected nucleotides A to I in RNA molecules. Recently, A-to-I editing has been explored for correcting disease-causing mutations in RNA using therapeutic guide oligonucleotides to direct ADAR editing at specific sites. Humans have two active ADARs whose preferences and specificities are not well understood. To investigate their substrate specificity, we introduced hADAR1 and hADAR2, respectively, into Schizosaccharomyces pombe (S. pombe), which lacks endogenous ADARs, and evaluated their editing activities in vivo. Using transcriptome sequencing of S. pombe cultured at optimal growth temperature (30 °C), we identified 483 A-to-I high-confident editing sites for hADAR1 and 404 for hADAR2, compared with the non-editing wild-type control strain. However, these sites were mostly divergent between hADAR1 and hADAR2-expressing strains, sharing 33 common sites that are less than 9% for each strain. Their differential specificity for substrates was attributed to their differential preference for neighboring sequences of editing sites. We found that at the -3-position relative to the editing site, hADAR1 exhibits a tendency toward T, whereas hADAR2 leans toward A. Additionally, when varying the growth temperature for hADAR1- and hADAR2-expressing strains, we observed increased editing sites for them at both 20 and 35 °C, compared with them growing at 30 °C. However, we did not observe a significant shift in hADAR1 and hADAR2's preference for neighboring sequences across three temperatures. The vast changes in RNA editing sites at lower and higher temperatures were also observed for hADAR2 previously in budding yeast, which was likely due to the influence of RNA folding at these different temperatures, among many other factors. We noticed examples of longer lengths of dsRNA around the editing sites that induced editing at 20 or 35 °C but were absent at the other two temperature conditions. We found genes' functions can be greatly affected by editing of their transcripts, for which over 50% of RNA editing sites for both hADAR1 and hADAR2 in S. pombe were in coding sequences (CDS), with more than 60% of them resulting in amino acid changes in protein products. This study revealed the extensive differences in substrate selectivity between the two active human ADARS, i.e., ADAR1 and ADAR2, and provided novel insight when utilizing the two different enzymes for in vivo treatment of human genetic diseases using the RNA editing approach.

Patient Perceptions of Microbiome-Based Therapies as Novel Treatments for Mood Disorders: A Mixed Methods Study: Perceptions des patients sur les thérapies basées sur le microbiome pour les troubles de l'humeur : une étude à méthodes mixtes.

OBJECTIVE: Medications are critical for treating major depressive disorder (MDD) and bipolar disorder (BD). Unfortunately, 30% to 40% of individuals do not respond well to current pharmacotherapy. Given the compelling growing body of research on the gut-brain axis, this study aims to assess patient perspectives regarding microbiome-based therapies (MBT) such as probiotics, prebiotics, dietary changes, or fecal microbiota transplantation (FMT) in the management of MDD and BD. METHODS: This single-centred observational study used quantitative and qualitative assessments to examine patient perceptions of MBT. Participants diagnosed with MDD or BD completed an anonymous questionnaire obtaining demographics, prior medication history, and symptom burden. Self-assessment questionnaires specific to each diagnosis were also used: Quick Inventory of Depressive Symptomatology Self-Report (QIDS-SR), Altman Self-Rating Mania Scale (ASRM), and General Anxiety Disorder Questionnaire (GAD-7). A logistic regression model analysed the association of MBT acceptance with disorder type, QIDS-SR, and GAD-7 scores. A bootstrap method assessed the proportion of MBT acceptance. The qualitative assessment consisted of 30-minute interviews to elicit perceptions and attitudes towards MBT. RESULTS: The qualitative assessment achieved information power with n = 20. Results from the 63-item MBT questionnaire (n = 43) showed probiotics (37.2%) as the top choice, followed by FMT (32.6%), dietary change (25.6%), and prebiotics (4.6%). A majority of participants (72.1%) expressed willingness to try MBT for their mood disorder, however, logistic regression analysis did not identify statistically significant predictors for MBT acceptance among disorder type, QIDS-SR, and GAD-7. CONCLUSION: There is an increased focus on the gut microbiota's role in mood disorders' etiology and treatment. Promising research and patient interest underscore the necessity for exploring and educating on patient perspectives and the factors influencing attitudes towards MBT.

Diverse performances for Pb(II) adsorption by in situ formed Fe(III) oxyhydroxide derived from ferrate(VI) reduction and ferrous oxidation.

Two in situ formed Fe(III) oxyhydroxides (FeOx) originated from ferrate reduction (designated FeOx-FeVI) and ferrous oxidation by H2O2 (designated FeOx-FeII) were compared in the aspects of morphology, hydrolyzed species, surface binding mechanism of lead. The theoretical maximum adsorption capacity calculated from the Langmuir model toward Pb(II) was 929.54 and 810.37 mg/g Fe by FeOx-FeVI and FeOx-FeII, respectively. At pH 6 and the same Fe/Pb ratio, the kinetic rate of Pb removal by the FeOx-FeVI process was 8 times faster. FTIR, SEM, and Ferron assay suggest FeOx-FeVI was associated with a lesser polymerization degree and contained more reactive hydroxyl-Fe polymers than those in the FeOx-FeII sample. SAXS verified that the particles possessed a smaller, more homogeneous, and open structure when Fe was hydrolyzed by ferrate reduction than ferrous oxidation. XPS coupled with fractal analysis suggests the different sorption capacities of Pb(II) can be ascribed to their distinct growth patterns. Fast cluster agglomeration during FeOx-FeII fabrication decreased the exposure of effective adsorption sites. In comparison, the incompact assemblies of FeOx-FeVI clusters facilitated Pb(II) ions to access the interstices of octahedral FeO6 units and formed an edge-sharing complex. This work provides new insight into mechanisms of particle fabrication and heavy metal removal of Fe(III) formed in situ.

Highly sensitive and specific detection of silver ions using a dual-color fluorescence co-localization strategy.

Ag+ ions are widely used in various fields of human life due to their unique properties and they threaten the environment and human health. The traditional methods for Ag+ detection commonly suffer from disadvantages including limited sensitivity, expensive equipment and complicated operating steps. Herein, we developed a highly specific dual-color fluorescence co-localization (DFC) strategy based on the C-Ag+-C structure for Ag+ detection. In this strategy, Ag+ ions can be captured to form C-Ag+-C base pairs, and these ions enable single-stranded DNAs to form double strands. The DFC strategy can exclude nonspecific interaction sites and greatly improve the sensitivity and specificity. By DFC of the QDs and Cy5 linked to the DNA strands, highly sensitive Ag+ detection was achieved in the concentration range from 0.14 pM to 200 nM, with a limit of detection (LOD) of 0.14 pM. Moreover, this method has been applied for the detection of Ag+ ions in real environmental samples with satisfactory recoveries. We believe that the DFC strategy is promising for Ag+ detection.

Enhanced Adsorption of Bromoform onto Microplastic Polyethylene Terephthalate Exposed to Ozonation and Chlorination.

This paper selected microplastic polyethylene terephthalate (PET), commonly found in water/wastewater plant effluent, to investigate the changes of PET oxidized under ozonation (designated as ozonized PET), followed by sodium hypochlorite oxidation (designated as ozonized-chlorinated PET) and studied their influence on the adsorption of the disinfection by-product bromoform (TBM). Fragmentation and cracks appeared on the oxidized PET surface. As the oxidation degree increased, the contact angle decreased from 137° to 128.90° and 128.50°, suggesting hydrophilicity was enhanced. FTIR and XPS analyses suggested that carbonyl groups increased on the surface of ozonized PET and ozonized-chlorinated PET, while the formation of intermolecular halogen bonds was possible when PET experienced dual oxidation. These physiochemical changes enhanced the adsorption of TBM. The adsorption capacity of TBM followed the order of ozonized-chlorinated PET (2.64 × 10−6 µg/µg) > ozonized PET (2.58 × 10−6 µg/µg) > pristine PET (2.43 × 10−6 µg/µg). The impact of raw water characteristics on the adsorption of TBM onto PETs, such as the pH, and the coexistence of inorganic ions and macromolecules (humic acid, surfactant, and bovine serum albumin) were studied. A different predominant adsorption mechanism between TBM and pristine PET or oxidized PETs was proposed.

Vernier assembly: controlling DNA polymerization via length mismatching.

Inspired by the principle of the Vernier scale, length mismatching was used to control the lengths of supramolecular DNA polymers.

Construction of RNA nanocages by re-engineering the packaging RNA of Phi29 bacteriophage.

RNA nanotechnology promises rational design of RNA nanostructures with wide array of structural diversities and functionalities. Such nanostructures could be used in applications such as small interfering RNA delivery and organization of in vivo chemical reactions. Though having impressive development in recent years, RNA nanotechnology is still quite limited and its programmability and complexity could not rival the degree of its closely related cousin: DNA nanotechnology. Novel strategies are needed for programmed RNA self-assembly. Here, we have assembled RNA nanocages by re-engineering a natural, biological RNA motif: the packaging RNA of phi29 bacteriophage. The resulting RNA nanostructures have been thoroughly characterized by gel electrophoresis, cryogenic electron microscopy imaging and dynamic light scattering.

Approaching the limit: can one DNA strand assemble into defined nanostructures?

This article reports a simple, symmetrical DNA building block (motif): a bulged DNA duplex consisting of two short, identical strands. Multiple copies of the same motif can interact with each other through T junctions. The resulting superstructures include predesigned 1D and 2D arrays that have been visualized by atomic force microscopy (AFM).

RNA-DNA hybrid origami: folding of a long RNA single strand into complex nanostructures using short DNA helper strands.

Quick folding of a long RNA strand using short DNA staple strands (at a 1 : 1 ratio) into various pre-designed nanostructures in high yields has been demonstrated.

Reversibly switching the surface porosity of a DNA tetrahedron.

The ability to reversibly switch the surface porosity of nanocages would allow controllable matter transport in and out of the nanocages. This would be a desirable property for many technological applications, such as drug delivery. To achieve such capability, however, is challenging. Herein we report a strategy for reversibly changing the surface porosity of a self-assembled DNA nanocage (a DNA tetrahedron) that is based on DNA hydridization and strand displacement. The involved DNA nanostructures were thoroughly characterized by multiple techniques, including polyacrylamide gel electrophoresis, dynamic light scattering, atomic force microscopy, and cryogenic electron microscopy. This work may lead to the design and construction of stimuli-responsive nanocages that might find applications as smart materials.

DNA polyhedra with T-linkage.

This paper reports a strategy for DNA self-assembly. Cross-over-based DNA nanomotifs are held together by T-junctions instead of commonly used sticky-end cohesion. We have demonstrated this strategy by assembling a DNA tetrahedron, an octahedron, and an icosahedron. The resulting DNA polyhedra contain out-pointing, short DNA hairpin spikes. These hairpins are well-structured relative to the polyhedra core and provide potential locations for introduction of functional chemicals such as proteins and gold nanoparticles. The T-linked DNA polyhedra have been characterized by polyacrylamide gel electrophoresis, atomic force microscopy, and dynamic light scattering.

A synthetic method for transition-metal chalcogenide nanocrystals.

In this paper, we prepared a series of chalcogenide semiconductor nanocrystals in controllable shape and size via a facile wet route using metal nitrates and sulfur or selenium powder as precursors and octadecylamine (ODA) as solvent. The as-obtained chalcogenides included CdS, MnS, Ag(2)S, PbS, Cu(1.8)S, Bi(2)S(3), ZnS, Zn(x)Cd(1-x)S, as well as Ag(2)Se, Cu(2-x)Se, CdSe, MnSe. Furthermore, these cyclohexane-soluble monodisperse nanocrystals were assembled to water-soluble colloidal spheres and the adjustment of assembly orderliness has been achieved by controlling the experimental parameters. The general synthesis and assembly of chalcogenide semiconductors provide ideal building blocks for various potential applications.

General synthesis of I-III-VI2 ternary semiconductor nanocrystals.

Metastable orthorhombic phase of AgInS2 nanocrystals with various shapes, including particles, rods, and worms, have been obtained to demonstrate a facile and effective one-pot chemical route for the synthesis of high quality I-III-VI2 ternary semiconductor nanocrystals (AgInS2, CuInS2, AgInSe2) with controllable shape and size.