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At least 487 records · Page 27

MAGNETIC FLUX CONSERVATION IN THE HELIOSHEATH INCLUDING SOLAR CYCLE VARIATIONS OF MAGNETIC FIELD INTENSITY

In the heliosheath (HS), Voyager 2 has observed a flow with constant radial velocity and magnetic flux conservation. Voyager 1, however, has observed a decrease in the flow’s radial velocity and an order of magnitude decrease in magnetic flux. We investigate the role of the 11 yr solar cycle variation of the magnetic field strength on the magnetic flux within the HS using a global 3D magnetohydrodynamic model of the heliosphere. We use time and latitude-dependent solar wind velocity and density inferred from Solar and Heliospheric Observatory/SWAN and interplanetary scintillations data and implemented solar cycle variations of the magnetic field derived from 27 day averages of the field magnitude average of the magnetic field at 1 AU from the OMNI database. With the inclusion of the solar cycle time-dependent magnetic field intensity, the model matches the observed intensity of the magnetic field in the HS along both Voyager 1 and 2. This is a significant improvement from the same model without magnetic field solar cycle variations, which was over a factor of two larger. The model accurately predicts the radial velocity observed by Voyager 2; however, the model predicts a flow speed ∼100 km s{sup −1} larger than that derived from LECP measurements at Voyager 1. In the model, magnetic flux is conserved along both Voyager trajectories, contrary to observations. This implies that the solar cycle variations in solar wind magnetic field observed at 1 AU does not cause the order of magnitude decrease in magnetic flux observed in the Voyager 1 data.

79 ASTRONOMY AND ASTROPHYSICS↗

Identification of conserved skeletal enhancers associated with craniosynostosis risk genes

Abstract Craniosynostosis, defined by premature fusion of one or multiple cranial sutures, is a common congenital defect affecting more than 1/2000 infants and results in restricted brain expansion. Single gene mutations account for 15%–20% of cases, largely as part of a syndrome, but the majority are nonsyndromic with complex underlying genetics. We hypothesized that the two noncoding genomic regions identified by a GWAS for craniosynostosis contain distal regulatory elements for the risk genes BMPER and BMP2. To identify such regulatory elements, we surveyed conserved noncoding sequences from both risk loci for enhancer activity in transgenic Danio rerio. We identified enhancers from both regions that direct expression to skeletal tissues, consistent with the endogenous expression of bmper and bmp2. For each locus, we also found a skeletal enhancer that also contains a sequence variant associated with craniosynostosis risk. We examined the activity of each enhancer during craniofacial development and found that the BMPER-associated enhancer is active in the restricted region of cartilage closely associated with frontal bone initiation. The same enhancer is active in mouse skeletal tissues, demonstrating evolutionarily conserved activity. Using enhanced yeast one-hybrid assays, we identified transcription factors that bind each enhancer and observed differential binding between alleles, implicating multiple signaling pathways. Our findings help unveil the genetic mechanism of the two craniosynostosis risk loci. More broadly, our combined in vivo approach is applicable to many complex genetic diseases to build a link between association studies and specific genetic mechanisms.

He(何璇), Xuan Anita (ORCID:0000000313221972)↗

Essential amino acids in the Plant-Conserved and Class-Specific Regions of cellulose synthases

The Plant-Conserved Region (P-CR) and the Class-Specific Region (CSR) are two plant-unique sequences in the catalytic core of cellulose synthases (CESAs) for which specific functions have not been established. Here, we used site-directed mutagenesis to replace amino acids and motifs within these sequences predicted to be essential for assembly and function of CESAs. We developed an in vivo method to determine the ability of mutated CesA1 transgenes to complement an Arabidopsis (Arabidopsis thaliana) temperature-sensitive root-swelling1 (rsw1) mutant. Replacement of a Cys residue in the CSR, which blocks dimerization in vitro, rendered the AtCesA1 transgene unable to complement the rsw1 mutation. Examination of the CSR sequences from 33 diverse angiosperm species showed domains of high-sequence conservation in a class-specific manner but with variation in the degrees of disorder, indicating a nonredundant role of the CSR structures in different CESA isoform classes. The Cys residue essential for dimerization was not always located in domains of intrinsic disorder. Expression of AtCesA1 transgene constructs, in which Pro417 and Arg453 were substituted for Ala or Lys in the coiled-coil of the P-CR, were also unable to complement the rsw1 mutation. Despite an expected role for Arg457 in trimerization of CESA proteins, AtCesA1 transgenes with Arg457Ala mutations were able to fully restore the wild-type phenotype in rsw1. Our data support that Cys662 within the CSR and Pro417 and Arg453 within the P-CR of Arabidopsis CESA1 are essential residues for functional synthase complex formation, but our data do not support a specific role for Arg457 in trimerization in native CESA complexes.

59 BASIC BIOLOGICAL SCIENCES↗

Phylogenetic conservation of soil bacterial responses to simulated global changes.

Soil bacterial communities are altered by anthropogenic drivers such as climate change-related warming and fertilization. However, we lack a predictive understanding of how bacterial communities respond to such global changes. Here, we tested whether phylogenetic information might be more predictive of the response of bacterial taxa to some forms of global change than others. We analysed the composition of soil bacterial communities from perturbation experiments that simulated warming, drought, elevated CO2 concentration and phosphorus (P) addition. Bacterial responses were phylogenetically conserved to all perturbations. The phylogenetic depth of these responses varied minimally among the types of perturbations and was similar when merging data across locations, implying that the context of particular locations did not affect the phylogenetic pattern of response. We further identified taxonomic groups that responded consistently to each type of perturbation. These patterns revealed that, at the level of family and above, most groups responded consistently to only one or two types of perturbations, suggesting that traits with different patterns of phylogenetic conservation underlie the responses to different perturbations. We conclude that a phylogenetic approach may be useful in predicting how soil bacterial communities respond to a variety of global changes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

54 ENVIRONMENTAL SCIENCES↗

Filling constraints on translation invariant dipole conserving systems

Systems with conserved dipole moment have drawn considerable interest in light of their realization in recent experiments on tilted optical lattices. Here, an important question for such systems is delineating the conditions under which they admit a unique gapped ground state that is consistent with all symmetries. Here, we study one-dimensional translation-invariant lattices that conserve U(1) charge and Z L dipole moment, where discreteness of the dipole symmetry is enforced by periodic boundary conditions, with L the system size. We show that in these systems, a symmetric, gapped, and non-degenerate ground state requires not only integer charge filling, but also a fixed value of the dipole filling, while other fractional dipole fillings enforce either a gapless or symmetry-breaking ground state. In contrast with prior results in the literature, we find that the dipole filling constraint depends both on the charge filling as well as the system size, emphasizing the subtle interplay of dipole symmetry with boundary conditions. We support our results with numerical simulations and exact results.

1-dimensional systems↗

Pre-equilibrium evolution of conserved charges with initial conditions in the ICCING Monte Carlo event generator

Heavy-ion collisions can be well described through relativistic viscous hydrodynamics, but questions still remain when hydrodynamics is applicable because the initial state may begin very far from equilibrium. Thus, a pre-equilibrium evolution phase is used to bridge the gap between the initial state and hydrodynamics. KøMPøST is one such pre-equilibrium model that propagates the energy-momentum tensor by decomposing it into the background and fluctuations around that background, whose evolution is captured by Green's functions. We extend this formalism to include conserved charges and calculate the corresponding nonequilibrium Green's functions in the relaxation-time approximation. The ICCING algorithm initializes conserved charges in the initial state by sampling $g$ → $q$$\overline{q}$ splitting probabilities and is, thus, perfectly positioned to implement Green's functions for charge propagation. As a result, we show that this method alters the initial-state charge geometries and is applicable in central to mid-central collisions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Strong optimized conservative Fermi-LAT constraints on dark matter models from the inclusive photon spectrum

Here, we set conservative, robust constraints on the annihilation and decay of dark matter into various Standard Model final states under various assumptions about the distribution of the dark matter in the Milky Way halo. We use the inclusive photon spectrum observed by the Fermi Gamma-ray Space Telescope through its main instrument, the Large Area Telescope. We use simulated data to first find the “optimal” regions of interest in the γ-ray sky, where the expected dark matter signal is largest compared with the expected astrophysical foregrounds. We then require the predicted dark matter signal to be less than the observed photon counts in the a priori optimal regions. This yields a very conservative constraint as we do not attempt to model or subtract astrophysical foregrounds. The resulting limits are competitive with other existing limits and, for some final states with cuspy dark-matter distributions in the Galactic Center region, disfavor the typical cross section required during freeze-out for a weakly interacting massive particle to obtain the observed relic abundance.

79 ASTRONOMY AND ASTROPHYSICS↗

Conservative Spin-Magnitude Change in Orbital Evolution in General Relativity

We show that physical scattering observables for compact spinning objects in general relativity can depend on additional degrees of freedom in the spin tensor beyond those described by the spin vector alone. The impulse, spin kick, and leading-order waveforms exhibit such a nontrivial dependence. A signal of this additional structure is the change in the magnitude of the spin vector under conservative Hamiltonian evolution, similar to our previous studies in electrodynamics. These additional degrees of freedom describe dynamical mass multipoles of compact objects and decouple for black holes. We also show that the conservative impulse, spin kick, and change of the additional degrees of freedom are encoded in the eikonal phase.

Classical black holes↗

Viscous Gubser flow with conserved charges to benchmark fluid simulations

We present semi-analytical solutions for the evolution of both the temperature and chemical potentials for viscous Gubser flow with conserved charges. Such a solution can be especially useful in testing numerical codes intended to simulate relativistic fluids with large chemical potentials. The freeze-out hypersurface profiles for constant energy density are calculated, along with the corresponding normal vectors, and presented as a new unit test for numerical codes. We also compare the influence of the equation of state on the semi-analytical solutions. We benchmark the newly developed smoothed particle hydrodynamics code ccake that includes both shear viscosity and three conserved charges. Here, the numerical solutions are in excellent agreement with the semi-analytical solution and are also able to accurately reproduce the hypersurface at freeze-out.

Hydrodynamic models↗

Rice Cellulose SynthaseA8 Plant-Conserved Region Is a Coiled-Coil at the Catalytic Core Entrance

The crystallographic structure of a rice (Oryza sativa) cellulose synthase, OsCesA8, plant-conserved region (P-CR), one of two unique domains in the catalytic domain of plant CesAs, was solved to 2.4 Å resolution. Two antiparallel α-helices form a coiled-coil domain linked by a large extended connector loop containing a conserved trio of aromatic residues. The P-CR structure was fit into a molecular envelope for the P-CR domain derived from small-angle X-ray scattering data. The P-CR structure and molecular envelope, combined with a homology-based chain trace of the CesA8 catalytic core, were modeled into a previously determined CesA8 small-angle X-ray scattering molecular envelope to produce a detailed topological model of the CesA8 catalytic domain. The predicted position for the P-CR domain from the molecular docking models places the P-CR connector loop into a hydrophobic pocket of the catalytic core, with the coiled-coil aligned near the entrance of the substrate UDP-glucose into the active site. In this configuration, the P-CR coiled-coil alone is unlikely to regulate substrate access to the active site, but it could interact with other domains of CesA, accessory proteins, or other CesA catalytic domains to control substrate delivery.

59 BASIC BIOLOGICAL SCIENCES↗

Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode

The host factor Hfq, as the bacterial branch of the Sm family, is an RNA-binding protein involved in the post-transcriptional regulation of mRNA expression and turnover. Hfq facilitates pairing between small regulatory RNAs (sRNAs) and their corresponding mRNA targets by binding both RNAs and bringing them into close proximity. Hfq homologs self-assemble into homo-hexameric rings with at least two distinct surfaces that bind RNA. Recently, another binding site, dubbed the `lateral rim', has been implicated in sRNA·mRNA annealing; the RNA-binding properties of this site appear to be rather subtle, and its degree of evolutionary conservation is unknown. An Hfq homolog has been identified in the phylogenetically deep-branching thermophile Aquifex aeolicus ( Aae ), but little is known about the structure and function of Hfq from basal bacterial lineages such as the Aquificae. Therefore, Aae Hfq was cloned, overexpressed, purified, crystallized and biochemically characterized. Structures of Aae Hfq were determined in space groups P 1 and P 6, both to 1.5 Å resolution, and nanomolar-scale binding affinities for uridine- and adenosine-rich RNAs were discovered. Co-crystallization with U 6 RNA reveals that the outer rim of the Aae Hfq hexamer features a well defined binding pocket that is selective for uracil. This Aae Hfq structure, combined with biochemical and biophysical characterization of the homolog, reveals deep evolutionary conservation of the lateral RNA-binding mode, and lays a foundation for further studies of Hfq-associated RNA biology in ancient bacterial phyla.

59 BASIC BIOLOGICAL SCIENCES↗

Structural insights into the interaction of the conserved mammalian proteins GAPR-1 and Beclin 1, a key autophagy protein

Mammalian Golgi-associated plant pathogenesis-related protein 1 (GAPR-1) is a negative autophagy regulator that binds Beclin 1, a key component of the autophagosome nucleation complex. Beclin 1 residues 267–284 are required for binding GAPR-1. Here, sequence analyses, structural modeling, mutagenesis combined with pull-down assays, X-ray crystal structure determination and small-angle X-ray scattering were used to investigate the Beclin 1–GAPR-1 interaction. Five conserved residues line an equatorial GAPR-1 surface groove that is large enough to bind a peptide. A model of a peptide comprising Beclin 1 residues 267–284 docked onto GAPR-1, built using the CABS-dock server, indicates that this peptide binds to this GAPR-1 groove. Mutation of the five conserved residues lining this groove, H54A/E86A/G102K/H103A/N138G, abrogates Beclin 1 binding. The 1.27 Å resolution X-ray crystal structure of this pentad mutant GAPR-1 was determined. Comparison with the wild-type (WT) GAPR-1 structure shows that the equatorial groove of the pentad mutant is shallower and more positively charged, and therefore may not efficiently bind Beclin 1 residues 267–284, which include many hydrophobic residues. Both WT and pentad mutant GAPR-1 crystallize as dimers, and in each case the equatorial groove of one subunit is partially occluded by the other subunit, indicating that dimeric GAPR-1 is unlikely to bind Beclin 1. SAXS analysis of WT and pentad mutant GAPR-1 indicates that in solution the WT forms monomers, while the pentad mutant is primarily dimeric. Thus, changes in the structure of the equatorial groove combined with the improved dimerization of pentad mutant GAPR-1 are likely to abrogate binding to Beclin 1.

59 BASIC BIOLOGICAL SCIENCES↗

Structural conservation of chemotaxis machinery across A rchaea and B acteria

Summary Chemotaxis allows cells to sense and respond to their environment. In B acteria, stimuli are detected by arrays of chemoreceptors that relay the signal to a two‐component regulatory system. These arrays take the form of highly stereotyped super‐lattices comprising hexagonally packed trimers‐of‐receptor‐dimers networked by rings of histidine kinase and coupling proteins. This structure is conserved across chemotactic B acteria, and between membrane‐bound and cytoplasmic arrays, and gives rise to the highly cooperative, dynamic nature of the signalling system. The chemotaxis system, absent in eukaryotes, is also found in A rchaea, where its structural details remain uncharacterized. Here we provide evidence that the chemotaxis machinery was not present in the last archaeal common ancestor, but rather was introduced in one of the waves of lateral gene transfer that occurred after the branching of Eukaryota but before the diversification of E uryarchaeota. Unlike in B acteria, the chemotaxis system then evolved largely vertically in A rchaea, with very few subsequent successful lateral gene transfer events. By electron cryotomography, we find that the structure of both membrane‐bound and cytoplasmic chemoreceptor arrays is conserved between B acteria and A rchaea, suggesting the fundamental importance of this signalling architecture across diverse prokaryotic lifestyles.

Briegel, Ariane↗

The Populus ARBORKNOX1 homeodomain transcription factor regulates woody growth through binding to evolutionarily conserved target genes of diverse function

Summary The class I KNOX homeodomain transcription factor ARBORKNOX1 (ARK1) is a key regulator of vascular cambium maintenance and cell differentiation in Populus . Currently, basic information is lacking concerning the distribution, functional characteristics, and evolution of ARK1 binding in the Populus genome. Here, we used chromatin immunoprecipitation sequencing (ChIP‐seq) technology to identify ARK1 binding loci genome‐wide in Populus . Computational analyses evaluated the distribution of ARK1 binding loci, the function of genes associated with bound loci, the effect of ARK1 binding on transcript levels, and evolutionary conservation of ARK1 binding loci. ARK1 binds to thousands of loci which are highly enriched proximal to the transcriptional start sites of genes of diverse functions. ARK1 target genes are significantly enriched in paralogs derived from the whole‐genome salicoid duplication event. Both ARK1 and a maize ( Zea mays ) homolog, KNOTTED1, preferentially target evolutionarily conserved genes. However, only a small portion of ARK1 target genes are significantly differentially expressed in an ARK1 over‐expression mutant. This study describes the functional characteristics and evolution of DNA binding by a transcription factor in an undomesticated tree, revealing complexities similar to those shown for transcription factors in model animal species.

Liu, Lijun↗

A human antibody reveals a conserved site on beta-coronavirus spike proteins and confers protection against SARS-CoV-2 infection

Broadly neutralizing antibodies (bnAbs) to coronaviruses (CoVs) are valuable in their own right as prophylactic and therapeutic reagents to treat diverse CoVs and as templates for rational pan-CoV vaccine design. We recently described a bnAb, CC40.8, from a CoV disease 2019 (COVID-19) convalescent donor that exhibits broad reactivity with human β-CoVs. Here, we showed that CC40.8 targets the conserved S2 stem helix region of the CoV spike fusion machinery. We determined a crystal structure of CC40.8 Fab with a SARS-CoV-2 S2 stem peptide at 1.6-Å resolution and found that the peptide adopted a mainly helical structure. Conserved residues in β-CoVs interacted with CC40.8 antibody, thereby providing a molecular basis for its broad reactivity. CC40.8 exhibited in vivo protective efficacy against SARS-CoV-2 challenge in two animal models. In both models, CC40.8-treated animals exhibited less weight loss and reduced lung viral titers compared to controls. Furthermore, we noted that CC40.8-like bnAbs are relatively rare in human COVID-19 infection, and therefore, their elicitation may require rational structure-based vaccine design strategies. Overall, our study describes a target on β-CoV spike proteins for protective antibodies that may facilitate the development of pan–β-CoV vaccines.

60 APPLIED LIFE SCIENCES↗

A dynamic protein interactome drives energy conservation and electron flux in Thermococcus kodakarensis

ABSTRACT Life is supported by energy gains fueled by catabolism of a wide range of substrates, each reliant on the selective partitioning of electrons through redox ( red uction and ox idation) reactions. Electron flux through tunable and regulated protein interactions provides dynamic routes for energy conservation, but how electron flux is regulated in vivo , particularly for archaeal metabolisms that support rapid growth at the thermodynamic limits of life, is poorly understood. Identification of bona fide in vivo protein assemblies and how such assemblies dictate the totality of electron flux is critical to our understanding of the regulation imposed on metabolism, energy production, and energy conservation. Here, 25 key proteins in central metabolic redox pathways in the model, genetically accessible, hyperthermophilic archaeon Thermococcus kodakarensis , were purified to reveal an extensive, dynamic, and tightly interconnected network of protein interactions that responds to environmental cues (such as the availability of various reductive sinks) to direct electron flux to maximize energetic gains. Interactions connecting disparate functions suggest many catabolic and anabolic activities occur in spatial proximity in vivo , and while protein complexes have been historically defined under optimal conditions, many of these complexes appear to maintain alternative partnerships in changing conditions. The totality of the results obtained redefines our understanding of in vivo assemblies driving ancient metabolic strategies supporting the growth of modern Archaea. IMPORTANCE Given the potential for rational genetic manipulations of biofuel- and biotech-promising archaea to yield transformative results for major markets, it is a priority to define how the metabolisms of such species are controlled, at least in part, by in vivo protein assemblies, and from such, define routes of energy flux that can be most efficiently altered toward biofuel or biotechnological gains. Proteinaceous electron carriers (PECs, such as ferredoxins) offer the potential for specific protein–protein interactions to coordinate selective reductive flow. Employing the model, genetically accessible, hyperthermophilic archaeon, Thermococcus kodakarensis , we establish the metabolic protein interactome of 25 key redox proteins, revealing that each redox active protein has a dynamic partnership profile, suggesting catabolic and anabolic activities may occur in concert and in temporal and spatial proximity in vivo . These results reveal critical importance in evaluating the newly identified partnerships and their role and utility in providing regulated redox flux in T. kodakarensis .

Williams, Sere A. (ORCID:0000000235509590)↗

Structural Basis of Pan-Ebolavirus Neutralization by a Human Antibody against a Conserved, yet Cryptic Epitope

ABSTRACT Only one naturally occurring human antibody has been described thus far that is capable of potently neutralizing all five ebolaviruses. Here we present two crystal structures of this rare, pan-ebolavirus neutralizing human antibody in complex with Ebola virus and Bundibugyo virus glycoproteins (GPs), respectively. The structures delineate the key protein and glycan contacts for binding that are conserved across the ebolaviruses, explain the antibody’s unique broad specificity and neutralization activity, and reveal the likely mechanism behind a known escape mutation in the fusion loop region of GP2. We found that the epitope of this antibody, ADI-15878, extends along the hydrophobic paddle of the fusion loop and then dips down into a highly conserved pocket beneath the N-terminal tail of GP2, a mode of recognition unlike any other antibody elicited against Ebola virus, and likely critical for its broad activity. The fold of Bundibugyo virus glycoprotein, not previously visualized, is similar to the fold of Ebola virus GP, and ADI-15878 binds to each virus’s GP with a similar strategy and angle of attack. These findings will be useful in deployment of this antibody as a broad-spectrum therapeutic and in the design of immunogens that elicit the desired broadly neutralizing immune response against all members of the ebolavirus genus and filovirus family. IMPORTANCE There are five different members of the Ebolavirus genus. Provision of vaccines and treatments able to protect against any of the five ebolaviruses is an important goal of public health. Antibodies are a desired result of vaccines and can be delivered directly as therapeutics. Most antibodies, however, are effective against only one or two, not all, of these pathogens. Only one human antibody has been thus far described to neutralize all five ebolaviruses, antibody ADI-15878. Here we describe the molecular structure of ADI-15878 bound to the relevant target proteins of Ebola virus and Bundibugyo virus. We explain how it achieves its rare breadth of activity and propose strategies to design improved vaccines capable of eliciting more antibodies like ADI-15878.

West, Brandyn R. (ORCID:0000000213990117)↗

Biophysical and Biochemical Characterization of TP0037, a D-Lactate Dehydrogenase, Supports an Acetogenic Energy Conservation Pathway in Treponema pallidum

A longstanding conundrum in Treponema pallidum biology concerns how the spirochete generates sufficient energy to fulfill its complex pathogenesis processes during human syphilitic infection. For decades, it has been assumed that the bacterium relies solely on glucose catabolism (via glycolysis) for generation of its ATP. However, the organism’s robust motility, believed to be essential for human tissue invasion and dissemination, would require abundant ATP likely not provided by the parsimony of glycolysis. As such, additional ATP generation, either via a chemiosmotic gradient, substrate-level phosphorylation, or both, likely exists in T. pallidum. Along these lines, we have hypothesized that T. pallidum exploits an acetogenic energy conservation pathway that relies on the redox chemistry of flavins. Central to this hypothesis is the apparent existence in T. pallidum of an acetogenic pathway for the conversion of d-lactate to acetate. Herein we have characterized the structural, biophysical, and biochemical properties of the first enzyme (d-lactate dehydrogenase [d-LDH]; TP0037) predicted in this pathway. Binding and enzymatic studies showed that recombinant TP0037 consumed d-lactate and NAD+ to produce pyruvate and NADH. The crystal structure of TP0037 revealed a fold similar to that of other d-acid dehydrogenases; residues in the cofactor-binding and active sites were homologous to those of other known d-LDHs. The crystal structure and solution biophysical experiments revealed the protein’s propensity to dimerize, akin to other d-LDHs. This study is the first to elucidate the enzymatic properties of T. pallidum’s d-LDH, thereby providing new compelling evidence for a flavin-dependent acetogenic energy conservation (ATP-generating) pathway in T. pallidum.

59 BASIC BIOLOGICAL SCIENCES↗