A cryptic RNA-binding domain mediates Syncrip recognition and exosomal partitioning of miRNA targets

Exosomal miRNA transfer is a mechanism for cell-cell communication that is important in the immune response, in the functioning of the nervous system and in cancer. Syncrip/hnRNPQ is a highly conserved RNA-binding protein that mediates the exosomal partition of a set of miRNAs. Here, we report that Syncrip's amino-terminal domain, which was previously thought to mediate protein-protein interactions, is a cryptic, conserved and sequence-specific RNA-binding domain, designated NURR (N-terminal unit for RNA recognition). The NURR domain mediates the specific recognition of a short hEXO sequence defining Syncrip exosomal miRNA targets, and is coupled by a non-canonical structural element to Syncrip's RRM domains to achieve high-affinity miRNA binding. As a consequence, Syncrip-mediated selection of the target miRNAs implies both recognition of the hEXO sequence by the NURR domain and binding of the RRM domains 5′ to this sequence. This structural arrangement enables Syncrip-mediated selection of miRNAs with different seed sequences. © 2018 The Author(s)

A cryptic RNA-binding domain mediates Syncrip recognition and exosomal partitioning of miRNA targets.

Exosomal miRNA transfer is a mechanism for cell–cell communication that is important in the immune response, in the functioning of the nervous system and in cancer. Syncrip/hnRNPQ is a highly conserved RNA-binding protein that mediates the exosomal partition of a set of miRNAs. Here, we report that Syncrip’s amino-terminal domain, which was previously thought to mediate protein–protein interactions, is a cryptic, conserved and sequence-specific RNA-binding domain, designated NURR (N-terminal unit for RNA recognition). The NURR domain mediates the specific recognition of a short hEXO sequence defining Syncrip exosomal miRNA targets, and is coupled by a non-canonical structural element to Syncrip’s RRM domains to achieve high-affinity miRNA binding. As a consequence, Syncrip-mediated selection of the target miRNAs implies both recognition of the hEXO sequence by the NURR domain and binding of the RRM domains 5′ to this sequence. This structural arrangement enables Syncrip-mediated selection of miRNAs with different seed sequences

TMVOC, a numerical simulator for three-phase non-isothermal flows of multicomponent hydrocarbon mixtures in saturated-unsaturated heterogeneous media

ii TMVOC is a numerical simulator for three-phase non-isothermal flow of water, soil gas, and a multicomponent mixture of volatile organic chemicals (VOCs) in multidimensional heterogeneous porous media. It is an extension of the TOUGH2 general-purpose simulation program developed at the Lawrence Berkeley National Laboratory. TMVOC is designed for applications to contamination problems that involve hydrocarbon fuel or organic solvent spills in saturated and unsaturated zones. It can model contaminant behavior under “natural ” environmental conditions, as well as for engineered systems, such as soil vapor extraction, groundwater pumping, or steam-assisted source remediation. This report is a self-contained guide to applications of TMVOC to subsurface contamination problems involving non-aqueous phase liquids (NAPLs). It gives a technical description of the TMVOC code, including a discussion of the physical processes modeled, and the mathematical and numerical methods used. Detailed instructions for preparing input data are presented along with illustrative sample problems

TMVOC, simulator for multiple volatile organic chemicals

TMVOC is a numerical simulator for three-phase non-isothermal flow of water, soil gas, and a multicomponent mixture of volatile organic chemicals (VOCs) in multidimensional heterogeneous porous media. It is an extension of the TOUGH2 general-purpose simulation program developed at the Lawrence Berkeley National Laboratory. TMVOC is designed for applications to contamination problems that involve hydrocarbon fuel or organic solvent spills in saturated and unsaturated zones. It can model contaminant behavior under ''natural'' environmental conditions, as well as for engineered systems, such as soil vapor extraction, groundwater pumping, or steam-assisted source remediation. TMVOC is upwards compatible with T2VOC (Falta et al., 1995) and can be initialized from T2VOC-style initial conditions. The main enhancements in TMVOC relative to T2VOC are as follows: a multicomponent mixture of volatile organic chemicals can be modeled; any and all combinations of the three phases water-oil-gas are treated; several non-condensible gases may be present; diffusion is treated in all phases in a manner that is fully coupled with phase partitioning. This paper gives a brief summary of the methodology used in TMVOC as well as highlighting some implementation issues. Simulation of a NAPL spill and subsequent remediation is discussed for a 2-D vertical section of a saturated-unsaturated flow problem

T2VOC Users Guide

This document was prepared as an account of work sponsored by the United States Government. While this document is believed to contain correct information, neither the United States Government nor any agency thereof, nor The Regents of the University of California, nor any of their employees, makes any warranty, express or implied, or assumes any legal responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by its trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or The Regents of the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Governmen

Interpretation of production tests in geothermal wells with T2Well-EWASG

In the geothermal sector, being able to simulate production tests by combining surface and downhole measurements can be extremely useful, improving data interpretation and reducing the impact of unavailable field data. This is possible with T2Well, a coupled wellbore-reservoir simulator. We plugged the EWASG equation of state for high enthalpy geothermal reservoirs into T2Well and extended the function to analytically compute the heat exchange between wellbore and formation at the short times. Changes to the analytical heat exchange function were verified by comparison with wellbore-formation heat exchange numerically simulated. T2Well-EWASG was validated by reproducing the flowing pressure and temperature logs taken from literature, and by using the software for the interpretation of a short production test. Simulation results indicate that T2Well-EWASG can be effectively used to improve the interpretation of production tests performed in geothermal well