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DOE OSTI2014

Conserved sequence-specific lincRNA-steroid receptor interactions drive transcriptional repression and direct cell fate

The majority of the eukaryotic genome is transcribed, generating a significant number of long intergenic noncoding RNAs (lincRNAs). Although lincRNAs represent the most poorly understood product of transcription, recent work has shown lincRNAs fulfill important cellular functions. In addition to low sequence conservation, poor understanding of structural mechanisms driving lincRNA biology hinders systematic prediction of their function. Here we report the molecular requirements for the recognition of steroid receptors (SRs) by the lincRNA growth arrest-specific 5 (Gas5), which regulates steroid-mediated transcriptional regulation, growth arrest and apoptosis. We identify the functional Gas5-SR interface and generate point mutations that ablate the SR-Gas5 lincRNA interaction, altering Gas5-driven apoptosis in cancer cell lines. Further, we find that the Gas5 SR-recognition sequence is conserved among haplorhines, with its evolutionary origin as a splice acceptor site. This study demonstrates that lincRNAs can recognize protein targets in a conserved, sequence-specific manner in order to affect critical cell functions.

Hudson, William H.↗

DOE OSTI2023

Crystal structure of a highly conserved enteroviral 5' cloverleaf RNA replication element

The extreme 5'-end of the enterovirus RNA genome contains a conserved cloverleaf-like domain that recruits 3CD and PCBP proteins required for initiating genome replication. Here, we report the crystal structure at 1.9 Å resolution of this domain from the CVB3 genome in complex with an antibody chaperone. The RNA folds into an antiparallel H-type four-way junction comprising four subdomains with co-axially stacked sA-sD and sB-sC helices. Long-range interactions between a conserved A40 in the sC-loop and Py-Py helix within the sD subdomain organize near-parallel orientations of the sA-sB and sC-sD helices. Our NMR studies confirm that these long-range interactions occur in solution and without the chaperone. The phylogenetic analyses indicate that our crystal structure represents a conserved architecture of enteroviral cloverleaf-like domains, including the A40 and Py-Py interactions. The protein binding studies further suggest that the H-shape architecture provides a ready-made platform to recruit 3CD and PCBP2 for viral replication.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus, and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., arm-preserving) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding surrounded by pericentromeric LINE/L1 elements. This work explores the structure of chromosomes across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible associations of centromeric chromatin and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Microbially mediated mechanisms underlie soil carbon accrual by conservation agriculture under decade-long warming

Increasing soil organic carbon (SOC) in croplands by switching from conventional to conservation management may be hampered by stimulated microbial decomposition under warming. Here, we test the interactive effects of agricultural management and warming on SOC persistence and underlying microbial mechanisms in a decade-long controlled experiment on a wheat-maize cropping system. Warming increased SOC content and accelerated fungal community temporal turnover under conservation agriculture (no tillage, chopped crop residue), but not under conventional agriculture (annual tillage, crop residue removed). Microbial carbon use efficiency (CUE) and growth increased linearly over time, with stronger positive warming effects after 5 years under conservation agriculture. According to structural equation models, these increases arose from greater carbon inputs from the crops, which indirectly controlled microbial CUE via changes in fungal communities. As a result, fungal necromass increased from 28 to 53%, emerging as the strongest predictor of SOC content. Collectively, our results demonstrate how management and climatic factors can interact to alter microbial community composition, physiology and functions and, in turn, SOC formation and accrual in croplands.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Numerical challenges for energy conservation in N -body simulations of collapsing self-interacting dark matter halos

Dark matter (DM) halos can be subject to gravothermal collapse if the DM is not collisionless, but engaged in strong self-interactions instead. When the scattering is able to efficiently transfer heat from the centre to the outskirts, the central region of the halo collapses and reaches densities much higher than those for collisionless DM. This phenomenon is potentially observable in studies of strong lensing. Current theoretical efforts are motivated by observations of surprisingly dense substructures. However, a comparison with observations requires accurate predictions. One method to obtain such predictions is to use N-body simulations. Collapsed halos are extreme systems that pose severe challenges when applying state-of-the-art codes to model self-interacting dark matter (SIDM). In this work, we investigate the root of such problems, with a focus on energy non-conservation. Moreover, we discuss possible strategies to avoid them. We ran N-body simulations, both with and without SIDM, of an isolated DM-only halo and we adjusted the numerical parameters to check the accuracy of the simulation. We find that not only the numerical scheme for SIDM can lead to energy non-conservation, but also the modelling of gravitational interaction and the time integration are problematic. The main issues we find are: (a) particles changing their time step in a non-time-reversible manner; (b) the asymmetry in the tree-based gravitational force evaluation; and (c) SIDM velocity kicks breaking the time symmetry. Tuning the parameters of the simulation to achieve a high level of accuracy allows us to conserve energy not only at early stages of the evolution, but also later on. However, the cost of the simulations becomes prohibitively large as a result. Some of the problems that make the simulations of the gravothermal collapse phase inaccurate can be overcome by choosing appropriate numerical schemes. However, other issues still pose a challenge. Our findings motivate further works on addressing the challenges in simulating strong DM self-interactions.

dark matter↗

DOE OSTI2014

Multi-scale coarse-graining of non-conservative interactions in molecular liquids

A new bottom-up procedure for constructing non-conservative (dissipative and stochastic) interactions for dissipative particle dynamics (DPD) models is described and applied to perform hierarchical coarse-graining of a polar molecular liquid (nitromethane). The distant-dependent radial and shear frictions in functional-free form are derived consistently with a chosen form for conservative interactions by matching two-body force-velocity and three-body velocity-velocity correlations along the microscopic trajectories of the centroids of Voronoi cells (clusters), which represent the dissipative particles within the DPD description. The Voronoi tessellation is achieved by application of the K-means clustering algorithm at regular time intervals. Consistently with a notion of many-body DPD, the conservative interactions are determined through the multi-scale coarse-graining (MS-CG) method, which naturally implements a pairwise decomposition of the microscopic free energy. A hierarchy of MS-CG/DPD models starting with one molecule per Voronoi cell and up to 64 molecules per cell is derived. The radial contribution to the friction appears to be dominant for all models. As the Voronoi cell sizes increase, the dissipative forces rapidly become confined to the first coordination shell. For Voronoi cells of two and more molecules the time dependence of the velocity autocorrelation function becomes monotonic and well reproduced by the respective MS-CG/DPD models. A comparative analysis of force and velocity correlations in the atomistic and CG ensembles indicates Markovian behavior with as low as two molecules per dissipative particle. The models with one and two molecules per Voronoi cell yield transport properties (diffusion and shear viscosity) that are in good agreement with the atomistic data. The coarser models produce slower dynamics that can be appreciably attributed to unaccounted dissipation introduced by regular Voronoi re-partitioning as well as by larger numerical errors in mapping out the dissipative forces. The framework presented herein can be used to develop computational models of real liquids which are capable of bridging the atomistic and mesoscopic scales.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Conservative algorithms for non-Maxwellian plasma kinetics

Here, we present a numerical model and a set of conservative algorithms for Non-Maxwellian plasma kinetics with inelastic collisions. These algorithms self-consistently solve for the time evolution of an isotropic electron energy distribution function interacting with an atomic state distribution function of an arbitrary number of levels through collisional excitation, deexcitation, as well as ionization and recombination. Electron-electron collisions, responsible for thermalization of the electron distribution, are also included in the model. The proposed algorithms guarantee mass/charge and energy conservation in a single step, and is applied to the case of non-uniform gridding of the energy axis in the phase space of the electron distribution function. Numerical test cases are shown to demonstrate the accuracy of the method and its conservation properties.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Conservation laws in coupled cluster dynamics at finite temperature

We extend the finite-temperature Keldysh non-equilibrium coupled cluster theory (Keldysh-CC) [A. F. White and G. K.-L. Chan, J. Chem. Theory Comput. 15, 6137–6253 (2019)] to include a time-dependent orbital basis. When chosen to minimize the action, such a basis restores local and global conservation laws (Ehrenfest’s theorem) for all one-particle properties while remaining energy conserving for time independent Hamiltonians. We present the time-dependent Keldysh orbital-optimized coupled cluster doubles method in analogy with the formalism for zero-temperature dynamics, extended to finite temperatures through the time-dependent action on the Keldysh contour. To demonstrate the conservation property and understand the numerical performance of the method, we apply it to several problems of nonequilibrium finite-temperature dynamics: a 1D Hubbard model with a time-dependent Peierls phase, laser driving of molecular H2, driven dynamics in warm-dense silicon, and transport in the single impurity Anderson model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Potential vorticity conservation for plasma turbulence in an inhomogeneous magnetic field: Theory and implications

The concept and theory of potential vorticity in drift wave turbulence are extended to the case of an inhomogeneous magnetic field. A one-field magnetic potential vorticity conserving equation is derived via the use of conservative gyrokinetics. The similarity between the corresponding systems for drift wave turbulence and shallow water theory is discussed in detail. Zonal flow physics in an inhomogeneous magnetic field is discussed. In particular, a Charney–Drazin type nonacceleration theorem is derived from the novel system, which conserves magnetic potential vorticity. Extensions of the turbulent equipartition theory to the transport of magnetic potential vorticity are proposed.

Physics↗

DOE OSTI2015

Background history and cosmic perturbations for a general system of self-conserved dynamical dark energy and matter

We determine the Hubble expansion and the general cosmic perturbation equations for a general system consisting of self-conserved matter, ρ{sub m}, and self-conserved dark energy (DE), ρ{sub D}. While at the background level the two components are non-interacting, they do interact at the perturbations level. We show that the coupled system of matter and DE perturbations can be transformed into a single, third order, matter perturbation equation, which reduces to the (derivative of the) standard one in the case that the DE is just a cosmological constant. As a nontrivial application we analyze a class of dynamical models whose DE density ρ{sub D}(H) consists of a constant term, C{sub 0}, and a series of powers of the Hubble rate. These models were previously analyzed from the point of view of dynamical vacuum models, but here we treat them as self-conserved DE models with a dynamical equation of state. We fit them to the wealth of expansion history and linear structure formation data and compare their fit quality with that of the concordance ΛCDM model. Those with C{sub 0}=0 include the so-called ''entropic-force'' and ''QCD-ghost'' DE models, as well as the pure linear model ρ{sub D}∼H, all of which appear strongly disfavored. The models with C{sub 0}≠0 , in contrast, emerge as promising dynamical DE candidates whose phenomenological performance is highly competitive with the rigid Λ-term inherent to the ΛCDM.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2016

Conservation of ζ with radiative corrections from heavy field

In this paper, we address a possible impact of radiative corrections from a heavy scalar field χ on the curvature perturbation ζ. Integrating out χ, we derive the effective action for ζ, which includes the loop corrections of the heavy field χ. When the mass of χ is much larger than the Hubble scale H, the loop corrections of χ only yield a local contribution to the effective action and hence the effective action simply gives an action for ζ in a single field model, where, as is widely known, ζ is conserved in time after the Hubble crossing time. Meanwhile, when the mass of χ is comparable to H, the loop corrections of χ can give a non-local contribution to the effective action. Because of the non-local contribution from χ, in general, ζ may not be conserved, even if the classical background trajectory is determined only by the evolution of the inflaton. In this paper, we derive the condition that ζ is conserved in time in the presence of the radiative corrections from χ. Namely, we show that when the dilatation invariance, which is a part of the diffeomorphism invariance, is preserved at the quantum level, the loop corrections of the massive field χ do not disturb the constant evolution of ζ at super Hubble scales. In this discussion, we show the Ward-Takahashi identity for the dilatation invariance, which yields a consistency relation for the correlation functions of the massive field χ.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2018

Conservative magnetic moment of runaway electrons and collisionless pitch-angle scattering

Recently, the validity of the guiding-center approach to model relativistic runaway electrons in tokamaks has been challenged by full-orbit simulations that demonstrate the breakdown of the standard magnetic moment conservation. In this paper, we derive a new expression for the magnetic moment of relativistic runaway electrons with p∥>>⊥, which is conserved significantly better than the standard one. The new result includes one of the second-order corrections in the standard guiding-center theory which, in case of runaway electrons with p∥>>⊥, can peculiarly be of the same order as the lowest-order term. The better conservation of the new magnetic moment also explains the collisionless pitch-angle-scattering effect observed in full-orbit simulations since it allows momentum transfer between the perpendicular and parallel directions when the runaway electron is accelerated by an electric field. In conclusion, while the derivation of the second-order correction to the magnetic moment in general case would require the full extent of the relativistic second-order guiding-center theory, we exploit the Lie-perturbation method at the limit p∥Gtp⊥ which simplifies the computations significantly. Consequently, we present the corresponding guiding-center equations applicable to runaway electrons.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Conservative discontinuous Galerkin scheme of a gyro-averaged Dougherty collision operator

Here, a conservative discontinuous Galerkin scheme for a non-linear Dougherty collision operator in full-f long-wavelength gyrokinetics is presented. Analytically this model operator has the advective-diffusive form of Fokker-Planck operators, it has a non-decreasing entropy functional, and conserves particles, momentum and energy. Discretely these conservative properties are maintained exactly as well, independent of numerical resolution. In this work the phase space discretization is performed using a novel version of the discontinuous Galerkin scheme, carefully constructed using concepts of weak equality and recovery. Discrete time advancement is carried out with an explicit time-stepping algorithm, whose stability limits we explore. The formulation and implementation within the long-wavelength gyrokinetic solver of Gkeyll are validated with relaxation tests, collisional Landau-damping benchmarks and the study of 5D gyrokinetic turbulence on helical, open field lines.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2018

Remodeling neuronal ER–PM junctions is a conserved nonconducting function of Kv2 plasma membrane ion channels

The endoplasmic reticulum (ER) and plasma membrane (PM) form junctions crucial to ion and lipid signaling and homeostasis. The Kv2.1 ion channel is localized at ER–PM junctions in brain neurons and is unique among PM proteins in its ability to remodel these specialized membrane contact sites. Here, we show that this function is conserved between Kv2.1 and Kv2.2, which differ in their biophysical properties, modulation, and cellular expression. Kv2.2 ER–PM junctions are present at sites deficient in the actin cytoskeleton, and disruption of the actin cytoskeleton affects their spatial organization. Kv2.2-containing ER–PM junctions overlap with those formed by canonical ER–PM tethers. The ability of Kv2 channels to remodel ER–PM junctions is unchanged by point mutations that eliminate their ion conduction but eliminated by point mutations within the Kv2-specific proximal restriction and clustering (PRC) domain that do not impact their ion channel function. The highly conserved PRC domain is sufficient to transfer the ER–PM junction–remodeling function to another PM protein. Last, brain neurons in Kv2 double-knockout mice have altered ER–PM junctions. Together, these findings demonstrate a conserved in vivo function for Kv2 family members in remodeling neuronal ER–PM junctions that is distinct from their canonical role as ion-conducting channels shaping neuronal excitability.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Structural basis for a highly conserved RNA-mediated enteroviral genome replication

Abstract Enteroviruses contain conserved RNA structures at the extreme 5′ end of their genomes that recruit essential proteins 3CD and PCBP2 to promote genome replication. However, the high-resolution structures and mechanisms of these replication-linked RNAs (REPLRs) are limited. Here, we determined the crystal structures of the coxsackievirus B3 and rhinoviruses B14 and C15 REPLRs at 1.54, 2.2 and 2.54 Å resolution, revealing a highly conserved H-type four-way junction fold with co-axially stacked sA-sD and sB-sC helices that are stabilized by a long-range A•C•U base-triple. Such conserved features observed in the crystal structures also allowed us to predict the models of several other enteroviral REPLRs using homology modeling, which generated models almost identical to the experimentally determined structures. Moreover, our structure-guided binding studies with recombinantly purified full-length human PCBP2 showed that two previously proposed binding sites, the sB-loop and 3′ spacer, reside proximally and bind a single PCBP2. Additionally, the DNA oligos complementary to the 3′ spacer, the high-affinity PCBP2 binding site, abrogated its interactions with enteroviral REPLRs, suggesting the critical roles of this single-stranded region in recruiting PCBP2 for enteroviral genome replication and illuminating the promising prospects of developing therapeutics against enteroviral infections targeting this replication platform.

Biochemistry & Molecular Biology↗

DOE OSTI2026

Sparsomycin inhibits translation through a conserved mechanism across all domains of life

Abstract Sparsomycin (SPA) is a broad-spectrum inhibitor of protein synthesis with activity across all three domains of life. Although SPA has long been known to target the ribosomal peptidyl transferase center (PTC), previous structural studies suggested that SPA binds differently to bacterial ribosomes compared to their archaeal and eukaryotic counterparts—an unexpected conclusion given the high evolutionary conservation of the ribosomal catalytic center. Here, we show that SPA inhibits a majority of elongation-competent bacterial ribosomal complexes and present X-ray crystal structures of Thermus thermophilus 70S ribosomes stalled by SPA at the initiation and early elongation stages of translation. These structures reveal that SPA binds to the bacterial ribosome in a manner essentially identical to that observed in archaeal and eukaryotic ribosomes, establishing a unified structural mechanism of SPA action across all domains of life. In this conserved binding mode, SPA occupies the A-site cleft of the PTC and forms an extensive network of interactions with universally conserved ribosomal RNA nucleotides and the CCA-end of the P-site transfer RNA (tRNA), thereby stabilizing the peptidyl-tRNA substrate while sterically blocking accommodation of an incoming aminoacyl-tRNA. By clarifying the mode of action of SPA on the bacterial ribosome, our work provides a structural framework for the rational design of SPA derivatives with improved potency and bacterial specificity.

Paranjpe, Madhura N [Department of Biological Scie↗

DOE OSTI2016

Conservation and Divergence of Mediator Structure and Function: Insights from Plants

The Mediator complex is a large, multisubunit, transcription co-regulator that is conserved across eukaryotes. Studies of the Arabidopsis Mediator complex and its subunits have shown that it functions in nearly every aspect of plant development and fitness. In addition to revealing mechanisms of regulation of plant-specific pathways, studies of plant Mediator complexes have the potential to shed light on the conservation and divergence of Mediator structure and function across Kingdoms and plant lineages. The majority of insights into plant Mediator function have come from Arabidopsis because it is the only plant from which Mediator has been purified and from which an array of Mediator mutants have been isolated by forward and reverse genetics. So far, these studies indicate that, despite low sequence similarity between many orthologous subunits, the overall structure and function of Mediator is well conserved between Kingdoms. Several studies have also expanded our knowledge of Mediator to other plant species, opening avenues of investigation into the role of Mediator in plant adaptation and fitness.

09 BIOMASS FUELS↗

DOE OSTI2018

Protection of the Queuosine Biosynthesis Enzyme QueF from Irreversible Oxidation by a Conserved Intramolecular Disulfide

QueF enzymes catalyze the nicotinamide adenine dinucleotide phosphate (NADPH)‐dependent reduction of the nitrile group of 7‐cyano‐7‐deazaguanine (preQ 0 ) to 7‐aminomethyl‐7‐deazaguanine (preQ 1 ) in the biosynthetic pathway to the tRNA modified nucleoside queuosine. The QueF‐catalyzed reaction involves the formation of a covalent thioimide intermediate with a conserved active site cysteine (Cys55) that is prone to oxidation in vivo under different conditions. Here, we report the crystal structure of a mutant of Bacillus subtilis QueF, which reveals an unanticipated intramolecular disulfide bond formed between the catalytically active Cys55 and a conserved Cys99 located near the active site. When compared to the substrate‐bound structure, this structure is more symmetric and exhibits major rearrangement of the loops responsible for substrate binding. It has been demonstrated that the disulfide does not play a catalytic role because mutation of Cys99 to Ala/Ser does not compromise enzyme activity. Inactivation of the wild‐type enzyme via peroxidation is reversible with thioredoxin, while such inactivation of the Cys99Ala/Ser mutants is irreversible. This is consistent with protection of Cys55 from irreversible oxidation by disulfide formation with Cys99. Conservation of the cysteine pair, and the reported in vivo interaction of QueF with the thioredoxin‐like hydroperoxide reductase AhpC in Escherichia coli suggest that regulation by the thioredoxin disulfide‐thiol exchange system may constitute a general protective mechanism of QueF from oxidative stress in vivo. Docking of QueF onto this enzyme complex sheds structural light on the mechanism of redox control and may inform future mutagenesis experiments. Support or Funding Information This project was supported by National Science Foundation grant CHE‐1309323 to D. Iwata‐Reuyl and M.A. Swairjo, National Institutes of Health (NIH) grant GM110588 to M.A. Swairjo and D. Iwata‐Reuyl, and NIH grant GM70641 to D. Iwata‐Reuyl. Use of the Stanford Synchrotron Radiation Lightsource (SSRL), Stanford Linear Accelerator Center National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE‐AC02‐76SF00515. The SSRL Structural Molecular Biology Program is supported by the Department of Energy Office of Biological and Environmental Research, by the NIH, and the National Institute of General Medical Sciences (NIGMS) (including grant P41GM103393). This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

Mohammad, Adeba↗