Structure of an RNA Aptamer that Can Inhibit HIV-1 by Blocking Rev-Cognate RNA (RRE) Binding and Rev-Rev Association
Abstract not provided
Dearborn, Altaira D.↗
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Representative Elementary Volume (REV) in spatio-temporal domain: A method to find REV for dynamic pores
One of the potential risks associated with subsurface storage of CO 2 is the seepage of CO 2 through existing faults and fractures. There have been a number of studies devoted to this topic. Some of these studies show that geochemistry, especially mineralization, plays an important role in rendering the faults as conduits for CO 2 movement while others show that mineralization due to CO 2 injection can result in seep migration and flow diversion. Therefore, understanding the changes in reservoir properties due to pore alterations is important to ensure safe long term CO 2 storage in the subsurface. We study the changes in the Representative Elementary Volume (REV) of a rock due to reactive kinetics over a time, using a statistical approach and pore-scale CO 2 -rock interactiondata. The goal of this study is to obtain the REV of a rock property that accounts for pore-scale changes over time due to reactive kinetics, and we call this as spatiotemporal REV. Scale-up results suggest that the REV changes with time when CO 2 -rock interaction is considered. It is hypothesized that the alteration in pore structure introduces more heterogeneity in the rock, and because of this the magnitude of REV increases. Furthermore, it is possible that these noticeable changes in REV at pore-scale may have an impact when analyzed at the reservoir scale.
54 ENVIRONMENTAL SCIENCES↗
Structural Mimicry Drives HIV-1 Rev-Mediated HERV-K Expression
Explore the source record for details and available documents.
O'Carroll, Ina P.↗
Quicklook overview of model changes in Melcor 2.2: Rev 6342 to Rev 9496
MELCOR 2.2 is a significant official release of the MELCOR code with many new models and model improvements. This report provides the code user with a quick review and characterization of new models added, changes to existing models, the effect of code changes during this code development cycle (rev 6342 to rev 9496), a preview of validation results with this code version. More detailed information is found in the code Subversion logs as well as the User Guide and Reference Manuals.
97 MATHEMATICS AND COMPUTING↗
Erratum: “The response of CR-39 nuclear track detector to 1–9 MeV protons” [Rev. Sci. Instrum.82, 103303 (2011)]
No abstract prepared.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Experimental Plan for EDF Energy Creep Rabbit Graphite Irradiations- Rev. 2 (replaces Rev. 0 ORNL/TM/2013/49)
The experimental results obtained here will assist in the development and validation of future models of irradiation induced creep of graphite by providing the following data: Inert creep stain data from low to lifetime AGR fluence Inert creep-property data (especially CTE) from low to lifetime AGR fluence Effect of oxidation on creep modulus (by indirect comparison with experiment 1 and direct comparison with experiment 3 NB. Experiment 1 and 3 are not covered here) Data to develop a mechanistic understanding, including: appropriate creep modulus (including pinning and high dose effects on structure), investigation of CTE-creep strain behavior under inert conditions oInformation on the effect of applied stress/creep strain on crystallite orientation (requires XRD), effect of creep strain on micro-porosity (requires tomography & microscopy) This document describes the experimental work planned to meet the requirements of project technical specification and EDF Energy requests for additional Pre-IE work. The PIE work is described in detail in this revision (Section 8 and 9).
Burchell, Timothy D.↗
Inhibition of Rev-erbα ameliorates muscular dystrophy
Highlights: • Rev-erbα ablation in mdx mice protects against muscle damage and wasting. • Loss of Rev-erbα promoted regenerative myogenesis in mdx mice. • Rev-erbα deficiency in dystrophic muscle reduced inflammatory response. • Loss of Rev-erbα in mdx primary myoblasts promoted proliferation and differentiation. Duchene muscular dystrophy leads to progressive muscle structural and functional decline due to chronic degenerative-regenerative cycles. Enhancing the regenerative capacity of dystrophic muscle provides potential therapeutic options. We previously demonstrated that the circadian clock repressor Rev-erbα inhibited myogenesis and Rev-erbα ablation enhanced muscle regeneration. Here we show that Rev-erbα deficiency in the dystrophin-deficient mdx mice promotes regenerative myogenic response to ameliorate muscle damage. Loss of Rev-erbα in mdx mice improved dystrophic pathology and muscle wasting. Rev-erbα-deficient dystrophic muscle exhibit augmented myogenic response, enhanced neo-myofiber formation and attenuated inflammatory response. In mdx myoblasts devoid of Rev-erbα, myogenic differentiation was augmented together with up-regulation of Wnt signaling and proliferative pathways, suggesting that loss of Rev-erbα inhibition of these processes contributed to the improvement in regenerative myogenesis. Collectively, our findings revealed that the loss of Rev-erbα function protects dystrophic muscle from injury by promoting myogenic repair, and inhibition of its activity may have therapeutic utilities for muscular dystrophy.
60 APPLIED LIFE SCIENCES↗
Stimulation of nuclear receptor REV-ERBs regulates tumor necrosis factor-induced expression of proinflammatory molecules in C6 astroglial cells
Under physiological conditions, astrocytes maintain homeostasis in the CNS. Following inflammation and injury to the CNS, however, activated astrocytes produce neurotoxic molecules such as cytokines and chemokines, amplifying the initial molecular-cellular events evoked by inflammation and injury. Nuclear receptors REV-ERBα and REV-ERBβ (REV-ERBs) are crucial in the regulation of inflammation- and metabolism-related gene transcription. The current study sought to elucidate a role of REV-ERBs in rat C6 astroglial cells on the expression of inflammatory molecules following stimulation with the neuroinflammatory cytokine tumor necrosis factor (TNF). Stimulation of C6 cells with TNF (10 ng/ml) significantly increased the mRNA expression of CCL2, interleukin-6 (IL-6), inducible nitric oxide synthase (iNOS), and matrix metalloprotease (MMP)-9, but not fibroblast growth factor-2 (FGF-2), cyclooxygenase-2 (COX-2) and MMP-2. Treatment with either REV-ERB agonists GSK4112 or SR9009 significantly blocked TNF-induced upregulation of CCL2 mRNA and MMP-9 mRNA, but not IL-6 mRNA and iNOS mRNA expression. Furthermore, treatment with RGFP966, a selective histone deacetylase 3 (HDAC3) inhibitor, potently reversed the inhibitory effects of GSK4112 on TNF-induced expression of MMP-9 mRNA, but not CCL2 mRNA. Expression of Rev-erbs mRNA in C6 astroglial cells, primary cultured rat cortical and spinal astrocytes was confirmed by reverse transcription polymerase chain reaction. Together, the findings demonstrate an anti-inflammatory effect, downregulating of MMP-9 and CCL2 transcription, of astroglial REV-ERBs activation through HDAC3-dependent and HDAC3-independent mechanisms. - Highlights: • Rev-erbα mRNA and Rev-erbβ mRNA are expressed in C6 astroglial cells. • TNF increases the expression of CCL2, IL-6, MMP-9 and iNOS mRNA. • REV-ERB activation inhibits CCL2 mRNA and MMP-9 mRNA expression. • HDAC3 activity is involved in the inhibitory effect of REV-ERB on MMP-9 induction.
60 APPLIED LIFE SCIENCES↗
Suppression of atherosclerosis by synthetic REV-ERB agonist
The nuclear receptors for heme, REV-ERBα and REV-ERBβ, play important roles in the regulation of metabolism and inflammation. Recently it was demonstrated that reduced REV-ERBα expression in hematopoetic cells in LDL receptor null mice led to increased atherosclerosis. We sought to determine if synthetic REV-ERB agonists that we have developed might have the ability to suppress atherosclerosis in this model. A previously characterized synthetic REV-ERB agonist, SR9009, was used to determine if activation of REV-ERB activity would affect atherosclerosis in LDL receptor deficient mice. Atherosclerotic plaque size was significantly reduced (p < 0.05) in mice administered SR9009 (100 mg/kg) for seven weeks compared to control mice (n = 10 per group). SR9009 treatment of bone marrow-derived mouse macrophages (BMDM) reduced the polarization of BMDMs to proinflammatory M1 macrophage while increasing the polarization of BMDMs to anti-inflammatory M2 macrophages. Our results suggest that pharmacological targeting of REV-ERBs may be a viable therapeutic option for treatment of atherosclerosis. - Highlights: • Synthetic REV-ERB agonist treatment reduced atherosclerosis in a mouse model. • Pharmacological activation of REV-ERB decreased M1 macrophage polarization. • Pharmacological activation of REV-ERB increased M2 macrophage polarization.
60 APPLIED LIFE SCIENCES↗
Structure of HIV-1 RRE stem-loop II identifies two conformational states of the high-affinity Rev binding site
During HIV infection, specific RNA-protein interaction between the Rev response element (RRE) and viral Rev protein is required for nuclear export of intron-containing viral mRNA transcripts. Rev initially binds the high-affinity site in stem-loop II, which promotes oligomerization of additional Rev proteins on RRE. Here, we present the crystal structure of RRE stem-loop II in distinct closed and open conformations. The high-affinity Rev-binding site is located within the three-way junction rather than the predicted stem IIB. The closed and open conformers differ in their non-canonical interactions within the three-way junction, and only the open conformation has the widened major groove conducive to initial Rev interaction. Rev binding assays show that RRE stem-loop II has high- and low-affinity binding sites, each of which binds a Rev dimer. We propose a binding model, wherein Rev-binding sites on RRE are sequentially created through structural rearrangements induced by Rev-RRE interactions.
60 APPLIED LIFE SCIENCES↗
RNA-guided assembly of Rev-RRE nuclear export complexes
HIV replication requires nuclear export of unspliced and singly spliced viral transcripts. Although a unique RNA structure has been proposed for the Rev-response element (RRE) responsible for viral mRNA export, how it recruits multiple HIV Rev proteins to form an export complex has been unclear. We show here that initial binding of Rev to the RRE triggers RNA tertiary structural changes, enabling further Rev binding and the rapid formation of a viral export complex. Analysis of the Rev-RRE assembly pathway using SHAPE-Seq and small-angle X-ray scattering (SAXS) reveals two major steps of Rev-RRE complex formation, beginning with rapid Rev binding to a pre-organized region presenting multiple Rev binding sites. This step induces long-range remodeling of the RNA to expose a cryptic Rev binding site, enabling rapid assembly of additional Rev proteins into the RNA export complex. This kinetic pathway may help maintain the balance between viral replication and maturation.
59 BASIC BIOLOGICAL SCIENCES↗
Structural basis for heme-dependent NCoR binding to the transcriptional repressor REV-ERBβ
Heme is the endogenous ligand for the constitutively repressive REV-ERB nuclear receptors, REV-ERBα (NR1D1) and REV-ERBβ (NR1D2), but how heme regulates REV-ERB activity remains unclear. Cellular studies indicate that heme is required for the REV-ERBs to bind the corepressor NCoR and repress transcription. However, fluorescence-based biochemical assays suggest that heme displaces NCoR; here, we show that this is due to a heme-dependent artifact. Using ITC and NMR spectroscopy, we show that heme binding remodels the thermodynamic interaction profile of NCoR receptor interaction domain (RID) binding to REV-ERBβ ligand-binding domain (LBD). We solved two crystal structures of REV-ERBβ LBD cobound to heme and NCoR peptides, revealing the heme-dependent NCoR binding mode. ITC and chemical cross-linking mass spectrometry reveals a 2:1 LBD:RID stoichiometry, consistent with cellular studies showing that NCoR-dependent repression of REV-ERB transcription occurs on dimeric DNA response elements. Our findings should facilitate renewed progress toward understanding heme-dependent REV-ERB activity.
59 BASIC BIOLOGICAL SCIENCES↗
A new HIV-1 Rev structure optimizes interaction with target RNA (RRE) for nuclear export
HIV-1 Rev mediates the nuclear export of unspliced and partially-spliced viral transcripts for the production of progeny genomes and structural proteins. In this process, four (or more) copies of Rev assemble onto a highly-structured 351-nt region in such viral transcripts, the Rev response element (RRE). How this occurs is not known. The Rev assembly domain has a helical-hairpin structure which associates through three (A-A, B-B and C-C) interfaces. The RRE has the topology of an upper-case letter A, with the two known Rev binding sites mapping onto the legs of the A. We have determined a crystal structure for the Rev assembly domain at 2.25 Å resolution, without resort to either mutations or chaperones. It shows that B-B dimers adopt an arrangement reversed relative to that previously reported, and join through a C-C interface to form tetramers. Here, the new subunit arrangement shows how four Rev molecules can assemble on the two sites on the RRE to form the specificity checkpoint, and how further copies add through A-A interactions. Residues at the C-C interface, specifically the Pro31-Trp45 axis, are a potential target for intervention.
59 BASIC BIOLOGICAL SCIENCES↗
Derivation of A Representative Elementary Volume (REV) for Upscaled Two-Phase Flow in Porous Media
Relative permeability plays an important role in the upscaling of multiphase flow in porous media from the pore scale to the Darcy scale. The entire concept of relative permeability is contingent on the existence of a representative elementary volume (REV). As we move to smaller samples to measure relative permeability, such as with digital core analysis, the concept of a classical REV has become increasingly unlikely when using the conventional approach to defining a representative volume. The “‘conventional”’ understanding of an REV is that a large enough volume must be considered such that spatial variability averages out. In digital rock methods, such as pore-scale simulations based on micro-computed tomography (CT) images, the domain size is typically 2 to 4 mm. This is approximately the length scale of a single-phase flow REV using the classic REV approach. However, the single-phase perspective does not consider the complex dynamics and fluctuations often observed in multiphase flow systems, even at centimeter-scale experiments and/or simulations. A fundamental question is, therefore, whether the domain size commonly used in digital rock simulations can provide a consistent energy budget such that the concept of relative permeability exists. Based on first principles, relative permeability accounts for the rate of energy dissipated in a stationary process. If the dynamics are fluctuating, the energy dissipated can vary but will average out over a long enough timescale. The key to determining the validity of the relative permeability is the timescale of the measurement, not the spatial scale. The conventional REV theory assumes that spatial, temporal, and ensemble averages are equivalent in an ergodic system, but it does not provide a way to test this assumption. We provide a formal way to identify the timescale where the relative permeability accurately captures energy dissipation as a way to validate relative permeability measurements and quantitatively assess their accuracy. This result will be tested for a practical SCAL test, determining how long a flow experiment needs to be run to accurately characterize the rate of energy dissipation by the flow. The outcome will be a best practice guide for the determination of relative permeability from core-scale experiments and/or digital core simulations that ensure the energy budget is fully accounted for in the relative permeability coefficient.
Mcclure, James [Virginia Tech, Blacksburg]↗
REV-INR: Regularized Evidential Implicit Neural Representation for Uncertainty-Aware Volume Visualization
Applications of Implicit Neural Representations (INRs) have emerged as a promising deep learning approach for compactly representing large volumetric datasets. These models can act as surrogates for volume data, enabling efficient storage and on-demand reconstruction via model predictions. However, conventional deterministic INRs only provide value predictions without insights into the model’s prediction uncertainty or the impact of inherent noisiness in the data. This limitation can lead to unreliable data interpretation and visualization due to prediction inaccuracies in the reconstructed volume. Identifying erroneous results extracted from model-predicted data may be infeasible, as raw data may be unavailable due to its large size. To address this challenge, we introduce REV-INR, Regularized Evidential Implicit Neural Representation, which learns to predict data values accurately along with the associated coordinate-level data uncertainty and model uncertainty using only a single forward pass of the trained REV-INR during inference. By comprehensively comparing and contrasting REV-INR with existing well-established deep uncertainty estimation methods, we show that REV-INR achieves the best volume reconstruction quality with robust data (aleatoric) and model (epistemic) uncertainty estimates using the fastest inference time. Consequently, we demonstrate that REV-INR facilitates assessment of the reliability and trustworthiness of the extracted isosurfaces and volume visualization results, enabling analyses to be solely driven by model-predicted data.
Saklani, Shanu [Indian Institute of Technology, Ka↗
The Renewable Energy Potential (reV) Model: A Geospatial Platform for Technical Potential and Supply Curve Modeling
The Renewable Energy Potential (reV) model is a platform for detailed assessment of renewable energy (RE) resources and their geospatial intersection with grid infrastructure and land use characteristics. The reV model currently supports photovoltaic (PV), concentrating solar power (CSP) and land-based wind turbine technologies. Modules in the reV framework function at different spatial and temporal resolutions, allowing for assessment of resource potential, technical potential and supply curves at varying levels of detail. The platform runs on NREL's High Performance Computing system, providing scalable and efficient performance from a single location all the way up to continental scales, for a single year or decades of time series resource data. Coupled with NREL's System Advisor Model (SAM), reV supports resource assessment from 5-minute to hourly temporal resolution and provides for analysis of long-term (i.e., year-on-year) variability of RE generation (e.g., interannual variability and exceedance probabilities). Technical potential is measured as a function of resource potential and limitations put on developable land area defined by the user. For example, the user can limit development by land ownership, terrain, land use/cover, and urban areas, as well as custom inputs. Technology, grid interconnection and operation costs, based on the latest market data and future projections, are also embedded in the model. The supply curve module is a spatial sorting algorithm based on plant siting, grid interconnection cost, and regional competition, which provides a geographically discrete estimate of levelized cost of electricity (LCOE) and supply (i.e., capacity) for specific renewable technologies. The reV model currently provides broad coverage across North America, South and Central Asia, South America and South Africa to inform national- and international-scale analyses as well as regional infrastructure and deployment planning.
13 HYDRO ENERGY↗
RNA helicase MOV10 functions as a co-factor of HIV-1 Rev to facilitate Rev/RRE-dependent nuclear export of viral mRNAs
Human immunodeficiency virus type 1 (HIV-1) exploits multiple host factors during its replication. The REV/RRE-dependent nuclear export of unspliced/partially spliced viral transcripts needs the assistance of host proteins. Recent studies have shown that MOV10 overexpression inhibited HIV-1 replication at various steps. However, the endogenous MOV10 was required in certain step(s) of HIV-1 replication. In this report, we found that MOV10 potently enhances the nuclear export of viral mRNAs and subsequently increases the expression of Gag protein and other late products through affecting the Rev/RRE axis. The co-immunoprecipitation analysis indicated that MOV10 interacts with Rev in an RNA-independent manner. The DEAG-box of MOV10 was required for the enhancement of Rev/RRE-dependent nuclear export and the DEAG-box mutant showed a dominant-negative activity. Our data propose that HIV-1 utilizes the anti-viral factor MOV10 to function as a co-factor of Rev and demonstrate the complicated effects of MOV10 on HIV-1 life cycle. - Highlights: • MOV10 can function as a co-factor of HIV-1 Rev. • MOV10 facilitates Rev/RRE-dependent transport of viral mRNAs. • MOV10 interacts with Rev in an RNA-independent manner. • The DEAG-box of MOV10 is required for the enhancement of Rev/RRE-dependent export.
60 APPLIED LIFE SCIENCES↗
reV (The Renewable Energy Potential Model - Open Source) [SWR-21-59, SWR-20-20 and SWR-17-34]
The Renewable Energy Potential (reV) model is a platform for the detailed assessment of renewable energy resources and their geospatial intersection with grid infrastructure and land use characteristics. The reV model currently supports photovoltaic (PV), concentrating solar power (CSP), and land-based wind turbine technologies. Modules in the reV framework function at different spatial and temporal resolutions, allowing for the assessment of resource potential, technical potential, and supply curves at varying levels of detail. The platform runs on the National Renewable Energy Laboratory’s (NREL’s) high-performance computing system, providing scalable and efficient performance from a single location up to a continent, for a single year or decades of time-series resource data. Coupled with NREL’s System Advisor Model (SAM), reV supports resource assessments from 5-minute to hourly temporal resolutions and supports the analysis of long-term (i.e., year-on-year) variability of renewable generation (e.g., interannual variability and exceedance probabilities).
Maclaurin, Galen↗