The ability to accurately quantify all the microRNAs (miRNAs) in a sample is important for understanding miRNA biology and for development of new biomarkers and therapeutic targets. We develop a new ...method for preparing miRNA sequencing libraries, RealSeq®-AC, that involves ligating the miRNAs with a single adapter and circularizing the ligation products. When compared to other methods, RealSeq®-AC provides greatly reduced miRNA sequencing bias and allows the identification of the largest variety of miRNAs in biological samples. This reduced bias also allows robust quantification of miRNAs present in samples across a wide range of RNA input levels.
MicroRNAs (miRNAs) regulate fundamental biological processes by silencing mRNA targets and are dysregulated in many diseases. Therefore, miRNA replacement or inhibition can be harnessed as potential ...therapeutics. However, existing strategies for miRNA modulation using oligonucleotides and gene therapies are challenging, especially for neurological diseases, and none have yet gained clinical approval. We explore a different approach by screening a biodiverse library of small molecule compounds for their ability to modulate hundreds of miRNAs in human induced pluripotent stem cell-derived neurons. We demonstrate the utility of the screen by identifying cardiac glycosides as potent inducers of miR-132, a key neuroprotective miRNA downregulated in Alzheimer's disease and other tauopathies. Coordinately, cardiac glycosides downregulate known miR-132 targets, including Tau, and protect rodent and human neurons against various toxic insults. More generally, our dataset of 1370 drug-like compounds and their effects on the miRNome provides a valuable resource for further miRNA-based drug discovery.
We have extensively characterized the DNA methylomes of 139 patients with chronic lymphocytic leukemia (CLL) with mutated or unmutated IGHV and of several mature B-cell subpopulations through the use ...of whole-genome bisulfite sequencing and high-density microarrays. The two molecular subtypes of CLL have differing DNA methylomes that seem to represent epigenetic imprints from distinct normal B-cell subpopulations. DNA hypomethylation in the gene body, targeting mostly enhancer sites, was the most frequent difference between naive and memory B cells and between the two molecular subtypes of CLL and normal B cells. Although DNA methylation and gene expression were poorly correlated, we identified gene-body CpG dinucleotides whose methylation was positively or negatively associated with expression. We have also recognized a DNA methylation signature that distinguishes new clinico-biological subtypes of CLL. We propose an epigenomic scenario in which differential methylation in the gene body may have functional and clinical implications in leukemogenesis.
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DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
For the development of redox responsive MRI probes based on the MnIII/MnII couple, stable complexation of both reduced and oxidized forms of the metal ion and appropriate tuning of the redox ...potential in the biologically relevant range are key elements. The water soluble fluorinated Mn-porphyrin derivative Mn-3 satisfies both requirements. In aqueous solutions, it can reversibly switch between MnIII/MnII oxidation states. In the presence of ascorbic acid or β-mercaptoethanol, the MnIII form undergoes reduction, which is slowly but fully reversed in the presence of air oxygen. A UV-Vis kinetic study of MnIII/MnII reduction under oxygen-free conditions yielded second-order rate constants, k2, of 46.1 M-1 s-1 and 13.8 M-1 s-1 for the reaction with ascorbic acid and β-mercaptoethanol, respectively. This could correspond, in the absence of oxygen, to a half-life of a few minutes in blood plasma and a few seconds in circulating immune cells where ascorbic acid reaches 20-40 μM and a few mM concentrations, respectively. In contrast to expectations based on the redox potential, reduction with glutathione or cysteine does not occur. It is prevented by the coordination of the glutathione carboxylate group(s) to MnIII in the axial position, as was evidenced by NMR data. Therefore, MnIII-3 acts as an ascorbate specific turn-on MRI probe, which in turn can be re-oxidized by oxygen. The relaxivity increase from the oxidized to the reduced form is considerably improved at medium frequencies (up to 80 MHz) with respect to the previously studied Mn-TPPS4 analogues; at 20 MHz, it amounts to 150%. No in vitro cytotoxicity is detectable for Mn-3 in the typical MRI concentration range. Finally, 19F NMR resonances of MnIII-3 are relatively sharp which could open further opportunities to exploit such complexes as paramagnetic 19F NMR probes.
We describe a computer code that simulates how a satellite observes optical radiation emitted by a lightning flash after it is scattered within an intervening cloud. Our code, CloudScat.jl, is ...flexible, fully open source and specifically tailored to modern instruments such as the Modular Multispectral Imaging Array (MMIA) component of the Atmosphere–Space Interactions Monitor (ASIM) that operates from the International Space Station. In this article, we describe the algorithms implemented in the code and discuss several applications and examples, with an emphasis on the interpretation of MMIA data.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Many eukaryotic genes contain embedded antisense transcripts and repetitive sequences of unknown function. We report that male germline-specific expression of an antisense transcript contained in an ...intron of C. elegans Target of Rapamycin (TOR, let-363) is associated with (1) accumulation of endo-small interfering RNAs (siRNAs) against an embedded Helitron transposon and (2) activation of an alternative 3′ splice site of TOR. The germline-specific Argonaute proteins PRG-1 and CSR-1, which participate in self/nonself RNA recognition, antagonistically regulate the generation of these endo-siRNAs, TOR mRNA levels, and 3′ splice-site selection. Supply of exogenous double-stranded RNA against the region of sense/antisense overlap reverses changes in TOR expression and splicing and suppresses the progressive multigenerational sterility phenotype of prg-1 mutants. We propose that recognition of a “nonself” intronic transposon by endo-siRNAs/the piRNA system provides physiological regulation of expression and alternative splicing of a host gene that, in turn, contributes to the maintenance of germline function across generations.
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•Worm male germline-specific antisense transcription is associated with a 3′ splice-site switch•Epigenetic memory of self/nonself RNA is co-opted for splicing regulation•TOR expression/alternative splicing influences germline mortality of Piwi mutants•Piwi-associated sterility is partially reversible and epigenetic
The role of antisense transcription and small RNAs in the physiological regulation of alternative splicing remains poorly understood. Barberán-Soler et al. now find an association among sperm-specific expression of an antisense transcript, Argonaute-dependent accumulation of small RNAs against an embedded transposon, and an alternative splicing switch in the C. elegans TOR gene. Disruption of this circuit might contribute to the progressive transgenerational sterility observed in piwi mutants, which would therefore be partly epigenetic in nature.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Empathy training in health sciences: A systematic review Bas-Sarmiento, Pilar; Fernández-Gutiérrez, Martina; Baena-Baños, María ...
Nurse education in practice,
March 2020, 2020-Mar, 2020-03-00, 20200301, Volume:
44
Journal Article
Peer reviewed
Effective empathy training interventions based on scientific evidence becomes essential. A theoretical framework should guide the proposed interventions and be coherent with the evaluation of the ...dimensions taking in account that empathy is currently a multidimensional concept. The study aimed to determine, in health care professionals and/or students, what is the effectiveness of experiential versus humanistic training, in terms of improvement of empathic ability (dimensions) and maintenance over time of what has been learned, and to establish the degree of coherence between the proposed theoretical model and the trained and evaluated dimensions. A systematic review using six databases was performed. The data were synthesised, and the risk of bias was analysed using the Equator Guidelines. Twenty-three articles were selected. Further evidence of the effectiveness of experiential intervention against humanistic educational strategies was observed. Most studies were not based on a solid theoretical framework and, in these cases, inconsistency between empathic trained dimensions and those evaluated was detected. Although a better understanding of training time variable is required, middle-term interventions are recommended. Increasing the multicentre controlled trials; specifying the intervention that includes the empathy dimensions; triangulating the data from health professionals, patients, and external observers; and including monitoring, becomes a necessity.
•Further evidence of the effectiveness of experiential empathy interventions.•Empathy training using simulations, roleplaying and feedback are more effective.•Lack of studies with experimental designs where empathy was a primary variable.•Incoherencies between the theoretical frame and the trained/evaluated dimensions.•Data triangulation using all measures (observation and self-reported) is necessary.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The electrochemical reduction of iodobenzene, 4-iodobenzonitrile and 4-iodonitrobenzene in DMF:benzene (2:8), in one-pot reaction and at room temperature, leads to cross-coupling products, biphenyl, ...4-phenylbenzonitrile and 4-phenylnitrobenzene in low to moderate yields. The proposed mechanism involves the formation of the aryl anion that is consistent with the number electrons transferred. The aryl anion reacts with benzene to form a σH-complex that is oxidized to the cross-coupling product in the reaction conditions. In identical conditions, 4-iodotoluene and 4-iodoanisole forms toluene and anisole, showing that electron donating groups in the iodoarene disfavour cross-coupling reaction.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Adjacent alternative 3' splice sites, those separated by ≤18 nucleotides, provide a unique problem in the study of alternative splicing regulation; there is overlap of the cis-elements that define ...the adjacent sites. Identification of the intron's 3' end depends upon sequence elements that define the branchpoint, polypyrimidine tract, and terminal AG dinucleotide. Starting with RNA-seq data from germline-enriched and somatic cell-enriched Caenorhabditis elegans samples, we identify hundreds of introns with adjacent alternative 3' splice sites. We identify 203 events that undergo tissue-specific alternative splicing. For these, the regulation is monodirectional, with somatic cells preferring to splice at the distal 3' splice site (furthest from the 5' end of the intron) and germline cells showing a distinct shift toward usage of the adjacent proximal 3' splice site (closer to the 5' end of the intron). Splicing patterns in somatic cells follow C. elegans consensus rules of 3' splice site definition; a short stretch of pyrimidines preceding an AG dinucleotide. Splicing in germline cells occurs at proximal 3' splice sites that lack a preceding polypyrimidine tract, and in three instances the germline-specific site lacks the AG dinucleotide. We provide evidence that use of germline-specific proximal 3' splice sites is conserved across Caenorhabditis species. We propose that there are differences between germline and somatic cells in the way that the basal splicing machinery functions to determine the intron terminus.
Alternative splicing allows for the generation of protein diversity and fine-tunes gene expression. Several model systems have been used for the in vivo study of alternative splicing. Here we review ...the use of the nematode Caenorhabditis elegans to study splicing regulation in vivo. Recent studies have shown that close to 25% of genes in the worm genome undergo alternative splicing. A big proportion of these events are functional, conserved, and under strict regulation either across development or other conditions. Several techniques like genome-wide RNAi screens and bichromatic reporters are available for the study of alternative splicing in worms. In this review, we focus, first, on the main studies that have been performed to dissect alternative splicing in this system and later on examples from genes that have human homologs that are implicated in cancer. The significant advancement towards understanding the regulation of alternative splicing and cancer that the C. elegans system has offered is discussed.
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FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
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