Differential ratio amplicons (Ramp) for the evaluation of RNA integrity extracted from complex environmental samples

Reliability and reproducibility of transcriptomics‐based studies are dependent on RNA integrity. In microbial ecology, microfluidics‐based techniques, such as the Ribosomal Integrity Number (RIN), targeting rRNA are currently the only approaches to evaluate RNA integrity. However, the relationship between rRNA and mRNA integrity is unknown. Here we present an integrity index, the Ratio Amplicon, Ramp, adapted from human clinical studies, to directly monitor mRNA integrity from complex environmental samples. We show, in a suite of experimental degradations of RNA extracted from sediment, that while the RIN generally reflected the degradation status of RNA the Ramp mapped mRNA degradation better. Furthermore, we examined the effect of degradation on transcript community structure by amplicon sequencing of 16S rRNA, amoA and glnA transcripts. We successfully sequenced transcripts for all three targets even from highly‐degraded RNA samples. While RNA degradation changed the community structure of the mRNA profiles, no changes were observed for the 16S rRNA transcript profiles. Since both RT‐Q‐PCR and sequencing results were obtained, even from highly degraded samples, we strongly recommend evaluating RNA integrity prior to downstream processing to ensure meaningful results. For this both the RIN and Ramp are useful, with the Ramp better evaluating mRNA integrity in this study

Nomenclature and semantic description of vascular lesions in small bowel capsule endoscopy: an international Delphi consensus statement

Background and study aims \u2002Nomenclature and descriptions of small bowel (SB) vascular lesions in capsule endoscopy (CE) are scarce in the medical literature. They are mostly based on the reader's opinion and thus differ between experts, with a potential negative impact on clinical care, teaching and research regarding SBCE. Our aim was to better define a nomenclature and to give a description of the most frequent vascular lesions in SBCE. Methods \u2002A panel of 18 European expert SBCE readers was formed during the UEGW 2016 meeting. Three experts constructed an Internet-based four-round Delphi consensus, but did not participate in the voting process. They built questionnaires that included various still frames of vascular lesions obtained with a third-generation SBCE system. The 15 remaining participants were asked to rate different proposals and description of the most common SB vascular lesions. A 6-point rating scale (varying from 'strongly disagree' to 'strongly agree') was used successive rounds. The consensus was reached when at least 80\u200a% voting members scored the statement within the 'agree' or 'strongly agree'. Results \u2002Consensual terms and descriptions were reached for angiectasia/angiodysplasia, erythematous patch, red spot/dot, and phlebectasia. A consensual description was reached for more subtle vascular lesions tentatively named "diminutive angiectasia" but no consensus was reached for this term. Conclusion \u2002An international group has reached a consensus on the nomenclature and descriptions of the most frequent and relevant SB vascular lesions in CE. These terms and descriptions are useful in daily practice, for teaching and for medical research purposes

Cardiac Glycosides Ouabain and Digoxin Interfere with the Regulation of Glutamate Transporter GLAST in Astrocytes Cultured from Neonatal Rat Brain

Glutamate transport (GluT) in brain is mediated chiefly by two transporters GLT and GLAST, both driven by ionic gradients generated by (Na+, K+)-dependent ATPase (Na+/K+-ATPase). GLAST is located in astrocytes and its function is regulated by translocations from cytoplasm to plasma membrane in the presence of GluT substrates. The phenomenon is blocked by a naturally occurring toxin rottlerin. We have recently suggested that rottlerin acts by inhibiting Na+/K+-ATPase. We now report that Na+/K+-ATPase inhibitors digoxin and ouabain also blocked the redistribution of GLAST in cultured astrocytes, however, neither of the compounds caused detectable inhibition of ATPase activity in cell-free astrocyte homogenates (rottlerin inhibited app. 80% of Pi production from ATP in the astrocyte homogenates, IC50 = 25 μM). Therefore, while we may not have established a direct link between GLAST regulation and Na+/K+-ATPase activity we have shown that both ouabain and digoxin can interfere with GluT transport and therefore should be considered potentially neurotoxic

ESKIMO1 Disruption in Arabidopsis Alters Vascular Tissue and Impairs Water Transport

Water economy in agricultural practices is an issue that is being addressed through studies aimed at understanding both plant water-use efficiency (WUE), i.e. biomass produced per water consumed, and responses to water shortage. In the model species Arabidopsis thaliana, the ESKIMO1 (ESK1) gene has been described as involved in freezing, cold and salt tolerance as well as in water economy: esk1 mutants have very low evapo-transpiration rates and high water-use efficiency. In order to establish ESK1 function, detailed characterization of esk1 mutants has been carried out. The stress hormone ABA (abscisic acid) was present at high levels in esk1 compared to wild type, nevertheless, the weak water loss of esk1 was independent of stomata closure through ABA biosynthesis, as combining mutant in this pathway with esk1 led to additive phenotypes. Measurement of root hydraulic conductivity suggests that the esk1 vegetative apparatus suffers water deficit due to a defect in water transport. ESK1 promoter-driven reporter gene expression was observed in xylem and fibers, the vascular tissue responsible for the transport of water and mineral nutrients from the soil to the shoots, via the roots. Moreover, in cross sections of hypocotyls, roots and stems, esk1 xylem vessels were collapsed. Finally, using Fourier-Transform Infrared (FTIR) spectroscopy, severe chemical modifications of xylem cell wall composition were highlighted in the esk1 mutants. Taken together our findings show that ESK1 is necessary for the production of functional xylem vessels, through its implication in the laying down of secondary cell wall components

Blood metabolomics uncovers inflammation-associated mitochondrial dysfunction as a potential mechanism underlying ACLF (vol 72, pg 688, 2020)

Cellular mechanisms in basic and clinical gastroenterology and hepatolog

Assessing lateral flows and solute transport during floods in a conduit-flow-dominated karst system using the inverse problem for the advection-diffusion equation

The aim of this study is to present a framework that provides new ways to characterize the spatio-temporal variability of lateral exchanges for water flow and solute transport in a karst conduit network during flood events, treating both the diffusive wave equation and the advectiondiffusion equation with the same mathematical approach, assuming uniform lateral flow and solute transport. A solution to the inverse problem for the advection-diffusion equations is then applied to data from two successive gauging stations to simulate flows and solute exchange dynamics after recharge. The study site is the karst conduit network of the Fourbanne aquifer in the French Jura Mountains, which includes two reaches characterizing the network from sinkhole to cave stream to the spring. The model is applied, after separation of the base from the flood components, on discharge and total dissolved solids (TDSs) in order to assess lateral flows and solute concentrations and compare them to help identify water origin. The results showed various lateral contributions in space -between the two reaches located in the unsaturated zone (R1), and in the zone that is both unsaturated and saturated (R2) -as well as in time, according to hydrological conditions. Globally, the two reaches show a distinct response to flood routing, with important lateral inflows on R1 and large outflows on R2. By combining these results with solute exchanges and the analysis of flood routing parameters distribution, we showed that lateral inflows on R1 are the addition of diffuse infiltration (observed whatever the hydrological conditions) and localized infiltration in the secondary conduit network (tributaries) in the unsaturated zone, except in extreme dry periods. On R2, despite inflows on the base component, lateral outflows are observed during floods. This pattern was attributed to the concept of reversal flows of conduit-matrix exchanges, inducing a complex water mixing effect in the saturated zone. From our results we build the functional scheme of the karst system. It demonstrates the impact of the saturated zone on matrix-conduit exchanges in this shallow phreatic aquifer and highlights the important role of the unsaturated zone on storage and transfer functions of the system