Structural basis of elongation factor 2 switching
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Fenwick, Michael K.↗
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Effect of copper content on the tensile elongation of Al–Cu–Mn–Zr alloys: Experiments and finite element simulations
Microstructures of cast aluminum alloys used in automotive engine applications often consist of intermetallic particles that can impact the tensile elongation of these alloys. Here in this paper, we investigate the effect of intermetallic grain boundary particles on tensile elongation by fabricating a series of alloys with Cu content varying between 6.0 - 9.0 wt% in cast Al–Cu–Mn–Zr (ACMZ) type compositions. The tensile elongation of as-aged ACMZ alloys decreases monotonically with increase in Cu content. While the microstructure within the grains and yield stress of the alloy remains invariant with Cu content, the decrease in tensile elongation correlates well with increase in the size and volume fraction of grain boundary particles. Microstructural observations are combined with finite element simulations to explain the trend in tensile elongation with changing Cu content. Crack initiation is found to occur by brittle fracture of the grain boundary particles. Increase in particle size promotes crack initiation by reduction in size dependent particle fracture strength. Lower inter-particle spacing at higher particle volume fraction further facilitates crack initiation by increasing stress within the particles caused by the interaction between stress fields of neighboring particles. Increase in particle volume fraction also accelerates crack propagation through the formation of macro shear zones in the microstructure. The increase in Cu content of cast ACMZ alloys, therefore, decreases tensile elongation by promoting both crack initiation and crack propagation.
36 MATERIALS SCIENCE↗
The role of CenKR in the coordination of Rhodobacter sphaeroides cell elongation and division
ABSTRACT Cell elongation and division are essential aspects of the bacterial life cycle that must be coordinated for viability and replication. The impact of misregulation of these processes is not well understood as these systems are often not amenable to traditional genetic manipulation. Recently, we reported on the CenKR two-component system (TCS) in the Gram-negative bacterium Rhodobacter sphaeroides that is genetically tractable, widely conserved in α-proteobacteria, and directly regulates the expression of components crucial for cell elongation and division, including genes encoding subunit of the Tol-Pal complex. In this work, we show that overexpression of cenK results in cell filamentation and chaining. Using cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), we generated high-resolution two-dimensional (2D) images and three-dimensional (3D) volumes of the cell envelope and division septum of wild-type cells and a cenK overexpression strain finding that these morphological changes stem from defects in outer membrane (OM) and peptidoglycan (PG) constriction. By monitoring the localization of Pal, PG biosynthesis, and the bacterial cytoskeletal proteins MreB and FtsZ, we developed a model for how increased CenKR activity leads to changes in cell elongation and division. This model predicts that increased CenKR activity decreases the mobility of Pal, delaying OM constriction, and ultimately disrupting the midcell positioning of MreB and FtsZ and interfering with the spatial regulation of PG synthesis and remodeling. IMPORTANCE By coordinating cell elongation and division, bacteria maintain their shape, support critical envelope functions, and orchestrate division. Regulatory and assembly systems have been implicated in these processes in some well-studied Gram-negative bacteria. However, we lack information on these processes and their conservation across the bacterial phylogeny. In R. sphaeroides and other α-proteobacteria, CenKR is an essential two-component system (TCS) that regulates the expression of genes known or predicted to function in cell envelope biosynthesis, elongation, and/or division. Here, we leverage unique features of CenKR to understand how increasing its activity impacts cell elongation/division and use antibiotics to identify how modulating the activity of this TCS leads to changes in cell morphology. Our results provide new insight into how CenKR activity controls the structure and function of the bacterial envelope, the localization of cell elongation and division machinery, and cellular processes in organisms with importance in health, host-microbe interactions, and biotechnology.
59 BASIC BIOLOGICAL SCIENCES↗
Wetlands harbor lactic acid-driven chain elongators
Wetlands are globally significant carbon storage hotspots. Recent research has suggested that microbially derived metabolites may contribute to soil organic matter formation. Identifying pathways driving the formation of such metabolites is critical to understand the global impact of wetland carbon cycling. Here, we evaluate the presence of chain-elongating organisms converting two to three carbon compounds (i.e., lactic and acetic acid) to medium-chain carboxylic acids (MCCA; i.e., six-carbon caproic acid) in wetland soils. We demonstrate the enrichment of a lactic acid-driven chain-elongating community from wetland soils producing a mixture of butyric and caproic acid. The enriched community was dominated by Clostridiaceae, Ruminococcaceae, and Lachnospiraceae, three families with known chain elongators. Amplicon sequencing identified three Ruminococcaceae and one Clostridiaceae zero-radius OTU (zOTU) that were (i) present in the soil, (ii) enriched over 1% relative abundance in the bioreactor, and (iii) were closely related to known chain elongators. Moreover, close relatives of the three Ruminococcaceae zOTU were also observed in several other wetland microbiomes. From this observation, we conclude that close relatives of known chain elongators, potentially capable of lactic acid-driven MCCA production themselves, are present in wetland soils. This observation may have implications for our understanding of carbon cycling and storage in wetland ecosystems.
59 BASIC BIOLOGICAL SCIENCES↗
Optimization of quasi-axisymmetric stellarators with varied elongation
An optimization study of Quasi-Axisymmetric (QA) stellarators with varied elongation has been carried out using the optimization code STELLOPT. The starting point of our optimization is a previously obtained QA stellarator with 3 field periods and aspect ratio of 6. Here, a series of QA stellarators are obtained at zero plasma beta with varied elongation value ranging from 2.5 to 3.7. Good quasi-symmetry is kept when the elongation value is reduced from the original value of 3.7. The rotational transform profile and aspect ratio are kept fixed. The plasma volume is ether kept fixed or varied linearly with elongation. Furthermore, finite beta QA stellarators are considered. The corresponding bootstrap currents are calculated using the kinetic code SFINCS. A series of kink-stable QA stellarators are obtained via optimization with varied plasma beta up to 5% and self-consistent bootstrap current. This work demonstrates that good QA stellarators with finite beta and varied elongation exist that are stable to external kink modes.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Influence of elongation and triangularity on plasma response to resonant magnetic perturbations
Abstract Systematic toroidal modeling of the plasma response to the n = 1–4 ( n is the toroidal mode number) resonant magnetic perturbation (RMP) field is carried out in order to understand the plasma-shaping effect on controlling the type-I edge-localized modes (ELMs) in tokamak experiments. Considered are large variations of the plasma elongation and triangularity at a fixed edge safety factor q a , for limiter plasmas with both single-null (SN) and double-null (DN) divertor-like boundary shapes. Numerical results assuming conformal 3D RMP coils show that (i) the optimum coil phasing between the upper and lower rows for ELM control becomes increasingly sensitive to the plasma elongation with higher- n toroidal spectra, (ii) the optimum coil phasing is however essentially independent of the plasma triangularity for all n = 1–4 RMP fields, (iii) with the same coil current and the optimum coil phasing, high elongation generally favors ELM control but it may be more challenging for plasmas with intermediate elongation and with lower- n ( n = 1–2) RMPs, and (iv) higher triangularity is generally always better for ELM control with all n = 1–4 fields for both DN and SN divertor-like plasma boundary shapes.
Physics↗
Chain elongators, friends, and foes
Bioproduction of medium chain carboxylic acids has recently emerged as an alternative strategy to valorize low-value organic waste and side-streams. Key to this route is chain elongation, an anaerobic microbial process driven by ethanol, lactic acid, or carbohydrates. Additionally, because these technologies use wastes as feedstocks, mixed microbial communities are often considered as biocatalysts. Understanding and steering these microbiomes is key to optimize bioprocess performance. From a meta-analysis of publicly available sequencing data, we (i) explore how the current collection of isolated chain elongators compares to microbiome members, (ii) discuss the main beneficial and antagonistic interactions with community partners, and (iii) identify the key research gaps and needs to help understand chain elongation microbiomes, and design/steer these novel bioproduction processes.
59 BASIC BIOLOGICAL SCIENCES↗
Adaptations for gas exchange enabled the elongation of lepidopteran proboscises
The extensive biodiversification of butterflies and moths (Lepidoptera) is partly attributed to their unique mouthparts (proboscis [Pr]) that can span in length from less than 1 mm to over 280mm in Darwin's sphinx moths. Lepi-doptera, similar to other insects, are believed to inhale and exhale respiratory gases only through valve-like spi-racles on their thorax and abdomen, making gas exchange through the narrow tracheae (Tr) challenging for the elongated Pr. How Lepidoptera overcome distance effects for gas transport to the Pr is an open question that is important to understanding how the Pr elongated over evolutionary time. Here, we show with scanning electron microscopy and X-ray imaging that distance effects on gas exchange are overcome by previously unreported micropores on the Pr surface and by superhydrophobic Tr that prevent water loss and entry. We find that the density of micropores decreases monotonically along the Pr length with the maxima proportional to the Pr length and that micropore diameters produce a Knudsen number at the boundary between the slip and transition flow regimes. By numerical estimation, we further show that the respiratory gas exchange for the Pr predominantly occurs via diffusion through the micropores. In conclusion, these adaptations are key innovations vital to Pr elongation, which likely facilitated lepidopteran biodiversification and the radiation of angiosperms by coevolutionary processes.
59 BASIC BIOLOGICAL SCIENCES↗
Response of Sulfonated Polystyrene Melts to Nonlinear Elongation Flows
Ionizable polymers form dynamic networks with domains controlled by two distinct energy scales, ionic interactions and van der Waals forces; both evolve under elongational flows during their processing into viable materials. A molecular level insight of their nonlinear response, paramount to controlling their structure, is attained by fully atomistic molecular dynamics simulations of a model ionizable polymer, polystyrene sulfonate. As a function of increasing elongational flow rate, the systems display an initial elastic response, followed by an ionic fraction-dependent strain hardening, stress overshoot, and eventually strain-thinning. As the sulfonation fraction increases, the chain elongation becomes more heterogeneous. Finally, flow-driven ionic assembly dynamics that continuously break and reform control the response of the system.
36 MATERIALS SCIENCE↗
Control of transcription elongation and DNA repair by alarmone ppGpp
Second messenger (p)ppGpp (collectively guanosine tetraphosphate and guanosine pentaphosphate) mediates bacterial adaptation to nutritional stress by modulating transcription initiation. More recently, ppGpp has been implicated in coupling transcription and DNA repair; however, the mechanism of ppGpp engagement remained elusive. Here we present structural, biochemical and genetic evidence that ppGpp controls Escherichia coli RNA polymerase (RNAP) during elongation via a specific site that is nonfunctional during initiation. Structure-guided mutagenesis renders the elongation (but not initiation) complex unresponsive to ppGpp and increases bacterial sensitivity to genotoxic agents and ultraviolet radiation. Thus, ppGpp binds RNAP at sites with distinct functions in initiation and elongation, with the latter being important for promoting DNA repair. Our data provide insights on the molecular mechanism of ppGpp-mediated adaptation during stress, and further highlight the intricate relationships between genome stability, stress responses and transcription.
59 BASIC BIOLOGICAL SCIENCES↗
The role of faceting and elongation on the magnetic anisotropy of magnetite Fe3O4 nanocrystals
Abstract Fe 3 O 4 nanoparticles are one of the most promising candidates for biomedical applications such as magnetic hyperthermia and theranostics due to their bio-compatibility, structural stability and good magnetic properties. However, much is unknown about the nanoscale origins of the observed magnetic properties of particles due to the dominance of surface and finite size effects. Here we have developed an atomistic spin model of elongated magnetite nanocrystals to specifically address the role of faceting and elongation on the magnetic shape anisotropy. We find that for faceted particles simple analytical formulae overestimate the magnetic shape anisotropy and that the underlying cubic anisotropy makes a significant contribution to the energy barrier for moderately elongated particles. Our results enable a better estimation of the effective magnetic anisotropy of highly crystalline magnetite nanoparticles and is a step towards quantitative prediction of the heating effects of magnetic nanoparticles.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Bioenergy sorghum stem density increases threefold following internode elongation due to continued accumulation of lignified cell walls and complex regulation of genes involved in cell wall biosynthesis
Bioenergy sorghum is a highly productive drought tolerant C4 grass that accumulates ~ 80% of its harvested biomass in ~ 4 m long stems comprised of > 40 internodes that develop sequentially during an extended vegetative growth phase. Following elongation of each internode, internode density increases ~ threefold to fourfold primarily due to the accumulation of cell walls composed of cellulose, glucuronoarabinoxylan and lignin. Lignin accumulates initially on cell walls of sclerenchyma cells surrounding vascular bundles and later on cell walls of the stem rind and stem core pith parenchyma. Many genes involved in cell wall biosynthesis were expressed continuously during the stem internode densification process whereas others showed dynamic patterns of expression (high to low, low to high). Several CESA genes involved in primary cell wall cellulose synthesis were expressed in the stem rind and core throughout the stem densification phase. In contrast, CESA genes involved in secondary cell wall biogenesis were expressed continuously in the stem rind but downregulated in the stem core shortly after completion of internode elongation. Overall, accumulation of cell wall biomass in elongated internodes during stem densification increases stem mechanical strength and biomass bulk density while modifying biomass composition in ways that could impact the amount and release of cellulosic sugars and lignin-derived bioproducts.
09 BIOMASS FUELS↗
Role of SaPCR2 in Zn Uptake in the Root Elongation Zone of the Zn/Cd Hyperaccumulator Sedum alfredii
Zn pollution is a potential toxicant for agriculture and the environment. Sedum alfredii is a Zn/Cd hyperaccumulator found in China and has been proven as a useful resource for the phytoremediation of Zn-contaminated sites. However, the molecular mechanism of Zn uptake in S. alfredii is limited. In this study, the function of SaPCR2 on Zn uptake in S. alfredii was identified by gene expression analysis, yeast function assays, Zn accumulation and root morphology analysis in transgenic lines to further elucidate the mechanisms of uptake and translocation of Zn in S. alfredii. The results showed that SaPCR2 was highly expressed in the root elongation zone of the hyperaccumulating ecotype (HE) S. alfredii, and high Zn exposure downregulated the expression of SaPCR2 in the HE S. alfredii root. The heterologous expression of SaPCR2 in yeast suggested that SaPCR2 was responsible for Zn influx. The overexpression of SaPCR2 in the non-hyperaccumulating ecotype (NHE) S. alfredii significantly increased the root uptake of Zn, but did not influence Mn, Cu or Fe. SR-μ-XRF technology showed that more Zn was distributed in the vascular buddle tissues, as well as in the cortex and epidermis in the transgenic lines. Root morphology was also altered after SaPCR2 overexpression, and a severe inhibition was observed. In the transgenic lines, the meristematic and elongation zones of the root were lower compared to the WT, and Zn accumulation in meristem cells was also reduced. These results indicate that SaPCR2 is responsible for Zn uptake, and mainly functions in the root elongation zone. This research on SaPCR2 could provide a theoretical basis for the use of genetic engineering technology in the modification of crops for their safe production and biological enhancement.
59 BASIC BIOLOGICAL SCIENCES↗
Why Interstellar Ice Dust Grains Should Be Elongated
Models of interstellar dust alignment assume that dust grains are elongated, but none of these models explain why dust grains should be elongated. On the other hand, models of interstellar dust grain growth assume that dust grains are spherical and not elongated. We show that when dusty plasma effects and the dipole moment of water molecules are together taken into account, ice grains in interstellar space should be prolate ellipsoids and not spheres. Dusty plasma analysis shows that an ice grain is charged to a negative potential that has magnitude nearly equal to that of the electron temperature. Several different mechanisms causing deviation from sphericity are identified; these mechanisms involve the interaction of the dipole moment of water molecules with electric fields associated with ice grain charging. These mechanisms include the focusing of water molecule trajectories, the migration of water molecules in a quasi-liquid layer on the grain surface toward regions where the electric field is strongest, the enhancement of this migration by the bombardment of energetic protons that gain energy upon falling into the ice grain negative potential, and mutual repulsion by electric charges having the same sign. Furthermore, the aspect ratio is established shortly after the ice grain is formed, and then is maintained as the grain grows.
79 ASTRONOMY AND ASTROPHYSICS↗
Elongated particles in flow: commentary on small-angle scattering investigations
Here, this work thoroughly examines several analytical tools, each possessing a different level of mathematical intricacy, for the purpose of characterizing the orientation distribution function of elongated objects under flow. Our investigation places an emphasis on connecting the orientation distribution to the small-angle scattering spectra measured experimentally. The diverse range of mathematical approaches investigated herein provide insights into the flow behavior of elongated particles from different perspectives and serve as powerful tools for elucidating the complex interplay between flow dynamics and the orientation distribution function.
36 MATERIALS SCIENCE↗
High planting density induces the expression of GA3-oxidase in leaves and GA mediated stem elongation in bioenergy sorghum
Abstract The stems of bioenergy sorghum hybrids at harvest are > 4 m long, contain > 40 internodes and account for ~ 80% of harvested biomass. In this study, bioenergy sorghum hybrids were grown at four planting densities (~ 20,000 to 132,000 plants/ha) under field conditions for 60 days to investigate the impact shading has on stem growth and biomass accumulation. Increased planting density induced a > 2-fold increase in sorghum internode length and a ~ 22% decrease in stem diameter, a typical shade avoidance response. Shade-induced internode elongation was due to an increase in cell length and number of cells spanning the length of internodes. SbGA3ox2 (Sobic.003G045900), a gene encoding the last step in GA biosynthesis, was expressed ~ 20-fold higher in leaf collar tissue of developing phytomers in plants grown at high vs. low density. Application of GA3 to bioenergy sorghum increased plant height, stem internode length, cell length and the number of cells spanning internodes. Prior research showed that sorghum plants lacking phytochrome B, a key photoreceptor involved in shade signaling, accumulated more GA1 and displayed shade avoidance phenotypes. These results are consistent with the hypothesis that increasing planting density induces expression of GA3-oxidase in leaf collar tissue, increasing synthesis of GA that stimulates internode elongation.
09 BIOMASS FUELS↗
Revealing reaction intermediates in one-carbon elongation by thiamine diphosphate/CoA-dependent enzyme family
2-Hydroxyacyl-CoA lyase/synthase (HACL/S) is a thiamine diphosphate (ThDP)-dependent versatile enzyme originally discovered in the mammalian α-oxidation pathway. HACL/S natively cleaves 2-hydroxyacyl-CoAs and, in its reverse direction, condenses formyl-CoA with aldehydes or ketones. The one-carbon elongation biochemistry based on HACL/S has enabled the use of molecules derived from greenhouse gases as biomanufacturing feedstocks. We investigated several HACL/S family members with high activity in the condensation of formyl-CoA and aldehydes, and distinct chain-length specificities and kinetic parameters. Our analysis revealed the structures of enzymes in complex with acyl-CoA substrates and products, several covalent intermediates, bound ThDP and ADP, as well as the C-terminal active site region. One of these observed states corresponds to the intermediary α–carbanion with hydroxymethyl-CoA covalently attached to ThDP. This research distinguishes HACL/S from related sub-families and identifies key residues involved in substrate binding and catalysis. These findings expand our knowledge of acyloin-condensation biochemistry and offer attractive prospects for biocatalysis using carbon elongation.
2-hydroxyacyl-CoA lyase↗
Different roles of elongation and triangularity in the H-mode pedestal height enhancement through strong plasma shaping
While the peeling–ballooning mode is known to be stabilized by strong plasma shaping in a high-confinement mode (H-mode), a significant difference is found in the roles of elongation and triangularity. The elongation mainly stabilizes the high-n ballooning branch, while the triangularity of the low-n peeling one with some destabilization of the high-n ballooning one, where n is the toroidal mode number. This difference is conjectured mainly due to the magnetic shear effect which is substantially enhanced in a high triangularity regime, giving a destabilization on the ballooning branch, while a stabilization on the peeling one. As shown here, an important consequence of these different roles of the two shape parameters is that they should work together to stabilize simultaneously both branches of the PBM, implying the necessity of synergy between them for the large pedestal height enhancement.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗