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Transcription Factors Controlling the Rhizobium–Legume Symbiosis: Integrating Infection, Organogenesis and the Abiotic Environment
Abstract Legume roots engage in a symbiotic relationship with rhizobia, leading to the development of nitrogen-fixing nodules. Nodule development is a sophisticated process and is under the tight regulation of the plant. The symbiosis initiates with a signal exchange between the two partners, followed by the development of a new organ colonized by rhizobia. Over two decades of study have shed light on the transcriptional regulation of rhizobium–legume symbiosis. A large number of transcription factors (TFs) have been implicated in one or more stages of this symbiosis. Legumes must monitor nodule development amidst a dynamic physical environment. Some environmental factors are conducive to nodulation, whereas others are stressful. The modulation of rhizobium–legume symbiosis by the abiotic environment adds another layer of complexity and is also transcriptionally regulated. Several symbiotic TFs act as integrators between symbiosis and the response to the abiotic environment. In this review, we trace the role of various TFs involved in rhizobium–legume symbiosis along its developmental route and highlight the ones that also act as communicators between this symbiosis and the response to the abiotic environment. Finally, we discuss contemporary approaches to study TF-target interactions in plants and probe their potential utility in the field of rhizobium–legume symbiosis.
Two interacting ethylene response factors regulate heat stress response
Abstract The ethylene response factor (ERF) transcription factors are integral components of environmental stress signaling cascades, regulating a wide variety of downstream genes related to stress responses and plant development. However, the mechanisms by which ERF genes regulate the heat stress response are not well understood. Here, we uncover the positive role of ethylene signaling, ERF95 and ERF97 in basal thermotolerance of Arabidopsis thaliana. We demonstrate that ethylene signaling-defective mutants exhibit compromised basal thermotolerance, whereas plants with constitutively activated ethylene response show enhanced basal thermotolerance. EIN3 physically binds to the promoters of ERF95 and ERF97. Ectopic constitutive expression of ERF95 or ERF97 increases the basal thermotolerance of plants. In contrast, erf95 erf96 erf97 erf98 quadruple mutants exhibit decreased basal thermotolerance. ERF95 and ERF97 genetically function downstream of EIN3. ERF95 can physically interact with ERF97, and this interaction is heat inducible. ERF95 and ERF97 regulate a common set of target genes, including known heat-responsive genes and directly bind to the promoter of HSFA2. Thus, our study reveals that the EIN3-ERF95/ERF97-HSFA2 transcriptional cascade may play an important role in the heat stress response, thereby establishing a connection between ethylene and its downstream regulation in basal thermotolerance of plants.
QCD Predictions for Meson Electromagnetic Form Factors at High Momenta: Testing Factorization in Exclusive Processes
We report the first lattice QCD computation of pion and kaon electromagnetic form factors, 𝐹 𝑀 (𝑄 2 ), at large momentum transfer up to 10 and 28 GeV 2 , respectively. Utilizing physical masses and two fine lattices, we achieve good agreement with JLab experimental results at 𝑄 2 ≲ 4 GeV 2 . For 𝑄 2 ≳ 4 GeV 2 , our results provide ab initio QCD benchmarks for the forthcoming experiments at JLab 12 GeV and future electron-ion colliders. We also test the QCD collinear factorization framework utilizing our high-𝑄 2 form factors at next-to-next-to-leading order in perturbation theory, which relates the form factors to the leading Fock-state meson distribution amplitudes. Comparisons with independent lattice QCD calculations using the same framework demonstrate, within estimated uncertainties, the universality of these nonperturbative quantities.
A Numerical Study of Factors Affecting Fracture-Fluid Cleanup and Produced Gas/Water in Marcellus Shale: Part II
Horizontal wells combined with successful multi-stage hydraulic fracture treatments are currently the most established method for effectively stimulating and enabling economic development of gas bearing organic-rich shale formations. Fracture cleanup in the Stimulated Reservoir Volume (SRV) is critical to stimulation effectiveness and long-term well performance. However, fluid cleanup is often hampered by formation damage, and post-fracture well performance frequently falls below expectations. A systematic study of the factors that hinder fracture fluid cleanup in shale formations can help optimize fracture treatments and better quantify long term volumes of produced water and gas. Fracture fluid cleanup is a complex process influenced by multi-phase flow through porous media (relative permeability hysteresis, capillary pressure etc.), reservoir rock and fluid properties, fracture fluid properties, proppant placement, fracture treatment parameters, and subsequent flowback and field operations. Changing SRV and fracture conductivity as production progresses further adds to the complexity of this problem. Numerical simulation is the best, and most practical approach to investigate such a complicated blend of mechanisms, parameters, their interactions, and subsequent impact on fracture fluid cleanup and well deliverability. In this paper, a 3-dimensional, 2-phase, dual-porosity model was used to investigate the impact of multiphase flow, proppant crushing, proppant diagenesis, shut-in time, reservoir rock compaction, gas slippage, and gas desorption on fracture fluid cleanup, and well performance in Marcellus shale. The research findings have shed light on the factors that substantially constrains efficient fracture fluid cleanup in gas shales, and provided guidelines for improved fracture treatment designs and water management.
Air Exchange Rate Impact on Activity Equilibrium Factors and Inhalation Fractional Equilibrium Factors for Rn, Xe, Kr, Ar, Ne, and Their Progeny in Vapor Intrusion, Risk, and Dose Models
Exposure to the radioactive noble gasses, especially radon, is of high concern and poses a significant risk to humans in an indoor air environment as the second leading cause of lung cancer in the United States. To evaluate and minimize the risks posed by these gasses, it is important to understand their radiological and physical properties. The EPA’s Radon Vapor Intrusion Screening Level (RVISL) calculator calculates indoor air RVISLs based on target working levels (WLs), target excess lifetime cancer risk (ELCR), and annual dose limits for the actinon (Rn-219), thoron (Rn-220), and radon (Rn-222) decay series. The RVISLs are based on inhalation and submersion in gas cloud exposure routes for residential and commercial settings. The RVISLs are analogous to preliminary remediation goals (PRGs) and dose compliance concentrations (DCCs), where the isotope-specific values are in units of activity concentration (activity per unit volume). If the concentration of a parent isotope of radon or its progeny is found to exceed the RVISL, then further action to ensure cleanup of the contaminant may be necessary. In residential and commercial settings, the RVISLs will vary based on the air exchange rate present. The EPA’s Radionuclide PRG and DCC Calculators also assess the risk/dose from noble gases in the air due to household use of water like showering. In this study, a computational method in MATLAB was developed to determine the impact of the air exchange rate on the activity equilibrium factor (A eq ) and the inhalation fractional equilibrium factor (F eq ). Both factors are values that reflect the equilibrium concentrations of progeny to their parent in the air. These factors have a direct impact on the RVISL, PRG, and DCC calculations of WL, ELCR, and annual dose, respectively. This study builds on a previous report that only focused on actinon, thoron, and radon by revisiting the original A eq and F eq calculation methods, as well as including the values for the Rn-207, Rn-209, Rn-210, Rn-211, Rn-215, Rn-216, Rn-217, Rn-218, Rn-223, Ne-24, Ar-42, Ar-43, Ar-44, Kr-74, Kr-75, Kr-76, Kr-77, Kr-88, Kr-89, Xe-120, Xe-121, Xe-122, Xe-123, Xe-135m, and Xe-138 decay chains, which are not currently available in literature. The EPA’s RVISL calculator will be updated to include the new A eq and F eq values for the actinon, thoron, and radon decay chains, while the rest of the calculators will incorporate all the new A eq and F eq values as appropriate.
Pd 2 Se 3 Monolayer: A Promising Two-Dimensional Thermoelectric Material with Ultralow Lattice Thermal Conductivity and High Power Factor
A high power factor and low lattice thermal conductivity are two essential ingredients of highly efficient thermoelectric materials. Although monolayers of transition-metal dichalcogenides possess high power factors, high lattice thermal conductivities significantly impede their practical applications. Our first-principles calculations show that these two ingredients are well fulfilled in the recently synthesized Pd 2 Se 3 monolayer, whose crystal structure is composed of [Se 2 ] 2- dimers, Se 2- anions, and Pd 2+ cations coordinated in a square-planar manner. Our detailed analysis of third-order interatomic force constants reveals that the anharmonicity and soft phonon modes associated with covalently bonded [Se 2 ] 2- dimers lead to ultralow lattice thermal conductivities in Pd 2 Se 3 monolayers (1.5 and 2.9 W m -1 K -1 along the a- and b-axes at 300 K, respectively), which are comparable to those of high-performance bulk thermoelectric materials such as PbTe. Moreover, the “pudding-mold” type band structure, caused by Pd 2+ (d 8 ) cations coordinated in a square-planar crystal field, leads to high power factors in Pd 2 Se 3 monolayers. Consequently, both electron- and hole-doped thermoelectric materials with a considerably high zT can be achieved at moderate carrier concentrations, suggesting that Pd 2 Se 3 is a promising two-dimensional thermoelectric material. Our results suggest that hierarchical chemical bonds, that is, coexistence of different types of chemical bonds, combined with a square-planar crystal field is a promising route for designing high-efficiency thermoelectric materials.
Stand development and other intrinsic factors largely control fine-root dynamics with only subtle modifications from resource availability
Forest productivity depends on resource acquisition by ephemeral roots and leaves. A combination of intrinsic and environmental factors influences ephemeral organs; however, difficulties in studying belowground organs impede mechanistic understanding of fine-root production and turnover. To quantify factors controlling fine-root dynamics, we grew a deciduous hardwood (Populus deltoides Bartr.) and an evergreen conifer (Pinus taeda L.) with distinct soil moisture and nutrient availability treatments. We monitored fine-root dynamics with minirhizotrons for 6 years during early stand development and expressed results on a root length, biomass and mortality-risk basis. Stand development and other intrinsic factors consistently influenced both species in the same direction and by similar magnitude. Live-root length increased to a peak during establishment and slowly declined after roots of neighboring trees overlapped. Root longevity was highest during establishment and decreased thereafter. Root longevity consistently increased with depth of appearance and initial root diameter. Season of appearance affected root longevity in the following order: spring > summer > fall > winter. The influence of soil resource availability on fine-root dynamics was inconsistent between species, and ranked below that of rooting depth, initial diameter, stand development and phenology. Fine-root biomass either increased or was unaffected by greater resource availability. Fine-root production and live root length decreased with irrigation for both species, and increased with fertilization only for poplar. Fine-root mortality risk both increased and decreased depending on species and amendment treatment. Differing responses to soil moisture and nutrient availability between species suggests we should carefully evaluate generalizations about the response of fine-root dynamics to resource availability. Finally, while attempting to describe and explain carbon allocation to fine-root production and turnover, modelers and physiologists should first consider consistent patterns of allocation caused by different depth, diameter, stand development, phenology and species before considering allocation due to soil resource availability.
Biota Modeling in EPA’s Preliminary Remediation Goal and Dose Compliance Concentration Calculators for Use in EPA Superfund Risk Assessment: Explanation of Intake Rate Derivation, Transfer Factor Compilation, and Mass Loading Factor Sources
The Preliminary Remediation Goal (PRG) and Dose Compliance Concentration (DCC) calculators are screening level risk assessment tools that set forth the Environmental Protection Agency’s (EPA) recommended approaches and currently available risk assessment guidance for response actions at Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) sites, commonly known as Superfund. The environmental screening levels derived by the PRG and DCC calculators are used to identify isotopes contributing the highest risk and dose as well as establish preliminary remediation goals. Each calculator has residential gardening and subsistence farmer exposure scenarios that model transfer of contaminants from soil and water into various types of biota (crops and animal products). New publications of human intake rates of biota; farm animal intakes of water, soil, and fodder; and soil to plant interactions require updates be implemented into the PRG and DCC calculators. Recent improvements in the biota modeling for these calculators include newly derived biota intake rates, enhanced soil mass loading factors (MLFs), and more comprehensive soil to plant transfer factors (BV’s) and soil to tissue transfer factors (TFs) for animals. New biota have been added in both the produce and animal products categories that greatly improve the accuracy and utility of the PRG and DCC calculators and encompass greater geographic diversity on a national and international scale.
Low-rank factorization of electron integral tensors and its application in electronic structure theory
In this letter, we introduce the reverse Cuthill-McKee (RCM) algorithm, which is often used for the bandwidth reduction of sparse tensors, to transform the two-electron integral tensors to their block diagonal forms. By further applying the pivoted Cholesky decomposition (CD) on each of the diagonal blocks, we are able to represent the high-dimensional two-electron integral tensors in terms of permutation matrices and low-rank Cholesky vectors. This representation facilitates the low-rank factorization of the high-dimensional tensor contractions that are usually encountered in post-Hartree-Fock calculations. In this letter, we discuss the second-order Møller-Plesset (MP2) method and linear coupled- cluster model with doubles (L-CCD) as two simple examples to demonstrate the efficiency of the RCM-CD technique in representing two-electron integrals in a compact form.
An expanded role for the transcription factor WRINKLED1 in the biosynthesis of triacylglycerols during seed development
The transcription factor WRINKLED1 ( WRI1 ) is known as a master regulator of fatty acid synthesis in developing oilseeds of Arabidopsis thaliana and other species. WRI1 is known to directly stimulate the expression of many fatty acid biosynthetic enzymes and a few targets in the lower part of the glycolytic pathway. However, it remains unclear to what extent and how the conversion of sugars into fatty acid biosynthetic precursors is controlled by WRI 1. To shortlist possible gene targets for future in-planta experimental validation, here we present a strategy that combines phylogenetic foot printing of cis-regulatory elements with additional layers of evidence. Upstream regions of protein-encoding genes in A. thaliana were searched for the previously described DNA-binding consensus for WRI1, the ASML1/WRI1 (AW)-box. For about 900 genes, AW-box sites were found to be conserved across orthologous upstream regions in 11 related species of the crucifer family. For 145 select potential target genes identified this way, affinity of upstream AW-box sequences to WRI1 was assayed by Microscale Thermophoresis. This allowed definition of a refined WRI1 DNA-binding consensus. We find that known WRI1 gene targets are predictable with good confidence when upstream AW-sites are phylogenetically conserved, specifically binding WRI1 in the in vitro assay, positioned in proximity to the transcriptional start site, and if the gene is co-expressed with WRI1 during seed development. When targets predicted in this way are mapped to central metabolism, a conserved regulatory blueprint emerges that infers concerted control of contiguous pathway sections in glycolysis and fatty acid biosynthesis by WRI1. Several of the newly predicted targets are in the upper glycolysis pathway and the pentose phosphate pathway. Of these, plastidic isoforms of fructokinase ( FRK 3) and of phosphoglucose isomerase ( PGI 1) are particularly corroborated by previously reported seed phenotypes of respective null mutations.
A fast two-stage algorithm for non-negative matrix factorization in smoothly varying data
This article reports the study of algorithms for non-negative matrix factorization (NMF) in various applications involving smoothly varying data such as time or temperature series diffraction data on a dense grid of points. Utilizing the continual nature of the data, a fast two-stage algorithm is developed for highly efficient and accurate NMF. In the first stage, an alternating non-negative least-squares framework is used in combination with the active set method with a warm-start strategy for the solution of subproblems. In the second stage, an interior point method is adopted to accelerate the local convergence. The convergence of the proposed algorithm is proved. The new algorithm is compared with some existing algorithms in benchmark tests using both real-world data and synthetic data. Furthermore, the results demonstrate the advantage of the algorithm in finding high-precision solutions.
Factor VIII moiety of recombinant Factor VIII Fc fusion protein impacts Fc effector function and CD16 + NK cell activation
Recombinant Factor VIII-Fc fusion protein (rFVIIIFc) is an enhanced half-life therapeutic protein product used for the management of hemophilia A. Recent studies have demonstrated that rFVIIIFc interacts with Fc gamma receptors (FcγR) resulting in the activation or inhibition of various FcγR-expressing immune cells. We previously demonstrated that rFVIIIFc, unlike recombinant Factor IX-Fc (rFIXFc), activates natural killer (NK) cells via Fc-mediated interactions with FcγRIIIA (CD16). Additionally, we showed that rFVIIIFc activated CD16 + NK cells to lyse a FVIII-specific B cell clone. Here, we used human NK cell lines and primary NK cells enriched from peripheral blood leukocytes to study the role of the FVIII moiety in rFVIIIFc-mediated NK cell activation. Following overnight incubation of NK cells with rFVIIIFc, cellular activation was assessed by measuring secretion of the inflammatory cytokine IFNγ by ELISA or by cellular degranulation. We show that anti-FVIII, anti-Fc, and anti-CD16 all inhibited indicating that these molecules were involved in rFVIIIFc-mediated NK cell activation. To define which domains of FVIII were involved, we used antibodies that are FVIII domain-specific and demonstrated that blocking FVIII C1 or C2 domain-mediated membrane binding potently inhibited rFVIIIFc-mediated CD16 + NK cell activation, while targeting the FVIII heavy chain domains did not. We also show that rFVIIIFc binds CD16 with about five-fold higher affinity than rFIXFc. Based on our results we propose that FVIII light chain-mediated membrane binding results in tethering of the fusion protein to the cell surface, and this, together with increased binding affinity for CD16, allows for Fc-CD16 interactions to proceed, resulting in NK cellular activation. Our working model may explain our previous results where we observed that rFVIIIFc activated NK cells via CD16, whereas rFIXFc did not despite having identical IgG1 Fc domains.
Effective Pressure Law for the Intrinsic Formation Factor in Low Permeability Sandstones: EPL law for the formation factor
The effective pressure law for the intrinsic formation factor of low permeability sandstones from the Ordos Basin (northwest of China) was studied experimentally by measuring the electrical resistivity of brine saturated rock samples while cycling the pore and confining pressures, p p and p c . We used a 100,000 ppm NaCl solution so that the results could be directly interpreted in terms of the intrinsic formation factor F. The Response Surface method was used to construct a quadratic function of pp and pc fitting the experimental data, from which the coefficient α of the effective pressure law, p eff = p c – αp p , was determined. We found that the coefficient α generally had low values, mainly from 0.2 to 0.4, thus contradicting the theoretical prediction that α should be equal to 1 for scale-invariant properties, such as F, in linear elastic materials having a homogeneous solid matrix. Since the two underlying assumptions, linear elasticity and homogeneity of the solid matrix, are likely violated in reservoir rocks, we tried to assess their effects on α using simple analytical models, based on idealized geometries of the pore and solid phases. Analysis of these models suggests that non-linear elasticity associated with the formation of solid–solid contacts in the compressed rocks (e.g., during closure of rough cracks or crack-like pores along the grain boundaries), may be more effective in producing the low α values observed than inhomogeneity of the solid matrix.
Manipulation of Ni Interstitials for Realizing Large Power Factor in TiNiSn-Based Materials
Not provided.
Monte Carlo calculation and verification of the geometrical factors for the NPDGamma experiment
The NPDGamma experiment measures the parity-violating asymmetry in gamma-ray emission in the capture of polarized neutrons on liquid parahydrogen. The sensitivity to the asymmetry for each detector in the array is used as a parameter in the extraction of the physics asymmetry from the measured data. The detector array is approximately cylindrically symmetric around the target and a step-wise sinusoidal function has been used for the sensitivity in the previous iteration of the NPDGamma experiment, but deviations from cylindrical symmetry necessitate the use of a Monte Carlo model to determine corrections to the geometrical factors. For the calculations, source code modifications to MCNPX were done in order to calculate the sensitivity of each cesium iodide detector to the physics asymmetry. We describe the MCNPX model and results from calculations and how the results are validated through measurement of the parity violating asymmetry of gamma-rays from neutron capture on chlorine.
Salinity-Induced Reduction of Interfacial Energies and Kinetic Factors during Calcium Carbonate Nucleation on Quartz
Abstract not provided