In vivo 5-ethynyluridine (EU) labelling detects reduced transcription in Purkinje cell degeneration mouse mutants, but can itself induce neurodegeneration.

Fluorescent staining of newly transcribed RNA via metabolic labelling with 5-ethynyluridine (EU) and click chemistry enables visualisation of changes in transcription, such as in conditions of cellular stress. Here, we tested whether EU labelling can be used to examine transcription in vivo in mouse models of nervous system disorders. We show that injection of EU directly into the cerebellum results in reproducible labelling of newly transcribed RNA in cerebellar neurons and glia, with cell type-specific differences in relative labelling intensities, such as Purkinje cells exhibiting the highest levels. We also observed EU-labelling accumulating into cytoplasmic inclusions, indicating that EU, like other modified uridines, may introduce non-physiological properties in labelled RNAs. Additionally, we found that EU induces Purkinje cell degeneration nine days after EU injection, suggesting that EU incorporation not only results in abnormal RNA transcripts, but also eventually becomes neurotoxic in highly transcriptionally-active neurons. However, short post-injection intervals of EU labelling in both a Purkinje cell-specific DNA repair-deficient mouse model and a mouse model of spinocerebellar ataxia 1 revealed reduced transcription in Purkinje cells compared to controls. We combined EU labelling with immunohistology to correlate altered EU staining with pathological markers, such as genotoxic signalling factors. These data indicate that the EU-labelling method provided here can be used to identify changes in transcription in vivo in nervous system disease models.

Determination of 5-fluorocytosine, 5-fluorouracil, and 5-fluorouridine in hospital wastewater by liquid chromatography-mass spectrometry.

Chemotherapeutics are pharmaceutical compounds the occurrence of which in the environment is of growing concern because of the increase in treatments against cancer diseases. They can reach the aquatic ecosystems after passing through wastewater treatment plants without complete removal. One of the most frequently used chemotherapeutics is 5-fluorouracil which exhibits a strong cytostatic effect. In this paper, an analytical methodology was developed, validated, and applied to determine 5-fluorouracil, its precursor, 5-fluorocytosine, and its major active metabolite, 5-fluorouridine, in hospital wastewater samples. Due to the expected low concentrations after dilution and interferences present in such a complex matrix, a very selective and sensitive detection method is required. Moreover, an extraction method must be implemented prior to the determination in order to purify the sample extract and preconcentrate the target analytes at micrograms per liter concentration levels. Solid-phase extraction followed by liquid chromatography with tandem mass spectrometry was the combination of choice and all included parameters were studied. Under optimized conditions for wastewater samples analysis, recoveries from 63 to 108% were obtained, while intraday and interday relative standard deviations never exceeded 20 and 25%, respectively. Limits of detection between 61 and 620 ng/L were achieved. Finally, the optimized method was applied to samples from hospital wastewater effluents.

A splice site-sensing conformational switch in U2AF2 is modulated by U2AF1 and its recurrent myelodysplasia-associated mutation.

An essential heterodimer of the U2AF1 and U2AF2 pre-mRNA splicing factors nucleates spliceosome assembly at polypyrimidine (Py) signals preceding the major class of 3' splice sites. U2AF1 frequently acquires an S34F-encoding mutation among patients with myelodysplastic syndromes (MDS). The influence of the U2AF1 subunit and its S34F mutation on the U2AF2 conformations remains unknown. Here, we employ single molecule Förster resonance energy transfer (FRET) to determine the influence of wild-type or S34F-substituted U2AF1 on the conformational dynamics of U2AF2 and its splice site RNA complexes. In the absence of RNA, the U2AF1 subunit stabilizes a high FRET value, which by structure-guided mutagenesis corresponds to a closed conformation of the tandem U2AF2 RNA recognition motifs (RRMs). When the U2AF heterodimer is bound to a strong, uridine-rich splice site, U2AF2 switches to a lower FRET value characteristic of an open, side-by-side arrangement of the RRMs. Remarkably, the U2AF heterodimer binds weak, uridine-poor Py tracts as a mixture of closed and open U2AF2 conformations, which are modulated by the S34F mutation. Shifts between open and closed U2AF2 may underlie U2AF1-dependent splicing of degenerate Py tracts and contribute to a subset of S34F-dysregulated splicing events in MDS patients.

Managing the column equilibration time in hydrophilic interaction chromatography.

For a wide variety of hydrophilic interaction chromatography stationary phases, a repeatable partial equilibration was demonstrated in gradient elution after purging with as little as 12 column volumes of mobile phase. Relative standard deviations of retention time of on average ~0.15% could be obtained after 1 or 2 conditioning (blank) runs. The equilibration period must be kept strictly constant, otherwise selectivity changes occur, but this is not problematic on modern instruments. Partial equilibration was largely independent of stationary phase or gradient slope. Alternatively, full column equilibration is favoured for stationary phases that do not trap extensive water layers, and for materials with a wider pore size that have a lower surface area. Temperatures somewhat above ambient also shorten the equilibration time. Some stationary phases under optimum conditions can achieve full column equilibration using purging with ~12 column volumes, which is useful for rapid set-up of isocratic separations or for conventional gradient analysis.

RNA modifications and the link to human disease.

Ribonucleic acid (RNA) is involved in translation and transcription, which are the mechanisms in which cells express genes (Alberts et al., 2002). The three classes of RNA discussed are transfer RNA (tRNA), messenger RNA (mRNA), and ribosomal RNA (rRNA). mRNA is the transcript encoded from DNA, rRNA is associated with ribosomes, and tRNA is associated with amino acids and is used to read mRNA transcripts to make proteins (Lodish, Berk, Zipursky, et al., 2000). Interestingly, the function of tRNA, rRNA, and mRNA can be significantly altered by chemical modifications at the co-transcriptional and post-transcriptional levels, and there are over 171 of these modifications identified thus far (Boccaletto et al., 2018; Modomics-Modified bases, 2017). Several of these modifications are linked to diseases such as cancer, diabetes, and neurological disorders. In this review, we will introduce a few RNA modifications with biological functions and how dysregulation of these RNA modifications is linked to human disease.

Determination of five nucleosides by LC-MS/MS and the application of the method to quantify N6 -methyladenosine level in liver messenger ribonucleic acid of an acetaminophen-induced hepatotoxicity mouse model.

Ribonucleic acid N6 -methyladenosine methylation plays an important role in a variety of biological processes and diseases. Acetaminophen-induced hepatotoxicity is one of the major challenges faced by clinicians. To date, the link between N6 -methyladenosine and acetaminophen-induced hepatotoxicity has not been studied. In this study, a simple ultra high performance liquid chromatography with tandem mass spectrometry method was developed for the simultaneous determination of five nucleosides (adenosine, uridine, cytidine, guanosine, and N6 -methyladenosine) in messenger ribonucleic acid. After enzymatic digestion of messenger ribonucleic acid, the nucleosides sample was separated on an Acquity UPLC column with gradient elution using methanol and 0.02% formic acid water, and detected by a Qtrap 4500 mass spectrometer with an electrospray ionization mode. The method was validated over the concentration ranges of 4-800 ng/mL for adenosine, uridine, cytidine, and guanosine and 0.1-20 ng/mL for N6 -methyladenosine. It was successfully applied to the determination of N6 -methyladenosine levels in liver messenger ribonucleic acid in an acetaminophen-induced hepatotoxicity mouse model and a control group. This study offers a method for the determination of nucleoside contents in epigenetic studies and constitutes the first step toward the investigation of ribonucleic acid methylation in acetaminophen-induced hepatotoxicity, which will facilitate the elucidation of its mechanism.

Identification and Characterization of Herbicide Penoxsulam Transformation Products in Aqueous Media by UPLC-QTOF-MS.

Photodegradation is an important non-biodegradation process of pesticide degradation in aquatic environments. In this study, the effect of different forms of nitrogen on the photodegradation kinetics of penoxsulam was investigated. The photodegradation of penoxsulam was accelerated by NO3- and NO2- but was not affected by NH4+. Ultra-high-performance liquid chromatography coupled with time-of-flight mass spectrometry was used to separate and identify the transformation products (TPs)converted by photodegradation of penoxsulam in an aqueous solution under UV-Vis (290-800 nm) irradiation. Seven major transformation products were identified based on mass spectral data. The structure was determined by elemental composition calculations, comparison of structural analogs, and existing literature. The main pathways of photodegradation were found to be sulfonamide bond cleavage, rearrangement, triazole ring cleavage, and hydroxylation. These findings are critical to elucidate the environmental fate of penoxsulam in aquatic ecosystems and provide a basis for further environmental risk assessment.

Osmium Tag for Post-transcriptionally Modified RNA.

5-Methylcytidine (m5 C) and 5-methyluridine (m5 U) are highly abundant post-transcriptionally modified nucleotides that are observed in various natural RNAs. Such nucleotides were labeled through a chemical approach, as both underwent oxidation at the C5=C6 double bond, leading to the formation of osmium-bipyridine complexes, which could be identified by mass spectrometry. This osmium tag made it possible to distinguished m5 C and m5 U from their isomers, 2'-O-methylcytidine and 2'-O-methyluridine, respectively. Queuosine and 2-methylthio-N6 -isopentenyladenosine in tRNA were also tagged through complex formation.

Toward a high-throughput method for determining vicine and convicine levels in faba bean seeds using flow injection analysis combined with tandem mass spectrometry.

Although faba bean provides environmental and health benefits, vicine and convicine (v-c) limit its use as a source of vegetable protein. Crop improvement efforts to minimize v-c concentration require low-cost, rapid screening methods to distinguish between high and low v-c genotypes to accelerate development of new cultivars and to detect out-crossing events. To assist crop breeders, we developed a unique and rapid screening method that uses a 60 s instrumental analysis step to accurately distinguish between high and low v-c genotypes. The method involves flow injection analysis (FIA) coupled with tandem mass spectrometry (i.e., selective reaction monitoring, SRM). Using seeds with known v-c levels as calibrants, measured v-c levels were comparable with liquid chromatography (LC)-SRM results and the method was used to screen 370 faba bean genotypes. Widespread use of FIA-SRM will accelerate breeding of low v-c faba bean, thereby alleviating concerns about anti-nutritional effects of v-c in this crop.

A practical toxicity bioassay for vicine and convicine levels in faba bean (Vicia faba).

BACKGROUND: Faba bean (Vicia faba) vicine and convicine (V-C) aglycones (divicine and isouramil respectively) provoke an acute hemolytic anemia called favism in individuals with a glucose-6-phosphate dehydrogenase (G6PD) enzyme defect in their red blood cells. Geneticists/plant breeders are working with faba bean to decrease V-C levels to improve public acceptance of this high-protein pulse crop. Here, we present a fast and simple ex vivo in vitro bioassay for V-C toxicity testing of faba bean or faba bean food products. RESULTS: We have shown that 1,3-bis (2-chloroethyl)-1-nitrosourea (BCNU)-treated (i.e., sensitized) normal red blood cells, like G6PD-defective blood, displayed (i) continuous glutathione (GSH) depletion with no regeneration as incubation time and the dose of aglycones increased, (ii) progressive accumulation of denatured hemoglobin products into high molecular weight (HMW) proteins with increased aglycone dose, (iii) both band 3 membrane proteins and hemichromes, in HMW protein aggregates. We have also demonstrated that sensitized red blood cells can effectively differentiate various levels of toxicity among faba bean varieties through the two hemolysis biomarkers: GSH depletion and HMW clumping. CONCLUSION: BCNU-sensitized red blood cells provide an ideal model for favism blood, to assess and compare the toxicity of faba bean varieties and their food products. © 2018 Society of Chemical Industry.

Nitrogen compounds in Phacelia tanacetifolia Benth. honey: First time report on occurrence of (-)-5-epi-lithospermoside, uridine, adenine and xanthine in honey.

Lacy phacelia (Phacelia tanacetifolia Borkh.) honey composition was screened by UHPLC-DAD-QqTOF-MS. The targeted analysis revealed 6 major nitrogen compounds including aromatic amino acids (tyrosine, phenylalanine), purine derivatives (adenine, xanthine), nucleoside (uridine) and rare non-cyanogenic cyanoglucoside, (-)-5-epi-lithospermoside ((2Z)-2-[(4R,5R,6S)-4,5-dihydroxy-6-(ß-d-glucopyranosyl)oxycyclohex-2-en-1-ylidene]acetonitrile). Their identity was confirmed by different analytical tools: HRMS, co-chromatography with standard compound or comprehensive NMR experiments. All the compounds, except amino acids, were reported and determined in honey for the first time. The amount of the compounds was quantified in 16 unifloral phacelia samples: adenine (18.45 ±â€¯4.63 mg/kg), xanthine (10.53 ±â€¯2.98 mg/kg), uridine (42.84 ±â€¯9.26 mg/kg), tyrosine (14.66 ±â€¯10.22 mg/kg), (-)-5-epi-lithospermoside (70.61 ±â€¯31.37 mg/kg) and phenylalanine (20.41 ±â€¯11.99 mg/kg). The (-)-5-epi-lithospermoside content is significantly correlated with P. tanacetifolia pollen percentage (R2 = 0.5612, p < 0.001) and it is proposed as a potential marker of botanical origin for phacelia honey.

Persistence Behavior of Penoxsulam Herbicide in Two Different Soils.

Penoxsulam, a new post emergence herbicide is suspected to be toxic to aquatic organisms, crop plants and also to soil microbial community even at low concentrations. Laboratory studies were therefore performed to examine the persistence of, penoxsulam in two different soils at two application rates (0.5 and 1.0 µg g-1). The study revealed that the dissipation followed the first order kinetics with a half life of 3.48 and 3.57 days at 0.5 µg g-1 and 4.1 and 4.17 days at 1.0 µg g-1 fortification rate. Both microbial- and photo-degradation seemed to play a vital role in the dissipation of penoxsulam. The results of LC MS/MS revealed that one minor and five major metabolites were formed during the degradation process of the herbicide and the cleavage of sulfonamide bridge served as the major metabolic pathway.

Analysis of the Uridylation of Both ARGONAUTE-Bound MiRNAs and 5' Cleavage Products of Their Target RNAs in Plants.

Uridylation (3' untemplated uridine addition) provides a mechanism to trigger the degradation of miRNAs and the 5' cleavage products (5' CP) that are produced from miRNA-directed ARGONAUTE (AGO) cleavage of target RNAs. We have recently shown that HEN1 SUPPRESSOR 1 (HESO1), a terminal uridylyltransferase, and its homolog UTP:RNA uridylyltransferase 1 (URT1) catalyze the uridylation of miRNAs and 5' CPs within the AGO complex in higher plants. In this chapter, we describe detailed protocols for analyzing 3' end uridylation of both AGO-bound miRNAs and 5' CP.

Label-free, direct localization and relative quantitation of the RNA nucleobase methylations m6A, m5C, m3U, and m5U by top-down mass spectrometry.

Nucleobase methylations are ubiquitous posttranscriptional modifications of ribonucleic acids (RNA) that can substantially increase the structural diversity of RNA in a highly dynamic fashion with implications for gene expression and human disease. However, high throughput, deep sequencing does not generally provide information on posttranscriptional modifications (PTMs). A promising alternative approach for the characterization of PTMs, i.e. their identification, localization, and relative quantitation, is top-down mass spectrometry (MS). In this study, we have investigated how specific nucleobase methylations affect RNA ionization in electrospray ionization (ESI), and backbone cleavage in collisionally activated dissociation (CAD) and electron detachment dissociation (EDD). For this purpose, we have developed two new approaches for the characterization of RNA methylations in mixtures of either isomers of RNA or nonisomeric RNA forms. Fragment ions from dissociation experiments were analyzed to identify the modification type, to localize the modification sites, and to reveal the site-specific, relative extent of modification for each site.

Age-related changes in skeletal muscle composition: A pilot nuclear magnetic resonance spectroscopy study in mice.

The composition of skeletal muscle was investigated in the quadriceps and gastrocnemius muscle of 13-month-old (n=15) and 23-month-old (n=19) mice by means of high-resolution nuclear magnetic resonance (NMR) spectroscopy. Muscle specimens were dissected out, frozen in liquid nitrogen and extracted in chloroform/methanol, and proton NMR spectra of the resulting aqueous and organic fractions were obtained at 600MHz. Several metabolites were unambiguously identified and quantified. Multivariate ANOVA (factor: age, muscle, age×muscle) showed a significant main effect of age (P=0.031) on the amount of muscle metabolites, suggesting that the aging process affects the composition of skeletal muscle. Univariate tests showed significant differences for lactate, acetate, taurine, and uridine in 13- and 23-month-old mice. A trend for the effect of muscle (quadriceps vs. gastrocnemius; P=0.128) was also found. No significant muscle x age interaction was present. When the same data were used in principal component analysis, the first two principal components separated muscles (quadriceps and gastrocnemius) and ages (13- and 23-month-old), explaining 66.7% of total variance. The results of this pilot study show that high-resolution NMR spectroscopy is able to detect age-associated changes in skeletal muscle metabolites, thereby paving the way to future detailed metabolomics investigation in sarcopenia of aging.

Effects of faba beans with different concentrations of vicine and convicine on egg production, egg quality and red blood cells in laying hens.

The faba bean (Vicia faba L.) is a potential source of proteins for poultry, mainly for laying hens whose protein requirements are lower than those of other birds such as growing broilers and turkeys. However, this feedstuff contains anti-nutritional factors, that is, vicine (V) and convicine (C) that are already known to reduce laying hen performance. The aim of the experiment reported here was to evaluate the effects of a wide range of dietary V and C concentrations in laying hens. Two trials were performed with laying hens fed diets including 20% or 25% of faba bean genotypes highly contrasting in V+C content. In Trial 1, faba beans from two tannin-containing cultivars, but with high or low V+C content were dehulled in order to eliminate the tannin effect. In addition to the contrasting levels of V+C in the two cultivars, two intermediate levels of V+C were obtained by mixing the two cultivars (70/30 and 30/70). In Trial 2, two isogenic zero-tannin faba bean genotypes with high or low V+C content were used. In both trials, a classical corn-soybean diet was also offered to control hens. Each experimental diet was given to 48 laying hens for 140 (Trial 1) or 89 (Trial 2) days. Laying performance and egg quality were measured. The redox sensitivity of red blood cells (RBCs) was assessed by measuring hemolysis and reduced glutathione (GSH) concentration in these cells. Egg weight was significantly reduced by the diets containing the highest concentrations of V+C (P<0.0001) in Trial 1 and slightly reduced (P<0.10) in Trial 2, but only weak linear relationships between egg weight and dietary V+C concentration were established. No negative effect of V+C level was observed for egg quality parameters. In contrast, certain parameters (i.e. Haugh units, yolk color) were improved by feeding low V+C diets (P<0.05). Hemolysis of RBCs was higher in hens fed high V+C diets. A decrease in GSH concentration in RBCs of hens fed the highest levels of V+C was observed. Faba bean genotypes with low concentrations of V+C can therefore be used in laying hen diets up to 25% without any detrimental effects on performance levels or egg characteristics, without any risk of hemolysis of RBCs.

Determination and stability of divicine and isouramil produced by enzymatic hydrolysis of vicine and convicine of faba bean.

The aglycones of vicine and convicine, divicine and isouramil, are the causative agents of favism and, therefore, should be analysed along with vicine and convicine in research seeking to eliminate them. This study investigated the stability of the aglycones produced by hydrolysis with ß-glucosidase. Reversed-phase, high-performance liquid chromatography (HPLC) with UV detection was shown to be able to observe both aglycone formation and further reactions in isolated fractions and extract made from faba bean and in faba bean suspension. Divicine and isouramil were unstable and degraded almost completely in extract in 60min and completely in fractions in 120min at a pH of 5 at 37°C. Adding sodium ascorbate delayed degradation of divicine. Divicine was more stable at 20°C than at 37°C. Being able to show formation and degradation of the aglycones, the proposed method allows monitoring of the vicine and convicine detoxification process.

Systematic Analysis of AU-Rich Element Expression in Cancer Reveals Common Functional Clusters Regulated by Key RNA-Binding Proteins.

Defects in AU-rich elements (ARE)-mediated posttranscriptional control can lead to several abnormal processes that underlie carcinogenesis. Here, we performed a systematic analysis of ARE-mRNA expression across multiple cancer types. First, the ARE database (ARED) was intersected with The Cancer Genome Atlas databases and others. A large set of ARE-mRNAs was over-represented in cancer and, unlike non-ARE-mRNAs, correlated with the reversed balance in the expression of the RNA-binding proteins tristetraprolin (TTP, ZFP36) and HuR (ELAVL1). Serial statistical and functional enrichment clustering identified a cluster of 11 overexpressed ARE-mRNAs (CDC6, KIF11, PRC1, NEK2, NCAPG, CENPA, NUF2, KIF18A, CENPE, PBK, TOP2A) that negatively correlated with TTP/HuR mRNA ratios and was involved in the mitotic cell cycle. This cluster was upregulated in a number of solid cancers. Experimentally, we demonstrated that the ARE-mRNA cluster is upregulated in a number of tumor breast cell lines when compared with noninvasive and normal-like breast cancer cells. RNA-IP demonstrated the association of the ARE-mRNAs with TTP and HuR. Experimental modulation of TTP or HuR expression led to changes in the mitosis ARE-mRNAs. Posttranscriptional reporter assays confirmed the functionality of AREs. Moreover, TTP augmented mitotic cell-cycle arrest as demonstrated by flow cytometry and histone H3 phosphorylation. We found that poor breast cancer patient survival was significantly associated with low TTP/HuR mRNA ratios and correlated with high levels of the mitotic ARE-mRNA signature. These results significantly broaden the role of AREs and their binding proteins in cancer, and demonstrate that TTP induces an antimitotic pathway that is diminished in cancer. Cancer Res; 76(14); 4068-80. ©2016 AACR.

Imazethapyr and imazapic, bispyribac-sodium and penoxsulam: zooplankton and dissipation in subtropical rice paddy water.

Herbicides are very effective at eliminating weed and are largely used in rice paddy around the world, playing a fundamental role in maximizing yield. Therefore, considering the flooded environment of rice paddies, it is necessary to understand the side effects on non-target species. Field experiment studies were carried out during two rice growing seasons in order to address how the commonly-used herbicides imazethapyr and imazapic, bispyribac-sodium and penoxsulam, used at recommended dosage, affect water quality and the non-target zooplankton community using outdoor rice field microcosm set-up. The shortest (4.9 days) and longest (12.2 days) herbicide half-life mean, estimated of the dissipation rate (k) is shown for imazethapyr and bispyribac-sodium, respectively. Some water quality parameters (pH, conductivity, hardness, BOD5, boron, potassium, magnesium, phosphorus and chlorides) achieved slightly higher values at the herbicide treatment. Zooplankton community usually quickly recovered from the tested herbicide impact. Generally, herbicides led to an increase of cladocera, copepods and nauplius population, while rotifer population decreased, with recovery at the end of the experiment (88 days after herbicide treatment).

Ambient infrared laser ablation mass spectrometry (AIRLAB-MS) of live plant tissue with plume capture by continuous flow solvent probe.

A new experimental setup for spatially resolved ambient infrared laser ablation-mass spectrometry (AIRLAB-MS) that uses an infrared microscope with an infinity-corrected reflective objective and a continuous flow solvent probe coupled to a Fourier transform ion cyclotron resonance mass spectrometer is described. The efficiency of material transfer from the sample to the electrospray ionization emitter was determined using glycerol/methanol droplets containing 1 mM nicotine and is ∼50%. This transfer efficiency is significantly higher than values reported for similar techniques. Laser desorption does not induce fragmentation of biomolecules in droplets containing bradykinin, leucine enkephalin and myoglobin, but loss of the heme group from myoglobin occurs as a result of the denaturing solution used. An application of AIRLAB-MS to biological materials is demonstrated for tobacco leaves. Chemical components are identified from the spatially resolved mass spectra of the ablated plant material, including nicotine and uridine. The reproducibility of measurements made using AIRLAB-MS on plant material was demonstrated by the ablation of six closely spaced areas (within 2 × 2 mm) on a young tobacco leaf, and the results indicate a standard deviation of <10% in the uridine signal obtained for each area. The spatial distribution of nicotine was measured for selected leaf areas and variation in the relative nicotine levels (15-100%) was observed. Comparative analysis of the nicotine distribution was demonstrated for two tobacco plant varieties, a genetically modified plant and its corresponding wild-type, indicating generally higher nicotine levels in the mutant.