Comparison of δ18O analyses on individual planktic foraminifer (Orbulina universa) shells by SIMS and gas-source mass spectrometry
Not provided.
Geochemistry & Geophysics↗
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Hydrogen-Bonding Bottlebrush Networks: Self-Healing Materials from Super-Soft to Stiff
The impact of polymer architecture on network dynamics and self-healing is presented using bottlebrushes containing side chains that are end-functionalized with 2-ureido-4[1H]-pyrimidinone (UPy). The synthesis of these materials is straightforward through a three-step process: (1) synthesizing rubbery poly(4-methylcaprolactone) macromonomers (p4MCL–OH) with a norbornene-based initiator, (2) functionalizing the terminal hydroxyl group with UPy–isocyanate (p4MCL–UPy), and (3) statistically copolymerizing p4MCL–OH and p4MCL–UPy via ring-opening metathesis polymerization (ROMP) to form hydrogen-bonding bottlebrushes having a fraction (p) of side chains functionalized with UPy. Attaching UPy to the free end of bottlebrush side chains dilutes the impact of friction from complementary UPy interactions on segmental dynamics, leading to a much weaker dependence of the glass-transition temperature (T g ) on p than observed in linear analogues, while the activation energy to dissociate UPy–UPy bonds (41–47 kJ/mol) remains mostly unchanged. Longer side chains result in a competition between reducing T g and inducing entanglements that influence hydrogen-bonded network dynamics. Increasing the backbone length extends the sticky Rouse region without affecting the network modulus (G x ) or UPy–UPy dissociation time (τ s ). Gx scales linearly with p and ranges from 27 kPa to 1.6 MPa, while τs remains nearly constant in contrast to linear telechelic ionomers, implying a similar self-healability across bottlebrush networks containing different amounts of UPy. Furthermore, these stretchable networks with p ≤ 0.25 undergo self-healing upon repeated rupture and melt pressing at ≤100 °C while retaining similar tensile properties. In summary, decorating bottlebrush polymers with hydrogen bonds creates opportunities to independently manipulate associative network dynamics and mechanical moduli.
36 MATERIALS SCIENCE↗
Influence of composition fluctuations on the linear viscoelastic properties of symmetric diblock copolymers near the order-disorder transition
Rheological evidence of composition fluctuations in disordered diblock copolymers near the order disorder transition (ODT) has been documented in the literature over the past three decades, characterized by a failure of time–temperature superposition (tTS) to reduce linear dynamic mechanical spectroscopy (DMS) data in the terminal viscoelastic regime to a temperature-independent form. However, for some materials, most notably poly(styrene-b-isoprene) (PS–PI), no signature of these rheological features has been found. We present small-angle X-ray scattering (SAXS) results on symmetric poly(cyclohexylethylene-b-ethylene) (PCHE–PE) diblock copolymers that confirm the presence of fluctuations in the disordered state and DMS measurements that also show no sign of the features ascribed to composition fluctuations. Assessment of DMS results published on five different diblock copolymer systems leads us to conclude that the effects of composition fluctuations can be masked by highly asymmetric block dynamics, thereby resolving a long-standing disagreement in the literature and reinforcing the importance of mechanical contrast in understanding the dynamics of ordered and disordered block polymers.
Hickey, Robert J.↗
A Functional Description of CymA, an Electron Transfer Hub Supporting Anaerobic Respiratory Flexibility in Shewanella
CymA is a member of the NapC/NirT family of quinol dehydrogenases. Essential for the anaerobic respiratory flexibility of shewanellae, CymA transfers electrons from menaquinol to various dedicated systems for the reduction of terminal electron acceptors including fumarate and insoluble minerals of Fe(III). Spectroscopic characterization of CymA from Shewanella oneidensis MR-1 identifies three low-spin His/His coordinated c-hemes and a single high-spin c-heme with His/H{sub 2}O coordination lying adjacent to the quinol binding site. At pH 7, binding of the menaquinol analogue, 2-heptyl-4-hydroxyquinoline-N-oxide, does not alter the mid-point potentials of the high-spin (ca. {approx}240 mV) and low-spin (ca. {approx}110, {approx}190 and {approx}265 mV) hemes that appear biased to transfer electrons from the high- to low-spin centres following quinol oxidation. CymA is reduced with menadiol (E{sub m} = {approx} 80 mV) in the presence of NADH (E{sub m} = {approx} 320 mV) and an NADH:menadione oxidoreductase, but not by menadiol alone. In cytoplasmic membranes reduction of CymA may then require the thermodynamic driving force from NADH, formate or H{sub 2} oxidation as the redox poise of the menaquinol pool in isolation is insufficient. Spectroscopic studies suggest that CymA requires a nonheme cofactor for quinol oxidation and that the reduced enzyme forms a 1:1 complex with its redox partner Fcc{sub 3}. The implications for CymA supporting the respiratory flexibility of shewanellae are discussed.
59 BASIC BIOLOGICAL SCIENCES↗
CO Oxidation Facilitated by Robust Surface States on Au-Covered Topological Insulators
Not Available
Chen, Hua↗
Dynamic molecular architecture of the synaptonemal complex
During meiosis, pairing between homologous chromosomes is stabilized by the assembly of the synaptonemal complex (SC). The SC ensures the formation of crossovers between homologous chromosomes and regulates their distribution. However, how the SC regulates crossover formation remains elusive. We isolated an unusual mutation in Caenorhabditis elegans that disrupts crossover interference but not SC assembly. This mutation alters the unique C terminal domain of an essential SC protein, SYP-4, a likely ortholog of the vertebrate SC protein SIX6OS1. We use three-dimensional stochastic optical reconstruction microscopy (3D-STORM) to interrogate the molecular architecture of the SC from wild-type and mutant C. elegans animals. Using a probabilistic mapping approach to analyze super-resolution image data, we detect changes in the organization of the synaptonemal complex in wild-type animals that coincide with crossover designation. We also found that our syp-4 mutant perturbs SC architecture. Our findings add to growing evidence that the SC is an active material whose molecular organization contributes to chromosome-wide crossover regulation.
59 BASIC BIOLOGICAL SCIENCES↗
Structural and Histone Binding Ability Characterizations of Human PWWP Domains
The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently. The PWWP domain has been shown to be a DNA binding domain, but sequence analysis and previous structural studies show that the PWWP domain exhibits significant similarity to other 'Royal Family' members, implying that the PWWP domain has the potential to bind histones. In order to further explore the function of the PWWP domain, we used the protein family approach to determine the crystal structures of the PWWP domains from seven different human proteins. Our fluorescence polarization binding studies show that PWWP domains have weak histone binding ability, which is also confirmed by our NMR titration experiments. Furthermore, we determined the crystal structures of the BRPF1 PWWP domain in complex with H3K36me3, and HDGF2 PWWP domain in complex with H3K79me3 and H4K20me3. PWWP proteins constitute a new family of methyl lysine histone binders. The PWWP domain consists of three motifs: a canonical {beta}-barrel core, an insertion motif between the second and third {beta}-strands and a C-terminal {alpha}-helix bundle. Both the canonical {beta}-barrel core and the insertion motif are directly involved in histone binding. The PWWP domain has been previously shown to be a DNA binding domain. Therefore, the PWWP domain exhibits dual functions: binding both DNA and methyllysine histones.
59 BASIC BIOLOGICAL SCIENCES↗
A model of polarized-beam AGS in the ray-tracing code Zgoubi
A model of the Alternating Gradient Synchrotron, based on the AGS snapramps, has been developed in the stepwise ray-tracing code Zgoubi. It has been used over the past 5 years in a number of accelerator studies aimed at enhancing RHIC proton beam polarization. It is also used to study and optimize proton and Helion beam polarization in view of future RHIC and eRHIC programs. The AGS model in Zgoubi is operational on-line via three different applications, ’ZgoubiFromSnaprampCmd’, ’AgsZgoubiModel’ and ’AgsModelViewer’, with the latter two essentially interfaces to the former which is the actual model ’engine’. All three commands are available from the controls system application launcher in the AGS ’StartUp’ menu, or from eponymous commands on shell terminals. Main aspects of the model and of its operation are presented in this technical note, brief excerpts from various studies performed so far are given for illustration, means and methods entering in ZgoubiFromSnaprampCmd are developed further in appendix.
43 PARTICLE ACCELERATORS↗
Multistage Stabilized Continuation for Indirect Optimal Control of Three-Dimensional Hypersonic Trajectories
This work presents the development of a multistaged stabilized continuation for the three-dimensional unpowered hypersonic trajectory planning problem using indirect optimal control methods. The stabilized continuation method is noniterative and guaranteed to terminate within a finite number of floating point operations, thereby making it well suited for onboard autonomous implementations. Here, we present a multistage formulation of the stabilized continuation scheme that involves starting with a “loose” integration tolerance during the first stage and ramping up toward a “strict” integration tolerance through subsequent stages. An important benefit of this approach is that even when the solution to the underlying optimal control problem is numerically unstable, such as with the hypersonic vehicle footprint generation problem, the stabilized continuation algorithm is shown to be successful in finding a solution while providing some additional insights into the underlying cause of the numerical instability.
33 ADVANCED PROPULSION SYSTEMS↗
Cosmogenic 21 Ne exposure ages on late Pleistocene moraines in Lassen Volcanic National Park, California, USA
We report new cosmogenic 21 Ne in quartz exposure ages from 18 samples on three distinct moraines deposited in the Lost Creek drainage, approximately 3–7 km down-valley from Lassen Peak in Lassen Volcanic National Park. Although measuring 21 Ne in quartz is generally straightforward, accurate 21Ne exposure dating of deposits of late Pleistocene is rarely possible due to the significant quantities of non-cosmogenic 21 Ne present in most lithologies. Young quartz-bearing volcanic rocks have been observed to be an exception. We take advantage of moraine boulders sourced from the ~28 ka dacite of Lassen Peak to generate a chronology of alpine deglaciation in Lassen Volcanic National Park. Ages from three distinct moraines are in stratigraphic order at 22.1 ± 3.8, 20.2 ± 2.4, and 15.3 ± 3.8 ka and generally agree with other terminal and some recessional moraine ages across the Cascade Range and Sierra Nevada of the western United States. To date, these are among the youngest surfaces ever dated using cosmogenic 21 Ne and provide a cost-effective proof-of-concept approach to dating moraines where applicable.
58 GEOSCIENCES↗
Surface termination structure of α-Ga{sub 2}O{sub 3} film grown by mist chemical vapor deposition
The surface structure of α-Ga{sub 2}O{sub 3}(0001) grown on an α-Al{sub 2}O{sub 3}(0001) substrate by mist chemical vapor deposition was studied by coaxial impact-collision ion scattering spectroscopy (CAICISS) and atomic force microscopy (AFM). The minimum step height observed in the AFM image was 0.21 ± 0.01 nm, coinciding with the height of three atomic layers of α-Ga{sub 2}O{sub 3}(0001). It was revealed by CAICISS analysis that the surface of α-Ga{sub 2}O{sub 3}(0001) is terminated by a Ga layer followed by an O layer, which is consistent with the surface termination of α-Al{sub 2}O{sub 3}(0001). A structural model taking surface relaxation into account was also constructed by fitting the simulated curve for the azimuth angle dependence of the Ga intensity to the experimental dependence. The resultant structural model is similar to the model of an α-Al{sub 2}O{sub 3}(0001) surface, which indicates analogous behavior in corundum crystals.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NbF{sub 5} and TaF{sub 5}: Assignment of {sup 19}F NMR resonances and chemical bond analysis from GIPAW calculations
The {sup 19}F isotropic chemical shifts (δ{sub iso}) of two isomorphic compounds, NbF{sub 5} and TaF{sub 5}, which involve six nonequivalent fluorine sites, have been experimentally determined from the reconstruction of 1D {sup 19}F MAS NMR spectra. In parallel, the corresponding {sup 19}F chemical shielding tensors have been calculated using the GIPAW method for both experimental and DFT-optimized structures. Furthermore, the [M{sub 4}F{sub 20}] units of NbF{sub 5} and TaF{sub 5} being held together by van der Waals interactions, the relevance of Grimme corrections to the DFT optimization processes has been evaluated. However, the semi-empirical dispersion correction term introduced by such a method does not show any significant improvement. Nonetheless, a complete and convincing assignment of the {sup 19}F NMR lines of NbF{sub 5} and TaF{sub 5} is obtained, ensured by the linearity between experimental {sup 19}F δ{sub iso} values and calculated {sup 19}F isotropic chemical shielding σ{sub iso} values. The effects of the geometry optimizations have been carefully analyzed, confirming among other matters, the inaccuracy of the experimental structure of NbF{sub 5}. The relationships between the fluorine chemical shifts, the nature of the fluorine atoms (bridging or terminal), the position of the terminal ones (opposite or perpendicular to the bridging ones), the fluorine charges, the ionicity and the length of the M–F bonds have been established. Additionally, for three of the {sup 19}F NMR lines of NbF{sub 5}, distorted multiplets, arising from {sup 1}J-coupling and residual dipolar coupling between the {sup 19}F and {sup 93}Nb nuclei, were simulated yielding to values of {sup 93}Nb–{sup 19}F {sup 1}J-coupling for the corresponding fluorine sites. - Graphical abstract: The complete assignment of the {sup 19}F NMR lines of NbF{sub 5} and TaF{sub 5} allow establishing relationships between the {sup 19}F δ{sub iso} values, the nature of the fluorine atoms (bridging or terminal), the position of the terminal ones (opposite or perpendicular to the bridging ones), the fluorine charges, the ionicity and the length of the M–F bonds. Display Omitted - Highlights: • The {sup 19}F δ{sub iso} values of NbF{sub 5} and TaF{sub 5} have been determined. • The {sup 19}F chemical shielding tensors have been calculated using the GIPAW method. • A confident assignment of the {sup 19}F NMR lines of NbF{sub 5} and TaF{sub 5} is obtained. • The relationships between the {sup 19}Fδ{sub iso} values and the M–F bonds features are established.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Mutation L232H Promotes Chromophore Maturation of EGFP-Based Fluorescent Fusion Proteins
The L232H mutant of the enhanced green fluorescent protein (EGFP) was expressed and crystallized. An X-ray diffraction data set was collected from the crystals to 1.53 Å resolution. An analysis of the three-dimensional structure revealed a stacking interaction between the amino-acid residues Н78 and Н232, which contributes to the fastening of the C-terminal region of the protein in the vicinity of the chromophore and influences chromophore maturation of hybrid fluorescent proteins produced by fusion of the target proteins with the C-terminus of EGFP. This hypothesis was experimentally confirmed by investigating chromophore maturation of the hybrid proteins fused to the N- and C-termini of EGFP and EGFP-L232H.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Staphylococcus aureus FtsZ and PBP4 bind to the conformationally dynamic N-terminal domain of GpsB
In the Firmicutes phylum, GpsB is a membrane associated protein that coordinates peptidoglycan synthesis with cell growth and division. Although GpsB has been studied in several bacteria, the structure, function, and interactome of Staphylococcus aureus GpsB is largely uncharacterized. To address this knowledge gap, we solved the crystal structure of the N-terminal domain of S. aureus GpsB, which adopts an atypical, asymmetric dimer, and demonstrates major conformational flexibility that can be mapped to a hinge region formed by a three-residue insertion exclusive to Staphylococci. When this three-residue insertion is excised, its thermal stability increases, and the mutant no longer produces a previously reported lethal phenotype when overexpressed in Bacillus subtilis. In S. aureus, we show that these hinge mutants are less functional and speculate that the conformational flexibility imparted by the hinge region may serve as a dynamic switch to fine-tune the function of the GpsB complex and/or to promote interaction with its various partners. Furthermore, we provide the first biochemical, biophysical, and crystallographic evidence that the N-terminal domain of GpsB binds not only PBP4, but also FtsZ, through a conserved recognition motif located on their C-termini, thus coupling peptidoglycan synthesis to cell division. Taken together, the unique structure of S. aureus GpsB and its direct interaction with FtsZ/PBP4 provide deeper insight into the central role of GpsB in S. aureus cell division.
59 BASIC BIOLOGICAL SCIENCES↗
A coevolution-guided model for the rotor of the bacterial flagellar motor
The Salmonella typhimurium trans-membrane FliF MS ring templates assembly of the rotary bacterial fagellar motor, which also contains a cytoplasmic C-ring. A full-frame fusion of FliF with the rotor protein FliG assembles rings in non-motile expression hosts. 3D electron microscopy reconstructions of these FliFFliG rings show three high electron-density sub-volumes. 3D-classifcation revealed heterogeneity of the assigned cytoplasmic volume consistent with FliG lability. We used residue coevolution to construct homodimer building blocks for ring assembly, with X-ray crystal structures from other species and injectisome analogs. The coevolution signal validates folds and, importantly, indicates strong homodimer contacts for three ring building motifs (RBMs), initially identified in injectisome structures. It also indicates that the cofolded domains of the FliG N-terminal domain (FliG_N) with embedded α-helical FliF carboxy-terminal tail homo-oligomerize. The FliG middle and C-terminal domains (FliG_MC) have a weak signal for homo-dimerization but have coevolved to conserve their stacking contact. The homodimers and their ring models ft well into the 3D reconstruction. We hypothesize that a stable FliF periplasmic hub provides a platform for FliG ring self-assembly, but the FliG_MC ring has only limited stability without the C-ring. We also present a mechanical model for torque transmission in the FliFFliG ring.
59 BASIC BIOLOGICAL SCIENCES↗
New examples of ferroelectric nematic materials showing evidence for the antiferroelectric smectic-Z phase
Abstract We present a new ferroelectric nematic material, 4-((4′-((trans)-5-ethyloxan-2-yl)-2′,3,5,6′-tetrafluoro-[1,1′-biphenyl]-4-yl)difluoromethoxy)-2,6-difluorobenzonitrile (AUUQU-2-N) and its higher homologues, the molecular structures of which include fluorinated building blocks, an oxane ring, and a terminal cyano group, all contributing to a large molecular dipole moment of about 12.5 D. We observed that AUUQU-2-N has three distinct liquid crystal phases, two of which were found to be polar phases with a spontaneous electric polarization P s of up to 6 µC cm –2 . The highest temperature phase is a common enantiotropic nematic (N) exhibiting only field-induced polarization. The lowest-temperature, monotropic phase proved to be a new example of the ferroelectric nematic phase (N F ), evidenced by a single-peak polarization reversal current response, a giant imaginary dielectric permittivity on the order of 10 3 , and the absence of any smectic layer X-ray diffraction peaks. The ordinary nematic phase N and the ferroelectric nematic phase N F are separated by an antiferroelectric liquid crystal phase which has low permittivity and a polarization reversal current exhibiting a characteristic double-peak response. In the polarizing light microscope, this antiferroelectric phase shows characteristic zig-zag defects, evidence of a layered structure. These observations suggest that this is another example of the recently discovered smectic Z A (SmZ A ) phase, having smectic layers with the molecular director parallel to the layer planes. The diffraction peaks from the smectic layering have not been observed to date but detailed 2D X-ray studies indicate the presence of additional short-range structures including smectic C-type correlations in all three phases—N, SmZ A and N F —which may shed new light on the understanding of polar and antipolar order in these phases.
36 MATERIALS SCIENCE↗
The structure of tubulin-binding cofactor A from Leishmania major infers a mode of association during the early stages of microtubule assembly
The structure of a tubulin-binding cofactor from L. major is reported and compared with yeast, plant and human orthologues. Tubulin-binding cofactor A (TBCA) participates in microtubule formation, a key process in eukaryotic biology to create the cytoskeleton. There is little information on how TBCA might interact with β-tubulin en route to microtubule biogenesis. To address this, the protozoan Leishmania major was targeted as a model system. The crystal structure of TBCA and comparisons with three orthologous proteins are presented. The presence of conserved features infers that electrostatic interactions that are likely to involve the C-terminal tail of β-tubulin are key to association. This study provides a reagent and template to support further work in this area.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Bus Design for the Poloidal Field Coils of the NSTX-Upgrade Fusion Device
The National Spherical Torus eXperiment (NSTX) has undergone a major upgrade to NSTX-U at Princeton Plasma Physics Laboratory (PPPL). NSTX upgrade (NSTX-U) will double the toroidal field, plasma current, and neutral beam injection heating power, as well as significantly increase the pulse duration. NSTX-U uses three poloidal field (PF) coils at the vessel top and three at the bottom near the divertor areas to control the local plasma shape there. These shaping coils operate at a maximum terminal voltage of 2 kV, corresponding to a maximum current about 20 kA. To supply the power to the PF coils, hard copper bus bars are typically used near the vacuum vessel, while water cooled flexible cables are used away from the vessel. The detailed design of the hard copper bus bars will be covered in this article. During operation, these hard bus bars are subject to high electromagnetic (EM) forces, thermal displacement loads, as well as plasma halo loads due to disruption. The EM, thermal, and structural analysis were performed, and the results revealed that, with the worst loads combined, the new design meets the NSTX-U thermal, structural, and fatigue cycle requirements. Finally, the manufacturing and installation process of the bus work will be discussed at the end of this article.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗