Structural Mimicry Drives HIV-1 Rev-Mediated HERV-K Expression
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O'Carroll, Ina P.↗
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Cantor-derived medium-entropy alloys: bridging the gap between traditional metallic and high-entropy alloys
The year 2004 marked the beginning of a new era in the design of metallic materials, as the concept of multiple principal component alloys, commonly known as High-Entropy Alloys (HEAs), was proposed by Cantor and Yeh. The unexpected single-phase microstructure, instead of the expected brittle intermetallic compounds, was attributed to the large entropy of mixing and immediately caught the attention of the scientific community. Today, HEAs are considered important advanced materials and a broad range of alloys using nominally the same design principle have been investigated. Despite that, the CrMnFeCoNi (Cantor) alloy stands out as the most successful HEA due to its outstanding mechanical properties and microstructure. In this scenario, variants of the Cantor alloy, named medium-entropy alloys (MEAs), are gaining significant interest as they display a better industrial potential than both HEAs and traditional alloys. These variants of the Cantor alloy with only three or four main elements result in 15 possible combinations. The microstructure of these alloys is discussed in terms of advanced characterization as well as thermodynamic parameters and computational simulation. Their phase stability is addressed over a wide range of temperatures and strain rates. The mechanical properties, especially the fracture toughness, of the CrFeCoNi and CrCoNi alloys have been reported to be even superior to those of the Cantor alloy and most modern engineering alloys. This is associated with the formation of a continuous sequence of strengthening mechanisms, including hierarchical twin networks, which serve to prolong the strain hardening. The present article reviews and critically assesses, for the first time, recent advances in these Cantor-derived MEAs.
36 MATERIALS SCIENCE↗
The effects of Ti content and quenching on phase transformations, microstructures, and mechanical properties in uranium-titanium alloys
In this work, the effect of Ti content on phase transformations, microstructures, and mechanical properties of U-Ti alloys are described for alloys containing 0.3 wt.% to 2.0 wt.%Ti. Rapid cooling is required to overcome diffusional decomposition of γ-phase and facilitate diffusionless transformation to supersaturated variants of α-phase. Critical cooling rate increases with increasing Ti content, opposite to the trend observed in U-Mo and U-Nb alloys. This difference occurs because the martensite transformation temperatures in these relatively dilute U-Ti alloys are above the knee of the C-curve for diffusional decomposition, unlike those in the more concentrated U-Mo and U-Nb alloys. In these U-Ti alloys critical cooling rate depends on the amount of undercooling required to reach M s , which increases with increasing Ti content, and the time for diffusional decomposition to occur just above M s , which decreases with increasing Ti content. The net result is that higher cooling rates are required as Ti content increases. Full quenching results in diffusionless transformation of γ-phase to supersaturated variants of α-phase. Very dilute alloys transform via a γ → β → α m sequence of massive transformations. Martensitic γ → α' a transformation begins at ~0.4%Ti, and 100% α' a microstructures are obtained from ~0.65% to ~1.4% Ti. A transition to banded α'b martensite occurs at ~1.5%Ti. Evidence suggests that the α' a to α' b transition may occur when the cubic γ-phase first transforms to tetragonal γ°, which in turn transforms to orthorhombic α' b via the sequence γ → γ° → α' b . Fully quenched alloys exhibit moderate strengths and ductilities, and their supersaturation with Ti makes them amenable to subsequent age hardening. Subcritical quenching typically results in two-phase microstructures with lower ductilities and near-zero Ti-supersaturation, eliminating the possibility of subsequent age hardening.
36 MATERIALS SCIENCE↗
The influence of nitrogen and nitrides on the structure and properties of proton irradiated ferritic/martensitic steel
The 12Cr1MoWV (wt%) ferritic/martensitic steel HT9 is a candidate material for fuel cladding in advanced nuclear reactors, such as the Versatile Test Reactor currently under development. As such, understanding the relationship between microstructure and mechanical properties in the context of irradiation environments for these steels is critical. N content, and more specifically interstitial N, has been hypothesized to be detrimental to irradiated properties at lower temperatures (less than 0.3T m ) to a total of 6 dpa; however, in this work at a dose of 1 dpa the irradiated microstructure was improved with added N, leading to less irradiation hardening. Three variants of HT9 were irradiated with 1.5 MeV protons to a dose of 1 dpa at 300°C. The HT9 variants included Low (10 ppm), Mid (190 ppm), and High (440 ppm) N alloys that were otherwise nearly identical. Changing the N content had a variety of effects on the irradiated defect structures. As N content increased, the average dislocation loop diameter decreased, while the number density of loops increased. Additionally, extensive Ni clustering was observed on dislocations and interfaces. The Mid and High N specimens exhibited significantly less hardening (ΔHV≃100) relative to the Low N specimen (ΔHV≃160). The decrease in hardening is attributed to vanadium carbonitride acting as a sink for Ni clusters that would otherwise form on dislocations. Under the irradiation conditions used, these results suggest increasing the N content in HT9 may have a desirable effect on the irradiated structure and properties at the dose studied, as well as the swelling resistance at higher doses. In other words, N content appears to be a powerful tool for tailoring the self-interstitial atom cluster mobility in F/M steels for different temperature and dose applications.
36 MATERIALS SCIENCE↗
Improved creep performance of CoCrFeNi high entropy alloys by Mo addition
The CoCrFeNi family of high entropy alloys has good mechanical and corrosion properties, performing like stainless steels with low yield stresses. They could, however, benefit from hardening methods for structural and high temperature applications. Here, this work investigates the potential for the CoCrFeNi alloy to be hardened with the addition of Mo. A series of CoCrFeNiMo alloys and their CoCrFeNi counterparts were subsequently manufactured at NETL and then mechanically creep tested at 650°C. The alloys were designed to possess a range of stacking fault energies which influence the mechanical properties of the alloys via the motion of their dislocations under stress. Results show that Mo-containing variants have creep rupture lives ranging from 4000 to 8000 hours, i.e., about two orders of magnitude longer than those for Mo-free variants. The significantly improved creep performance of the Mo-containing alloys is due to a combination of solid solution strengthening and precipitation strengthening from µ-phase and carbides.
36 MATERIALS SCIENCE↗
Two-step deformation-induced martensitic transformation in additively manufactured High-Si stainless steel
Deformation-induced phase transformation in the additively manufactured (AM) Fe–18Cr–8Ni-5.5Si (in wt.%) alloy was analyzed using the in-situ electron backscattered diffraction (EBSD) record during uniaxial tensile testing in a scanning electron microscope (SEM). Analysis of EBSD data was focused to investigate phase transformation behavior during deformation with consideration of mechanical interactions among phases and grains in the ultrafine AM microstructure. The initial EBSD phase map illustrated that the as-built microstructure was a duplex structure consisting of major austenite (γ) and minor ferrite phases, some of which showed non-traditional orientation relationship since the rapid solidification in the AM process has produced non-equilibrium state in phase formation. In the deformed as-built AM alloy, the two-step martensitic transformation (γ→ε→α´) was identified as the main deformation-induced transformation mechanism. Martensitic transformation steps were found to be associated with glides of Shockley partial dislocations on closed packed (111) planes under the influence of atomic disturbance in the γ and ε phases, respectively. Using the closed-packed plane pole figures and unit cell orientations, their evolutions and mechanisms accompanying with the transformation were analyzed. Finally, the results indicate that one variant of ε-martensite forms from their parent γ phase, while two variants of α´ form from their parent ε phase.
36 MATERIALS SCIENCE↗
Influence of intermediate carbon content on the microstructure and high-temperature mechanical properties of cast and wrought Ni-based superalloy nimonic 105
NIMONIC® 105 variants with three different carbon concentrations were manufactured. Here, the medium carbon content variant shows inferior creep properties due to a bimodal grain size distribution and non-uniform carbides repartition leading to plastic strain accumulation between the two domains. Here, this eventually facilitated facile cracking and void formation during high-temperature creep.
36 MATERIALS SCIENCE↗
Synthetic proteins for COVID-19 diagnostics
There is an urgent need for inexpensive, rapid and specific antigen-based assays to test for vaccine efficacy and detect infection with SARS-CoV-2 and its variants. We have identified a small, synthetic protein (JS7), representing a region of maximum variability within the receptor binding domain (RBD), which binds antibodies in sera from nine patients with PCR-verified COVID-19 of varying severity. Antibodies binding to either JS7 or the SARS-CoV-2 recombinant RBD, as well as those that disrupt binding between a fragment of the ACE2 receptor and the RBD, are proportional to disease severity and clinical outcome. Binding to JS7 was inhibited by linear peptides from the RBD interface with ACE2. Variants of JS7, such as E484K or N501Y, can be quickly synthesized in pure form in large quantities by automated methods. JS7 and related synthetic antigens can provide a basis for specific diagnostics for SARS-CoV-2 infections.
59 BASIC BIOLOGICAL SCIENCES↗
Metabolic engineering of β-oxidation to leverage thioesterases for production of 2-heptanone, 2-nonanone and 2-undecanone
Medium-chain length methyl ketones are potential blending fuels due to their cetane numbers and low melting temperatures. Biomanufacturing offers the potential to produce these molecules from renewable resources such as lignocellulosic biomass. Here, we designed and tested metabolic pathways in Escherichia coli to specifically produce 2-heptanone, 2-nonanone and 2-undecanone. We achieved substantial production of each ketone by introducing chain-length specific acyl-ACP thioesterases, blocking the β-oxidation cycle at an advantageous reaction, and introducing active β-ketoacyl-CoA thioesterases. Using a bioprospecting approach, we identified fifteen homologs of E. coli β-ketoacyl-CoA thioesterase (FadM) and evaluated the in vivo activity of each against various chain length substrates. The FadM variant from Providencia sneebia produced the most 2-heptanone, 2-nonanone, and 2-undecanone, suggesting it has the highest activity on the corresponding β-ketoacyl-CoA substrates. We further tested enzyme variants, including acyl-CoA oxidases, thiolases, and bi-functional 3-hydroxyacyl-CoA dehydratases to maximize conversion of fatty acids to β-keto acyl-CoAs for 2-heptanone, 2-nonanone, and 2-undecanone production. In order to address the issue of product loss during fermentation, we applied a 20% (v/v) dodecane layer in the bioreactor and built an external water cooling condenser connecting to the bioreactor heat-transferring condenser coupling to the condenser. Finally, using these modifications, we were able to generate up to 4.4 g/L total medium-chain length methyl ketones.
2-Heptanone↗
Gene Amplification, Laboratory Evolution, and Biosensor Screening Reveal MucK as a Terephthalic Acid Transporter in Acinetobacter baylyi ADP1
Microbial terephthalic acid (TPA) catabolic pathways are conserved among the few bacteria known to turnover this xenobiotic aromatic compound. However, to date there are few reported cases in which this pathway has been successfully expressed in heterologous hosts to impart efficient utilization of TPA as a sole carbon source. In this work, we aimed to engineer TPA conversion in Acinetobacter baylyi ADP1 via the heterologous expression of catabolic and transporter genes from a native TPA-utilizing bacterium. Specifically, we obtained ADP1-derived strains capable of growing on TPA as the sole carbon source using chromosomal insertion and targeted amplification of the tph catabolic operon from Comamonas sp. E6. Adaptive laboratory evolution was then used to improve growth on this substrate. TPA consumption rates of the evolved strains, which retained multiple copies of the tph genes, were ~0.2 g/L/h (or ~1 g TPA/g cells/h), similar to that of Comamonas sp. E6 and almost 2-fold higher than that of Rhodococcus jostii RHA1, another native TPA-utilizing strain. To evaluate TPA transport in the evolved ADP1 strains, we engineered a TPA biosensor consisting of the transcription factor TphR and a fluorescent reporter. In combination with whole-genome sequencing, the TPA biosensor revealed that transport of TPA was not mediated by the heterologous proteins from Comamonas sp. E6. Instead, the endogenous ADP1 muconate transporter MucK, a member of the major facilitator superfamily, was responsible for TPA transport in several evolved strains in which MucK variants were found to enhance TPA uptake. Furthermore, the IclR-type transcriptional regulator DcaS was identified as a repressor of mucK expression. Overall, this work presents an unexpected function of a native protein identified through gene amplification, adaptive laboratory evolution, and a combination of screening methods. This study also provides a TPA biosensor for application in ADP1 and identifies transporter variants for use in metabolic engineering applications focused on plastic upcycling of polyesters.
59 BASIC BIOLOGICAL SCIENCES↗
Quasi-periodic travelling gravity–capillary waves
We present a numerical study of spatially quasi-periodic travelling waves on the surface of an ideal fluid of infinite depth. This is a generalization of the classic Wilton ripple problem to the case when the ratio of wavenumbers satisfying the dispersion relation is irrational. We propose a conformal mapping formulation of the water wave equations that employs a quasi-periodic variant of the Hilbert transform to compute the normal velocity of the fluid from its velocity potential on the free surface. We develop a Fourier pseudo-spectral discretization of the travelling water wave equations in which one-dimensional quasi-periodic functions are represented by two-dimensional periodic functions on the torus. This leads to an overdetermined nonlinear least-squares problem that we solve using a variant of the Levenberg–Marquardt method. We investigate various properties of quasi-periodic travelling waves, including Fourier resonances, time evolution in conformal space on the torus, asymmetric wave crests, capillary wave patterns that change from one gravity wave trough to the next without repeating and the dependence of wave speed and surface tension on the amplitude parameters that describe a two-parameter family of waves.
97 MATHEMATICS AND COMPUTING↗
Mechanically induced localisation of SECONDARY WALL INTERACTING bZIP is associated with thigmomorphogenic and secondary cell wall gene expression
Plant growth requires the integration of internal and external cues, perceived and transduced into a developmental programme of cell division, elongation and wall thickening. Mechanical forces contribute to this regulation, and thigmomorphogenesis typically includes reducing stem height, increasing stem diameter, and a canonical transcriptomic response. We present data on a bZIP transcription factor involved in this process in grasses. Brachypodium distachyon SECONDARY WALL INTERACTING bZIP (SWIZ) protein translocated into the nucleus following mechanostimulation. Classical touch-responsive genes were upregulated in B. distachyon roots following touch, including significant induction of the glycoside hydrolase 17 family, which may be unique to grass thigmomorphogenesis. SWIZ protein binding to an E-box variant in exons and introns was associated with immediate activation followed by repression of gene expression. SWIZ overexpression resulted in plants with reduced stem and root elongation. These data further define plant touch-responsive transcriptomics and physiology, offering insights into grass mechanotranduction dynamics.
Coomey, Joshua↗
Hyperfusogenic Mutations Destabilize the Postfusion Six-Helix Bundle of the Measles Virus Fusion Glycoprotein
Fusion of the host membrane and viral envelope by class I viral fusion proteins is driven by the assembly of a postfusion six-helix bundle formed through antiparallel interactions between N-terminal (HR1) and C-terminal (HR2) heptad-repeat regions. Although mutations in these regions of the measles virus (MeV) fusion (F) glycoprotein are known to promote neuropathogenic and hyperfusogenic phenotypes, their effects on postfusion core stability have not been systematically examined. Here, we combine peptide biophysics and X-ray crystallography to interrogate how mutations within the HR2 domain, present in native neuropathogenic MeV isolates (e.g., L454W and N462K) and laboratory-generated hyperfusogenic variants (e.g., L454M and T461A), influence postfusion 6HB assembly. Circular dichroism (CD) spectroscopy reveals that, with few exceptions, these mutations decrease postfusion core stability, despite their association with enhanced fusion activity. We also report the first crystal structure of the wild-type MeV postfusion core as well as structures of six hyperfusogenic variants, enabling high-resolution comparison of the molecular basis of destabilization. Structural analysis shows that these effects arise from localized perturbations to steric packing, hydrogen bonding networks, and helix-stabilizing interactions within HR2, while the overall 6HB architecture remains conserved. Together, these results indicate that hyperfusogenic mutations are not associated with stabilization of the postfusion state and are instead consistent with models in which hyperfusogenicity arises from a reduction in the energetic barrier to fusion, potentially through effects on prefusion stability or triggering efficiency. These findings establish key sequence-structure–stability relationships governing coiled-coil assembly and provide a framework for the design of HR1- and HR2-based fusion inhibitors.
Genetics↗
Cofactor Complexes of DesD, a Model Enzyme in the Virulence-related NIS Synthetase Family
The understudied nonribosomal-peptide-synthetase-independent siderophore (NIS) synthetase family has been increasingly associated with virulence in bacterial species due to its key role in the synthesis of hydroxamate and carboxylate "stealth" siderophores. We have identified a model family member, DesD, from Streptomyces coelicolor , to structurally characterize using a combination of a wild-type and a Arg306Gln variant in apo , cofactor product AMP-bound, and cofactor reactant ATP-bound complexes. The kinetics in the family has been limited by solubility and reporter assays, so we have developed a label-free kinetics assay utilizing a single-injection isothermal-titration-calorimetry-based method. We report second-order rate constants that are 50 times higher than the previous estimations for DesD. Our Arg306Gln DesD variant was also tested under identical buffer and substrate conditions, and its undetectable activity was confirmed. These are the first reported structures for DesD, and they describe the critical cofactor coordination. This is also the first label-free assay to unambiguously determine the kinetics for an NIS synthetase.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Kinetics and Optimization of the Lysine–Isopeptide Bond Forming Sortase Enzyme from Corynebacterium diphtheriae
Site-specifically modified protein bioconjugates have important applications in biology, chemistry, and medicine. Functionalizing specific protein side chains with enzymes using mild reaction conditions is of significant interest, but remains challenging. Recently, the lysine–isopeptide bond forming activity of the sortase enzyme that builds surface pili in Corynebacterium diphtheriae ( Cd SrtA) has been reconstituted in vitro. A mutationally activated form of Cd SrtA was shown to be a promising bioconjugating enzyme that can attach Leu-Pro-Leu-Thr-Gly peptide fluorophores to a specific lysine residue within the N-terminal domain of the SpaA protein ( N SpaA), enabling the labeling of target proteins that are fused to N SpaA. Here we present a detailed analysis of the Cd SrtA catalyzed protein labeling reaction. We show that the first step in catalysis is rate limiting, which is the formation of the Cd SrtA-peptide thioacyl intermediate that subsequently reacts with a lysine ε-amine in N SpaA. This intermediate is surprisingly stable, limiting spurious proteolysis of the peptide substrate. We report the discovery of a new enzyme variant ( Cd SrtA Δ ) that has significantly improved transpeptidation activity, because it completely lacks an inhibitory polypeptide appendage (“lid”) that normally masks the active site. We show that the presence of the lid primarily impairs formation of the thioacyl intermediate and not the recognition of the N SpaA substrate. Quantitative measurements reveal that Cd SrtA Δ generates its cross-linked product with a catalytic turnover number of 1.4 ± 0.004 h –1 and that it has apparent K M values of 0.16 ± 0.04 and 1.6 ± 0.3 mM for its N SpaA and peptide substrates, respectively. Cd SrtA Δ is 7-fold more active than previously studied variants, labeling >90% of N SpaA with peptide within 6 h. The results of this study further improve the utility of Cd SrtA as a protein labeling tool and provide insight into the enzyme catalyzed reaction that underpins protein labeling and pilus biogenesis.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Solving the “Coloring Problem” in InPd 3– x Ag x ( x = 0–0.7) by Phase Diagrams Modeling and Diffraction Experiments
Here, a series of InPd 3–x Ag x (x = 0–1) compositions were synthesized by conventional high-temperature synthesis, and as-synthesized samples were characterized by powder X-ray diffraction experiments. Up to x = 0.7, InPd 3–x Ag x adopts the ternary substitutional variant of the InPd 3 structure (TiAl 3 -type), when x > 0.7, elemental Ag starts to segregate along with the main phase. Accurate structural characterization in InPd 3–x Ag x faces a critical challenge due to the narrow X-ray scattering contrast among constituents In, Pd, and Ag and nearly identical neutron scattering lengths of Pd and Ag. To overcome this “coloring problem”, a combination of calculation of phase diagrams modeling (CALPHAD) and diffraction techniques (X-ray and neutron) was employed. In the compositional range 0 ≤ x ≤ 0.7, InPd 3–x Ag x presents a ternary variant of the TiAl 3 -type structure, where Ag atoms selectively substitute one (the 2b Wyckoff site) of the two Pd sites in InPd 3 . Notably, in contrast to the isologous InPd 3–x Cu x (x = 0–1) system, Ag substitution does not form an ordered VRh 2 Sn-type structure at the limiting composition. The distinct site preference in InPd 3–x Ag x is elucidated by charge population analysis, electronic structure calculations, and orbital-resolved chemical bonding investigations, and the extent of substitution is supported by formation free energy calculations.
36 MATERIALS SCIENCE↗
Robust Tensor Hypercontraction of the Particle–Particle Ladder Term in Equation-of-Motion Coupled Cluster Theory
One method of representing a high-rank tensor as a (hyper-)product of lower-rank tensors is the tensor hypercontraction (THC) method of Hohenstein et al. This strategy has been found to be useful for reducing the polynomial scaling of coupled-cluster methods by representation of a four-dimensional tensor of electron-repulsion integrals in terms of five two-dimensional matrices. Pierce et al. have already shown that the application of a robust form of THC to the particle–particle ladder (PPL) term reduces the cost of this term in couple-cluster singles and doubles (CCSD) from O(N 6 ) to O(N 5 ) with negligible errors in energy with respect to the density-fitted variant. In this work, we have implemented the least-squares variant of THC (LS-THC) which does not require a nonlinear tensor factorization, including the robust form (R-LS-THC), for the calculation of the excitation and electron attachment energies using equation-of-motion coupled cluster methods EOMEE-CCSD and EOMEA-CCSD, respectively. We have benchmarked the effect of the R-LS-THC-PPL approximation on excitation energies using the comprehensive QUEST database and the accuracy of electron attachment energies using the NAB22 database. Here, we find that errors on the order of 1 meV are achievable with a reduction in total calculation time of approximately 5x.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Perspectives on van der Waals Density Functionals: The Case of TiS 2
The van der Waals interaction is of foundational importance for a wide variety of physical systems. In particular, van der Waals forces lie at the heart of potential device technologies that may be realized from the functional organization of layered two-dimensional (2D) nanomaterials. Furthermore, for intermediate to large-scale applications modeling, van der Waals density functionals have become the de facto choice for first-principles calculations. In particular, the vdW-DF family of functionals have provided a systematic approach to this theoretically challenging problem. While much progress has been made, there remains room for improvement in the microscopic description of vdW forces from these density functionals. In this work, we compute benchmark results for the binding energy and the electronic density response to binding in TiS2 via accurate diffusion quantum Monte Carlo calculations. We compare these benchmark data to results obtained from local, semilocal, and van der Waals functionals. In particular, we gauge the quality of the original vdW-DF/vdW-DF2 functionals, as well as updated variants such as vdW-DF-C09, vdW-DF-optB88, vdW-DF-optB86b, and vdW-DF2-B86R. We find a close relationship between the accuracy of predicted interlayer separation distances and binding energies for TiS 2 , with the vdW-DF-optB88 functional performing very well in terms of both quantities. In general, the more recently developed functionals are systematic improvements over older ones. However, when considering the response of the electron density to binding, we find that local-density approximation (LDA) and PBEsol generally outperform the vdW-DF functionals in describing the interlayer charge accumulation with vdW-DF-C09 variants performing the best overall.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗