SUR1 Receptor Interaction with Hesperidin and Linarin Predicts Possible Mechanisms of Action of Valeriana officinalis in Parkinson.

Parkinson's disease (PD) is one of the most common neurodegenerative disorders. A theoretical approach of our previous experiments reporting the cytoprotective effects of the Valeriana officinalis compounds extract for PD is suggested. In addiction to considering the PD as a result of mitochondrial metabolic imbalance and oxidative stress, such as in our previous in vitro model of rotenone, in the present manuscript we added a genomic approach to evaluate the possible underlying mechanisms of the effect of the plant extract. Microarray of substantia nigra (SN) genome obtained from Allen Brain Institute was analyzed using gene set enrichment analysis to build a network of hub genes implicated in PD. Proteins transcribed from hub genes and their ligands selected by search ensemble approach algorithm were subjected to molecular docking studies, as well as 20 ns Molecular Dynamics (MD) using a Molecular Mechanic Poison/Boltzman Surface Area (MMPBSA) protocol. Our results bring a new approach to Valeriana officinalis extract, and suggest that hesperidin, and probably linarin are able to relieve effects of oxidative stress during ATP depletion due to its ability to binding SUR1. In addition, the key role of valerenic acid and apigenin is possibly related to prevent cortical hyperexcitation by inducing neuronal cells from SN to release GABA on brain stem. Thus, under hyperexcitability, oxidative stress, asphyxia and/or ATP depletion, Valeriana officinalis may trigger different mechanisms to provide neuronal cell protection.Fil: Santos, Gesivaldo. Universidade Estadual do Sudoeste da Bahia; BrasilFil: Giraldez Alvarez, Lisandro Diego. Universidade Estadual do Sudoeste da Bahia; BrasilFil: Ávila Rodriguez, Marco. Pontificia Universidad Javeriana; ColombiaFil: Capani, Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Cardiológicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Cardiológicas; ArgentinaFil: Galembeck, Eduardo. Universidade Estadual de Campinas; BrasilFil: Gôes Neto, Aristóteles. Universidade Estadual de Feira de Santana; BrasilFil: Barreto, George E.. Pontificia Universidad Javeriana; ColombiaFil: Andrade, Bruno. Universidade Estadual do Sudoeste da Bahia; Brasi

Accuracy, Reproducibility And Bias Of Next Generation Sequencing For Quantitative Small RNA Profiling: A Multiple Protocol Study Across Multiple Laboratories [preprint]

Small RNA-seq is increasingly being used for profiling of small RNAs. Quantitative characteristics of long RNA-seq have been extensively described, but small RNA-seq involves fundamentally different methods for library preparation, with distinct protocols and technical variations that have not been fully and systematically studied. We report here the results of a study using common references (synthetic RNA pools of defined composition, as well as plasma-derived RNA) to evaluate the accuracy, reproducibility and bias of small RNA-seq library preparation for five distinct protocols and across nine different laboratories. We observed protocol-specific and sequence-specific bias, which was ameliorated using adapters for ligation with randomized end-nucleotides, and computational correction factors. Despite this technical bias, relative quantification using small RNA-seq was remarkably accurate and reproducible, even across multiple laboratories using different methods. These results provide strong evidence for the feasibility of reproducible cross-laboratory small RNA-seq studies, even those involving analysis of data generated using different protocols

FABRICATION OF WINDOW SADDLES FOR NIF CRYOGENIC HOHLRAUMS

OAK-B135 A planar diagnostic viewing port attached to the cylindrical wall of the NIF cryogenic hohlraum requires a saddle-like transition piece. While the basic design of this window saddle is straightforward, its fabrication is not, given the scale and precision of the component. They solved the problem through the use of a two segment copper mandrel to electroform the gold window saddle. The segments were micro-machined using a combination of single-point diamond turning and single point diamond milling. These processes as well as the electroplating conditions, final machining and mandrel removal are described in this paper

Description of the idealized bed roughness effects on tracer transport in water flumes by applying the strange attractor multifractal analysis

River hydrodynamicsTurbulent open channel flow and transport phenomen

Long-Term water stress and drought assessment of Mediterranean oak savanna vegetation using thermal remote sensing

Drought is a devastating natural hazard that is difficult to define, detect and quantify. The increased availability of both meteorological and remotely sensed data provides an opportunity to develop new methods to identify drought conditions and characterize how drought changes over space and time. In this paper, we applied the surface energy balance model, SEBS (Surface Energy Balance System), for the period 2001 2018, to estimate evapotranspiration and other energy fluxes over the dehesa area of the Iberian Peninsula, with a monthly temporal resolution and 0.05° pixel size. A satisfactory agreement was found between the fluxes modeled and the measurements obtained for 3 years by two flux towers located over representative sites (RMSD = 21 W m-2 and R2 = 0.76, on average, for all energy fluxes and both sites). The estimations of the convective fluxes (LE and H) showed higher deviations, with RMSD = 26 W m-2 on average, than Rn and G, with RMSD = 15 W m-2. At both sites, annual evapotranspiration (ET) was very close to total precipitation, with the exception of a few wet years in which intense precipitation events that produced high runoff were observed. The analysis of the anomalies of the ratio of ET to reference ET (ETo) was used as an indicator of agricultural drought on monthly and annual scales. The hydrological years 2004/2005 and 2011/2012 stood out for their negative values. The first one was the most severe of the series, with the highest impact observed on vegetation coverage and grain production. On a monthly scale, this event was also the longest and most intense, with peak negative values in January February and April May 2005, explaining its great impact on cereal production (up to 45 % reduction). During the drier events, the changes in the grasslands and oak trees ground cover allowed for a separate analysis of the strategies adopted by the two strata to cope with water stress. These results indicate that the drought events characterized for the period did not cause any permanent damage to the vegetation of dehesa systems. The approach tested has proven useful for providing insight into the characteristics of drought events over this ecosystem and will be helpful to identify areas of interest for future studies at finer resolutions

Sur1 Receptor Interaction With Hesperidin And Linarin Predicts Possible Mechanisms Of Action Of Valeriana Officinalis In Parkinson

Parkinson's disease (PD) is one of the most common neurodegenerative disorders. A theoretical approach of our previous experiments reporting the cytoprotective effects of the Valeriana officinalis compounds extract for PD is suggested. In addiction to considering the PD as a result of mitochondrial metabolic imbalance and oxidative stress, such as in our previous in vitro model of rotenone, in the present manuscript we added a genomic approach to evaluate the possible underlying mechanisms of the effect of the plant extract. Microarray of substantia nigra (SN) genome obtained from Allen Brain Institute was analyzed using gene set enrichment analysis to build a network of hub genes implicated in PD. Proteins transcribed from hub genes and their ligands selected by search ensemble approach algorithm were subjected to molecular docking studies, as well as 20 ns Molecular Dynamics (MD) using a Molecular Mechanic Poison/Boltzman Surface Area (MMPBSA) protocol. Our results bring a new approach to Valeriana officinalis extract, and suggest that hesperidin, and probably linarin are able to relieve effects of oxidative stress during ATP depletion due to its ability to binding SUR1. In addition, the key role of valerenic acid and apigenin is possibly related to prevent cortical hyperexcitation by inducing neuronal cells from SN to release GABA on brain stem. Thus, under hyperexcitability, oxidative stress, asphyxia and/or ATP depletion, Valeriana officinalis may trigger different mechanisms to provide neuronal cell protection. © 2016 Santos, Giraldez-Alvarez, ávila-Rodriguez, Capani, Galembeck, Neto, Barreto and Andrade.8MA

Detecting microRNA binding and siRNA off-target effects from expression data.

Sylamer is a method for detecting microRNA target and small interfering RNA off-target signals in 3' untranslated regions from a ranked gene list, sorted from upregulated to downregulated, after a microRNA perturbation or RNA interference experiment. The output is a landscape plot that tracks occurrence biases using hypergeometric P-values for all words across the gene ranking. We demonstrated the utility, speed and accuracy of this approach on several datasets