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At least 271 records · Page 15

Crystal truncation rods from miscut surfaces with alternating terminations

Miscut surfaces of layered crystals can exhibit a stair-like sequence of terraces having periodic variation in their atomic structure. For hexagonal close-packed and related crystal structures with an αβαβ stacking sequence, there have been long-standing questions regarding how the differences in adatom attachment kinetics at the steps separating the terraces affect the fractional coverage of α vs. β termination during crystal growth. To demonstrate how surface X-ray scattering can help address these questions, we develop a general theory for the intensity distributions along crystal truncation rods (CTRs) for miscut surfaces with a combination of two terminations. We consider half-unit-cell-height steps, and variation of the coverages of the terraces above each step. Example calculations are presented for the GaN (0001) surface with various reconstructions. These show which CTR positions are most sensitive to the fractional coverage of the two terminations. We compare the CTR profiles for exactly oriented surfaces to those for vicinal surfaces having a small miscut angle, and investigate the circumstances under which the CTR profile for an exactly oriented surface is equal to the sum of the intensities of the corresponding family of CTRs for a miscut surface.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Influence of ion site occupancies on the unit cell parameters, specific volumes, and densities of M 8 (AlSiO 4 ) 6 X 2 sodalites where M = Li, Na, K, Rb, and Ag and X = Cl, Br, and I

Here, this paper discusses the effects of composition on the unit cell parameter (a), unit cell volume (V), specific volume (v), and density (ρ) of various sodalite compositions including $M^+_8$(AlSiO 4 ) 6 Cl 2 (M = Li, Na, K, Rb, and/or Ag) and Na8(AlSiO 4 ) 6 $X^-_2$(X = Cl, Br, and/or I). Compositional models were developed, and the results show that the models are successful at predicting a, V, and v (and thus ρ) within the compositional range available in the literature. Discussion is included on the correlation between the ionic radii of the alkali metals and halides in the sodalite β-cages and the measured values of a, V, v, and ρ. The data show linear increases in a and ρ with increases in the average ionic radii of the M + and X - constituents (data for v show a linear decrease).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Texture Formation in Polycrystalline Thin Films of All‐Inorganic Lead Halide Perovskite

Abstract Controlling grain orientations within polycrystalline all‐inorganic halide perovskite solar cells can help increase conversion efficiencies toward their thermodynamic limits; however, the forces governing texture formation are ambiguous. Using synchrotron X‐ray diffraction, mesostructure formation within polycrystalline CsPbI 2.85 Br 0.15 powders as they cool from a high‐temperature cubic perovskite (α‐phase) is reported. Tetragonal distortions (β‐phase) trigger preferential crystallographic alignment within polycrystalline ensembles, a feature that is suggested here to be coordinated across multiple neighboring grains via interfacial forces that select for certain lattice distortions over others. External anisotropy is then imposed on polycrystalline thin films of orthorhombic (γ‐phase) CsPbI 3‐ x Br x perovskite via substrate clamping, revealing two fundamental uniaxial texture formations; i) I‐rich films possess orthorhombic‐like texture (<100> out‐of‐plane; <010> and <001> in‐plane), while ii) Br‐rich films form tetragonal‐like texture (<110> out‐of‐plane; <110> and <001> in‐plane). In contrast to relatively uninfluential factors like the choice of substrate, film thickness, and annealing temperature, Br incorporation modifies the γ‐CsPbI 3− x Br x crystal structure by reducing the orthorhombic lattice distortion (making it more tetragonal‐like) and governs the formation of the different, energetically favored textures within polycrystalline thin films.

Steele, Julian A.↗

Phase transitions in high-purity zirconium under dynamic compression

In this work, we present results from ramp compression experiments on high-purity Zr that show the α → ω, ω → β, as well as reverse β → ω phase transitions. Simulations with a multi-phase equation of state and phenomenological kinetic model match the experimental wave profiles well. While the dynamic α ! ! transition occurs ~ 9 GPa above the equilibrium phase boundary, the ω → β transition occurs within 0.9 GPa of equilibrium. We estimate that the dynamic compression path intersects the equilibrium ω – β line at P = 29:2 GPa, and T = 490 K. The thermodynamic path in the interior of the sample lies ~ 100 K above the isentrope at the point of the ω → β transition. Approximately half of this dissipative temperature rise is due to plastic work, and half is due to the non-equilibrium α → ω transition. The inferred rate of the α → ω transition is several orders of magnitude higher than that measured in dynamic diamond anvil cell (DDAC) experiments in an overlapping pressure range. We discuss a model for the influence of shear stress on the nucleation rate. We find that the shear stress s ji has the same effect on the nucleation rate as a pressure increase δP = cϵ ij s ji /(ΔV/V); where c is a geometric constant ~ 1 and, ϵ ij are the transformation shear strains. The small fractional volume change ΔV/V ≈ 0:1 at the α → ω transition amplifies the effect of shear stress, and we estimate that for this case δP is in the range of several GPa. Correcting our transition rate to a hydrostatic rate brings it approximately into line with the DDAC results, suggesting that shear stress plays a significant role in the transformation rate.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Atp7b-dependent choroid plexus dysfunction causes transient copper deficit and metabolic changes in the developing mouse brain

Copper (Cu) has a multifaceted role in brain development, function, and metabolism. Two homologous Cu transporters, Atp7a (Menkes disease protein) and Atp7b (Wilson disease protein), maintain Cu homeostasis in the tissue. Atp7a mediates Cu entry into the brain and activates Cu-dependent enzymes, whereas the role of Atp7b is less clear. We show that during postnatal development Atp7b is necessary for normal morphology and function of choroid plexus (ChPl). Inactivation of Atp7b causes reorganization of ChPl’ cytoskeleton and cell-cell contacts, loss of Slc31a1 from the apical membrane, and a decrease in the length and number of microvilli and cilia. In ChPl lacking Atp7b, Atp7a is upregulated but remains intracellular, which limits Cu transport into the brain and results in significant Cu deficit, which is reversed only in older animals. Cu deficiency is associated with down-regulation of Atp7a in locus coeruleus and catecholamine imbalance, despite normal expression of dopamine-β-hydroxylase. In addition, there are notable changes in the brain lipidome, which can be attributed to inhibition of diacylglyceride-to-phosphatidylethanolamine conversion. These results identify the new role for Atp7b in developing brain and identify metabolic changes that could be exacerbated by Cu chelation therapy.

59 BASIC BIOLOGICAL SCIENCES↗

Chloroplast Sec14-like 1 (CPSFL1) is essential for normal chloroplast development and affects carotenoid accumulation in Chlamydomonas

Plastid isoprenoid-derived carotenoids serve essential roles in chloroplast development and photosynthesis. Although nearly all enzymes that participate in the biosynthesis of carotenoids in plants have been identified, the complement of auxiliary proteins that regulate synthesis, transport, sequestration, and degradation of these molecules and their isoprenoid precursors have not been fully described. To identify such proteins that are necessary for the optimal functioning of oxygenic photosynthesis, we screened a large collection of nonphotosynthetic (acetate-requiring) DNA insertional mutants of Chlamydomonas reinhardtii and isolated cpsfl1 . The cpsfl1 mutant is extremely light-sensitive and susceptible to photoinhibition and photobleaching. The CPSFL1 gene encodes a CRAL-TRIO hydrophobic ligand-binding (Sec14) domain protein. Proteins containing this domain are limited to eukaryotes, but some may have been retargeted to function in organelles of endosymbiotic origin. The cpsfl1 mutant showed decreased accumulation of plastidial isoprenoid-derived pigments, especially carotenoids, and whole-cell focused ion-beam scanning-electron microscopy revealed a deficiency of carotenoid-rich chloroplast structures (e.g., eyespot and plastoglobules). The low carotenoid content resulted from impaired biosynthesis at a step prior to phytoene, the committed precursor to carotenoids. The CPSFL1 protein bound phytoene and β-carotene when expressed in Escherichia coli and phosphatidic acid in vitro. We suggest that CPSFL1 is involved in the regulation of phytoene synthesis and carotenoid transport and thereby modulates carotenoid accumulation in the chloroplast.

59 BASIC BIOLOGICAL SCIENCES↗

Fractal dimensions of jammed packings with power-law particle size distributions in two and three dimensions

Static structure factors are computed for large-scale, mechanically stable, jammed packings of frictionless spheres (three dimensions) and disks (two dimensions) with broad, power-law size dispersity characterized by the exponent -β. Here, the static structure factor exhibits diverging power-law behavior for small wave numbers, allowing us to identify a structural fractal dimension d f . In three dimensions, d f ≈ 2.0 for 2.5≤ β ≤ 3.8, such that each of the structure factors can be collapsed onto a universal curve. In two dimensions, we instead find 1.0≲ d f ≲1.34 for 2.1≤ β ≤ 2.9. Furthermore, we show that the fractal behavior persists when rattler particles are removed, indicating that the long-wavelength structural properties of the packings are controlled by the large particle backbone conferring mechanical rigidity to the system. A numerical scheme for computing structure factors for triclinic unit cells is presented and employed to analyze the jammed packings.

97 MATHEMATICS AND COMPUTING↗

Inferring assembly-curving trends of bacterial micro-compartment shell hexamers from crystal structure arrangements

Bacterial microcompartments (BMC) are complex macromolecular assemblies that participate in varied chemical processes in about one fourth of bacterial species. BMC-encapsulated enzymatic activities are segregated from other cell contents by means of semipermeable shells, justifying why BMC are viewed as prototype nano-reactors for biotechnological applications. Herein, we undertook a comparative study of bending propensities of BMC hexamers (BMC-H), the most abundant shell constituents. Published data show that some BMC-H, like β -carboxysomal CcmK, tend to assemble flat whereas other BMC-H often build curved objects. Inspection of available crystal structures presenting BMC-H in tiled arrangements permitted us to identify two major assembly modes with a striking connection with experimental trends. All-atom molecular dynamics (MD) supported that BMC-H bending is triggered robustly only from the arrangement adopted in crystals by BMC-H that experimentally form curved objects, leading to very similar arrangements to those found in structures of recomposed BMC shells. Simulations on triplets of planar-behaving hexamers, which were previously reconfigured to comply with such organization, confirmed that bending propensity is mostly defined by the precise lateral positioning of hexamers, rather than by BMC-H identity. Finally, an interfacial lysine was pinpointed as the most decisive residue in controlling PduA spontaneous curvature. Globally, results presented herein should contribute to improve our understanding of the variable mechanisms of biogenesis characterized for BMC, and of possible strategies to regulate BMC size and shape.

59 BASIC BIOLOGICAL SCIENCES↗

Proteogenomic insights suggest druggable pathways in endometrial carcinoma

We characterized a prospective endometrial carcinoma (EC) cohort containing 138 tumors and 20 enriched normal tissues using 10 different omics platforms. Targeted quantitation of two peptides can predict antigen processing and presentation machinery activity, and may inform patient selection for immunotherapy. Association analysis between MYC activity and metformin treatment in both patients and cell lines suggests a potential role for metformin treatment in non-diabetic patients with elevated MYC activity. PIK3R1 in-frame indels are associated with elevated AKT phosphorylation and increased sensitivity to AKT inhibitors. CTNNB1 hotspot mutations are concentrated near phosphorylation sites mediating pS45-induced degradation of β-catenin, which may render Wnt-FZD antagonists ineffective. Deep learning accurately predicts EC subtypes and mutations from histopathology images, which may be useful for rapid diagnosis. Overall, this study identified molecular and imaging markers that can be further investigated to guide patient stratification for more precise treatment of EC.

60 APPLIED LIFE SCIENCES↗

High pressure structural and lattice dynamics study of α-In2Se3

Layered α-In2Se3 has been studied using a combined in situ synchrotron angle-dispersive powder x-ray diffraction and Raman spectroscopy study in a diamond anvil cell up to 60+ GPa, at room temperature. Helium, which remains fairly hydrostatic up to the highest pressure in this study, was used as the pressure-transmitting medium. The results from both experimental methods reveal a pressure-induced structural phase transition from α-In2Se3 to a monoclinic β'-In2Se3 structure at ≈1 GPa, in agreement with previous studies. Based on our detailed measurements using both experimental techniques and the F-f formalism, the β'-In2Se3 structure remains stable up to 45 GPa, without a clear indication of a phase transition toward the previously reported β-In2Se3 phase. Above this pressure, In2Se3 adopts a disordered solid-solution-like orthorhombic structure, phase IV. The results are discussed in comparison with the relevant previous studies of α-In2Se3 under pressure.

Feng, Shiyu↗

Atypical Carboxysome Loci: JEEPs or Junk?

Carboxysomes, responsible for a substantial fraction of CO 2 fixation on Earth, are proteinaceous microcompartments found in many autotrophic members of domain Bacteria, primarily from the phyla Proteobacteria and Cyanobacteria. Carboxysomes facilitate CO 2 fixation by the Calvin-Benson-Bassham (CBB) cycle, particularly under conditions where the CO 2 concentration is variable or low, or O 2 is abundant. These microcompartments are composed of an icosahedral shell containing the enzymes ribulose 1,5-carboxylase/oxygenase (RubisCO) and carbonic anhydrase. They function as part of a CO 2 concentrating mechanism, in which cells accumulate HCO 3 - in the cytoplasm via active transport, HCO 3 - enters the carboxysomes through pores in the carboxysomal shell proteins, and carboxysomal carbonic anhydrase facilitates the conversion of HCO 3 - to CO 2 , which RubisCO fixes. Two forms of carboxysomes have been described: α-carboxysomes and β-carboxysomes, which arose independently from ancestral microcompartments. The α-carboxysomes present in Proteobacteria and some Cyanobacteria have shells comprised of four types of proteins [CsoS1 hexamers, CsoS4 pentamers, CsoS2 assembly proteins, and α-carboxysomal carbonic anhydrase (CsoSCA)], and contain form IA RubisCO (CbbL and CbbS). In the majority of cases, these components are encoded in the genome near each other in a gene locus, and transcribed together as an operon. Interestingly, genome sequencing has revealed some α-carboxysome loci that are missing genes encoding one or more of these components. Some loci lack the genes encoding RubisCO, others lack a gene encoding carbonic anhydrase, some loci are missing shell protein genes, and in some organisms, genes homologous to those encoding the carboxysome-associated carbonic anhydrase are the only carboxysome-related genes present in the genome. Given that RubisCO, assembly factors, carbonic anhydrase, and shell proteins are all essential for carboxysome function, these absences are quite intriguing. In this review, we provide an overview of the most recent studies of the structural components of carboxysomes, describe the genomic context and taxonomic distribution of atypical carboxysome loci, and propose functions for these variants. We suggest that these atypical loci are JEEPs, which have modified functions based on the presence of Just Enough Essential Parts.

59 BASIC BIOLOGICAL SCIENCES↗

Sensor Domain of Histidine Kinase VxrA of Vibrio cholerae : Hairpin-Swapped Dimer and Its Conformational Change

VxrA and VxrB are cognate histidine kinase (HK)-response regulator (RR) pairs of a two-component signaling system (TCS) found in Vibrio cholerae, a bacterial pathogen that causes cholera. The VxrAB TCS positively regulates virulence, the type VI secretion system, biofilm formation, and cell wall homeostasis in V. cholerae, providing protection from environmental stresses and contributing to the transmission and virulence of the pathogen. The VxrA HK has a unique periplasmic sensor domain (SD) and, remarkably, lacks a cytoplasmic linker domain between the second transmembrane helix and the dimerization and histidine phosphotransfer (DHp) domain, indicating that this system may utilize a potentially unique signal sensing and transmission TCS mechanism. Here, we have determined several crystal structures of VxrA-SD and its mutants. These structures reveal a novel structural fold forming an unusual β hairpin-swapped dimer. A conformational change caused by relative rotation of the two monomers in a VxrA-SD dimer could potentially change the association of transmembrane helices and, subsequently, the pairing of cytoplasmic DHp domains. Based on the structural observation, we propose a putative scissor-like closing regulation mechanism for the VxrA HK. IMPORTANCE V. cholerae has a dynamic life cycle, which requires rapid adaptation to changing external conditions. Two-component signal transduction (TCS) systems allow V. cholerae to sense and respond to these environmental changes. The VxrAB TCS positively regulates a number of important V. cholerae phenotypes, including virulence, the type six secretion system, biofilm formation, and cell wall homeostasis. Here, we provide the crystal structures of the VxrA sensor histidine kinase sensing domain and propose a mechanism for signal transduction. The cognate signal for VxrAB remains unknown; however, in this work we couple our structural analysis with functional assessments of key residues to further our understanding of this important TCS.

59 BASIC BIOLOGICAL SCIENCES↗

Non-thermal electron acceleration from magnetically driven reconnection in a laboratory plasma

Magnetic reconnection rapidly converts magnetic energy into some combination of plasma flow energy, thermal energy and non-thermal energetic particles. Various reconnection acceleration mechanisms have been theoretically proposed and numerically studied in different collisionless and low-β environments, where β refers to the plasma-to-magnetic pressure ratio. These mechanisms include Fermi acceleration, betatron acceleration, parallel electric field acceleration along magnetic fields and direct acceleration by the reconnection electric field. However, none of them have been experimentally confirmed, as the direct observation of non-thermal particle acceleration in laboratory experiments has been difficult due to short Debye lengths for in situ measurements and short mean free paths for ex situ measurements. Here we report the direct measurement of accelerated non-thermal electrons from magnetically driven reconnection at low β in experiments using a laser-powered capacitor coil platform. We use kilojoule lasers to drive parallel currents to reconnect megagauss-level magnetic fields in a quasi-axisymmetric geometry. The angular dependence of the measured electron energy spectrum and the resulting accelerated energies, supported by particle-in-cell simulations, indicate that the mechanism of direct electric field acceleration by the out-of-plane reconnection electric field is at work. Scaled energies using this mechanism show direct relevance to astrophysical observations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Oral delivery of a functional algal-expressed TGF-β mimic halts colitis in a murine DSS model

Inflammatory bowel disease (IBD) is a set of immunological disorders which can generate chronic pain and fatigue associated with the inflammatory symptoms. The treatment of IBD remains a significant hurdle with current therapies being only partially effective or having significant side effects, suggesting that new therapies that elicit different modes of action and delivery strategies are required. TGM1 is a TGF-β mimic that was discovered from the intestinal helminth parasite Heligmosomoides polygyrus and is thought to be produced by the parasite to suppress the intestinal inflammation response to help evade host immunity, making it an ideal candidate to be developed as a novel anti-inflammatory bio-therapeutic. Here we utilized the expression system of the edible green algae Chlamydomonas reinhardtii in order to recombinantly produce active TGM1 in a form that could be ingested. C. reinhardtii robustly expressed TGM1, and the resultant recombinant protein is biologically active as measured by regulatory T cell induction. When delivered orally to mice, the algal expressed TGM1 is able to ameliorate weight loss, lymphadenopathy, and disease symptoms in a mouse model of DSS-induced colitis, demonstrating the potential of this biologic as a novel treatment of IBD.

09 BIOMASS FUELS↗

Genetic and structural studies of RABL3 reveal an essential role in lymphoid development and function

The small GTPase RABL3 is an oncogene of unknown physiological function. Homozygous knockout alleles of mouse Rabl3 were embryonic lethal, but a viable hypomorphic allele (xiamen [xm]) causing in-frame deletion of four amino acids from the interswitch region resulted in profound defects in lymphopoiesis. Impaired lymphoid progenitor development led to deficiencies of B cells, T cells, and natural killer (NK) cells in Rabl3 xm/xm mice. T cells and NK cells exhibited impaired cytolytic activity, and mice infected with mouse cytomegalovirus (MCMV) displayed elevated titers in the spleen. Myeloid cells were normal in number and function. Further, biophysical and crystallographic studies demonstrated that RABL3 formed a homodimer in solution via interactions between the effector binding surfaces on each subunit; monomers adopted a typical small G protein fold. RABL3 xm displayed a large compensatory alteration in switch I, which adopted a β-strand configuration normally provided by the deleted interswitch residues, thereby permitting homodimer formation. Dysregulated effector binding due to conformational changes in the switch I–interswitch–switch II module likely underlies the xm phenotype. One such effector may be GPR89, putatively an ion channel or G protein-coupled receptor (GPCR). RABL3, but not RABL3 xm , strongly associated with and stabilized GPR89, and an N-ethyl-N-nitrosourea (ENU)-induced mutation (explorer) in Gpr89 phenocopied Rabl3 xm .

59 BASIC BIOLOGICAL SCIENCES↗

[ 89 Zr]Zr-DFO-TOC: a novel radiopharmaceutical for PET imaging of somatostatin receptor positive neuroendocrine tumors

Neuroendocrine tumors (NETs) are clinically diverse types of tumors that can arise anywhere in the body. Previous studies have shown that somatostatin receptors (SSTRs) are overexpressed on NET cell membranes relative to healthy tissue, allowing for tumor targeting through radiolabeled somatostatin analogs (SSAs). This work aims to develop a novel 89 Zr-labeled tracer incorporating the SSA, octreotide (TOC), for positron emission tomography (PET) imaging of SSTR + NETs and predictive dosimetry calculations, leveraging the excellent nuclear (t ½ = 3.27 days, β+ = 22.3%, β + avg = 395.5 keV) and chemical characteristics (+ 4 oxidation state, preferential coordination number of 7/8, favorable aqueous chemistry) of 89 Zr. In combination with 89 Zr, the known radiochemistry with the chelator deferoxamine (DFO) gives reason to believe that this radiopharmaceutical incorporating an octreotide conjugate will be successful in studying the suitability of detecting SSTR + NETs.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Evolution of structure and spectroscopic properties of a new 1,3-diacetylpyrene polymorph with temperature and pressure

A new polymorph of 1,3-diacetylpyrene has been obtained from its melt and thoroughly characterized using single-crystal X-ray diffraction, steady-state UV–Vis spectroscopy and periodic density functional theory calculations. Experimental studies covered the temperature range from 90 to 390 K and the pressure range from atmospheric to 4.08 GPa. Optimal sample placement in a diamond anvil cell according to our previously presented methodology ensured over 80% data coverage up to 0.8 Å for a monoclinic sample. Unrestrained Hirshfeld atom refinement of the high-pressure crystal structures was successful and anharmonic behavior of carbonyl oxygen atoms was observed. Unlike the previously characterized polymorph, the structure of 2°AP-β is based on infinite π-stacks of antiparallel 2°AP molecules. 2°AP-β displays piezochromism and piezofluorochromism which are directly related to the variation in interplanar distances within the π-stacking. The importance of weak intermolecular interactions is reflected in the substantial negative thermal expansion coefficient of -55.8 (57) MK -1 in the direction of C—H∙∙∙O interactions.

36 MATERIALS SCIENCE↗

Insight into the autoproteolysis mechanism of the RsgI9 anti‐σ factor from Clostridium thermocellum

Abstract Clostridium thermocellum is a potential microbial platform to convert abundant plant biomass to biofuels and other renewable chemicals. It efficiently degrades lignocellulosic biomass using a surface displayed cellulosome, a megadalton sized multienzyme containing complex. The enzymatic composition and architecture of the cellulosome is controlled by several transmembrane biomass‐sensing RsgI‐type anti‐σ factors. Recent studies suggest that these factors transduce signals from the cell surface via a conserved RsgI extracellular (CRE) domain (also called a periplasmic domain) that undergoes autoproteolysis through an incompletely understood mechanism. Here we report the structure of the autoproteolyzed CRE domain from the C. thermocellum RsgI9 anti‐σ factor, revealing that the cleaved fragments forming this domain associate to form a stable α/β/α sandwich fold. Based on AlphaFold2 modeling, molecular dynamics simulations, and tandem mass spectrometry, we propose that a conserved Asn‐Pro bond in RsgI9 autoproteolyzes via a succinimide intermediate whose formation is promoted by a conserved hydrogen bond network holding the scissile peptide bond in a strained conformation. As other RsgI anti‐σ factors share sequence homology to RsgI9, they likely autoproteolyze through a similar mechanism.

Takayesu, Allen↗