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At least 685 records · Page 38

Modification of cell wall polysaccharide guides cell division in Streptococcus mutans

In ovoid-shaped, Gram-positive bacteria, MapZ guides FtsZ-ring positioning at cell equators. The cell wall of the ovococcus Streptococcus mutans contains peptidoglycan decorated with serotype c carbohydrates (SCCs). In the present study, we identify the major cell separation autolysin AtlA as an SCC-binding protein. AtlA binding to SCC is attenuated by the glycerol phosphate (GroP) modification. Using fluorescently labeled AtlA constructs, we mapped SCC distribution on the streptococcal surface, revealing enrichment of GroP-deficient immature SCCs at the cell poles and equators. The immature SCCs co-localize with MapZ at the equatorial rings throughout the cell cycle. In GroP-deficient mutants, AtlA is mislocalized, resulting in dysregulated cellular autolysis. These mutants display morphological abnormalities associated with MapZ mislocalization, leading to FtsZ-ring misplacement. Altogether, our data support a model in which maturation of a cell wall polysaccharide provides the molecular cues for the recruitment of cell division machinery, ensuring proper daughter cell separation and FtsZ-ring positioning.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Domain coupling in activation of a family C GPCR

Abstract The G protein-coupled metabotropic glutamate receptors form homodimers and heterodimers with highly diverse responses to glutamate and varying physiological functions. We employ molecular dynamics, single-molecule spectroscopy and hydrogen–deuterium exchange to dissect the activation pathway triggered by glutamate. We find that activation entails multiple loosely coupled steps, including formation of an agonist-bound, pre-active intermediate whose transition to active conformations forms dimerization interface contacts that set efficacy. The agonist-bound receptor populates at least two additional intermediates en route to G protein-coupling conformations. Sequential transitions into these states act as ‘gates’, which attenuate the effects of glutamate. Thus, the agonist-bound receptor is remarkably dynamic, with low occupancy of G protein-coupling conformations, providing considerable headroom for modulation by allosteric ligands. Sequence variation within the dimerization interface, as well as altered conformational coupling in receptor heterodimers, may contribute to precise decoding of glutamate signals over broad spatial and temporal scales.

Biochemistry & Molecular Biology↗

Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA

The interbacterial deaminase toxin DddA catalyzes cytosine-to-uracil conversion in double-stranded (ds) DNA and enables CRISPR-free mitochondrial base editing, but the molecular mechanisms underlying its unique substrate selectivity have remained elusive. Here, we report crystal structures of DddA bound to a dsDNA substrate containing the 5'-TC target motif. These structures show that DddA binds to the minor groove of a sharply bent dsDNA and engages the target cytosine extruded from the double helix. DddA Phe1375 intercalates in dsDNA and displaces the 5' (-1) thymine, which in turn replaces the target (0) cytosine and forms a noncanonical T–G base pair with the juxtaposed guanine. This tandem displacement mechanism allows DddA to locate a target cytosine without flipping it into the active site. Biochemical experiments demonstrate that DNA base mismatches enhance the DddA deaminase activity and relax its sequence selectivity. On the basis of the structural information, we further identified DddA mutants that exhibit attenuated activity or altered substrate preference. Our studies may help design new tools useful in genome editing or other applications.

59 BASIC BIOLOGICAL SCIENCES↗

An infrared, Raman, and X-ray database of battery interphase components

Further improvements to lithium-ion and emerging battery technologies can be enabled by an improved understanding of the chemistry and working mechanisms of interphases that form at electrochemically active battery interfaces. However, it is difficult to collect and interpret spectra of interphases for several reasons, including the presence of a variety of compounds. To address this challenge, we herein present a vibrational spectroscopy and X-ray diffraction data library of ten compounds that have been identified as interphase constituents in lithium-ion or emerging battery chemistries. The data library includes attenuated total reflectance Fourier transform infrared spectroscopy, Raman spectroscopy, and X-ray diffraction data, collected in inert atmospheres provided by custom sample chambers. The data library presented in this work (and online repository) simplifies access to reference data that is otherwise either diffusely spread throughout the literature or non-existent, and provides energy storage researchers streamlined access to vital interphase-relevant data that can accelerate battery research efforts.

25 ENERGY STORAGE↗

Time-resolved 3D imaging of two-phase fluid flow inside a steel fuel injector using synchrotron X-ray tomography

The multiphase flow inside a diesel injection nozzle is imaged using synchrotron X-rays from the Advanced Photon Source at Argonne National Laboratory. Through acquisitions performed at several viewing angles and subsequent tomographic reconstruction, in-situ 3D visualization is achieved for the first time inside a steel injector at engine-like operating conditions. The morphology of the internal flow reveals strong flow separation and vapor-filled cavities (cavitation), the degree of which correlates with the nozzle's asymmetric inlet corner profile. Micron-scale surface features, which are artifacts of manufacturing, are shown to influence the morphology of the resulting liquid-gas interface. The data obtained at 0.1 ms time resolution exposes transient flow features and the flow development timescales are shown to be correlated with in-situ imaging of the fuel injector's hydraulically-actuated valve (needle). As more than 98.5% of the X-ray photon flux is attenuated within the steel injector body itself, we are posed with a unique challenge for imaging the flow within. Time-resolved imaging under these low-light conditions is achieved by exploiting both the refractive and absorptive properties of X-ray photons. The data-processing strategy converted these images with a signal-to-noise ratio of similar to 10 into a meaningful dataset for understanding internal flow and cavitation in a nozzle of diameter 200 mu m enclosed within 1-2 millimeters of steel.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

An interphase pool of KIF11 localizes at the basal bodies of primary cilia and a reduction in KIF11 expression alters cilia dynamics

KIF11 is a homotetrameric kinesin that peaks in protein expression during mitosis. It is a known mitotic regulator, and it is well-described that KIF11 is necessary for the formation and maintenance of the bipolar spindle. However, there has been a growing appreciation for non-mitotic roles for KIF11. KIF11 has been shown to function in such processes as axon growth and microtubule polymerization. We previously demonstrated that there is an interphase pool of KIF11 present in glioblastoma cancer stem cells that drives tumor cell invasion. Here, we identified a previously unknown association between KIF11 and primary cilia. We confirmed that KIF11 localized to the basal bodies of primary cilia in multiple cell types, including neoplastic and non-neoplastic cells. Further, we determined that KIF11 has a role in regulating cilia dynamics. Upon the reduction of KIF11 expression, the number of ciliated cells in asynchronously growing populations was significantly increased. We rescued this effect by the addition of exogenous KIF11. Lastly, we found that depleting KIF11 resulted in an increase in cilium length and an attenuation in the kinetics of cilia disassembly. These findings establish a previously unknown link between KIF11 and the dynamics of primary cilia and further support non-mitotic functions for this kinesin.

59 BASIC BIOLOGICAL SCIENCES↗

Three-dimensional imaging of mitochondrial cristae complexity using cryo-soft X-ray tomography

Mitochondria are dynamic organelles that change morphology to adapt to cellular energetic demands under both physiological and stress conditions. Cardiomyopathies and neuronal disorders are associated with structure-related dysfunction in mitochondria, but three-dimensional characterizations of the organelles are still lacking. In this study, we combined high-resolution imaging and 3D electron density information provided by cryo-soft X-ray tomography to characterize mitochondria cristae morphology isolated from murine. Using the linear attenuation coefficient, the mitochondria were identified (0.247 ± 0.04 µm -1 ) presenting average dimensions of 0.90 ± 0.20 µm in length and 0.63 ± 0.12 µm in width. The internal mitochondria structure was successfully identified by reaching up the limit of spatial resolution of 35 nm. The internal mitochondrial membranes invagination (cristae) complexity was calculated by the mitochondrial complexity index (MCI) providing quantitative and morphological information of mitochondria larger than 0.90 mm in length. The segmentation to visualize the cristae invaginations into the mitochondrial matrix was possible in mitochondria with MCI ≥ 7. Altogether, we demonstrated that the MCI is a valuable quantitative morphological parameter to evaluate cristae modelling and can be applied to compare healthy and disease state associated to mitochondria morphology.

3-D reconstruction↗

Quantitative imaging and automated fuel pin identification for passive gamma emission tomography

Compliance of member States to the Treaty on the Non-Proliferation of Nuclear Weapons is monitored through nuclear safeguards. The Passive Gamma Emission Tomography (PGET) system is a novel instrument developed within the framework of the International Atomic Energy Agency (IAEA) project JNT 1510, which included the European Commission, Finland, Hungary and Sweden. The PGET is used for the verification of spent nuclear fuel stored in water pools. Advanced image reconstruction techniques are crucial for obtaining high-quality cross-sectional images of the spent-fuel bundle to allow inspectors of the IAEA to monitor nuclear material and promptly identify its diversion. In this work, we have developed a software suite to accurately reconstruct the spent-fuel cross sectional image, automatically identify present fuel rods, and estimate their activity. Unique image reconstruction challenges are posed by the measurement of spent fuel, due to its high activity and the self-attenuation. While the former is mitigated by detector physical collimation, we implemented a linear forward model to model the detector responses to the fuel rods inside the PGET, to account for the latter. The image reconstruction is performed by solving a regularized linear inverse problem using the fast-iterative shrinkage-thresholding algorithm. We have also implemented the traditional filtered back projection (FBP) method based on the inverse Radon transform for comparison and applied both methods to reconstruct images of simulated mockup fuel assemblies. Higher image resolution and fewer reconstruction artifacts were obtained with the inverse-problem approach, with the mean-square-error reduced by 50%, and the structural-similarity improved by 200%. We then used a convolutional neural network (CNN) to automatically identify the bundle type and extract the pin locations from the images; the estimated activity levels finally being compared with the ground truth. The proposed computational methods accurately estimated the activity levels of the present pins, with an associated uncertainty of approximately 5%.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Fracture-matrix fluid exchange in oil-bearing unconventional mudstones

The poromechanical properties of unconventional reservoir materials are in large part dictated by their mineralogy. Since these properties govern the response to stress experienced during hydraulic fracturing, fluid production, and fluid injection, they play a central role in the formation of microcracks or bedding delaminations which ultimately dominate mass transport. In this work we study access to the porosity of end member unconventional reservoir materials, where the end members are predominantly dictated by carbonate content. Access to the porosity is quantified using state of the art 3D x-ray computed tomography coupled with physics informed data analytics. Xenon gas, which attenuates x-rays, provides a spatiotemporal map of access to the porosity. The accessible porosity is quantified over a range of net confining stress relevant to the manmade disturbances listed above. These experiments demonstrate that heavily carbonated mudstones are nearly impermeable at the core (~ cm) scale, while carbonate free analogues afford better access to the microstructure. Consistent with previous qualitative 2D radiographs, access to the interior of the clastic mudstones is first observed along planar microcracks, followed by slow penetration into the surrounding matrix. Physics informed data analytics of the 3D tomography measurements presented here show that these microcracks do not permit uniform access to the adjacent rock matrix. In addition, variation of the effective pressure elucidates the mechanisms that govern fracture/matrix fluid exchange. Under conditions consistent with hydrocarbon production fluid accumulates in the immediate vicinity of the nearest microcrack. While there is clear evidence that, as intended, part of this accumulation is from the more distant matrix, fluid is also squeezed out of the microcrack. The fluid build-up at the microcrack indicates that migration out of the rock is hindered by the coupled poroelastic response of the microcrack and adjacent rock matrix. We show that these mechanisms ultimately account for the meager oil recovery factors realized in practice. These insights have implications for making reservoir scale predictions based on core scale observations, and provide a basis for devising new asset development techniques to access more porosity, and enhance fluid extraction. Finally, these findings shed light on key features and mechanisms that govern shale storage capacity, with relevance to other important industrial processes, such as geologic CO 2 storage.

58 GEOSCIENCES↗

Enhancing the Cherenkov over scintillation ratio using dichroic filters in BGO and TlCl for TOF-PET

Abstract The Cherenkov emission in inorganic crystal scintillators has been shown to dramatically improve time resolution for time-of-flight positron emission tomography (TOF-PET) for in slow scintillators with a high refractive index such as bismuth germanium oxide (BGO). This is due to the faster nature of the Cherenkov emission (tens of picoseconds) with respect to scintillation (nanosecond). However, the presence of slower scintillation light and the inability of existing detectors to distinguish between Cherenkov and scintillation make it difficult for BGO to achieve a good CTR for all the detected coincidence events. In this paper, we exploit the difference between the Cherenkov and scintillation emission spectra and use dichroic filters to enhance the Cherenkov over scintillation ratio. Dichroic filters transmit or reflect photons based on their wavelength, with a photon attenuation lower than 10%. We investigate several shortpass and longpass dichroic filters in a single-photon configuration with BGO and find the optimal filter that maximizes the Cherenkov over scintillation ratio. We demonstrate that we can enhance the ratio of Cherenkov to scintillation photons by a factor of 2.17 ± 0.38 by employing a shortpass dichroic filter with a cut-off wavelength of 450 nm for BGO, and by a factor of 2.87 ± 0.40 using a longpass dichroic filter with a cut-on wavelength of 550 nm for iodine/beryllium-doped thallium chloride.

Science & Technology - Other Topics↗

Advances in detection for neutron reflectometry with time-resolved imaging detectors

Thermal neutron detection in neutron scattering science is a challenging endeavour due to a limited number of technologies which are sensitive to these weakly interacting particles. While many improvements to conventional detectors are underway at various facilities, there is a great opportunity to make a leap in performance by combining the spatial resolution benefits of imaging and the temporal resolution and background discrimination of event-driven radiation detectors. This idea has been realized by using a neutron sensitive scintillator read out by a single-photon sensitive camera based on a Timepix3 ASIC. We demonstrate how such data-driven imaging sensors can enable unprecedented performance in neutron reflectometry using the ASTERIX instrument at the Los Alamos Neutron Scattering Center. Several samples were measured with both the new and a conventional 3 He detector systems. The results from this work demonstrate that these imaging based systems can satisfy performance parameters for the future QIKR reflectometer to be built at the Second Target Station at Oak Ridge National Laboratory. Further improvements to the detector are already underway which will allow streamlined and expedited experiments. We demonstrate at least a two order of magnitude increase in detection rate at an acceptable dead time and introduce a new way of tuning the detector efficiency using light collecting optics to accommodate highly intense direct beams which cannot be measured with any current detectors without severe attenuation. This will allow measurements of complete reflectometry profiles and using a single sample measurement combined with fewer direct beam calibration measurements on QIKR and potentially other reflectometers.

36 MATERIALS SCIENCE↗

Linking international technical specifications for acoustic characterization of marine energy converter sounds with environmental compliance criteria

As new ocean energy technologies emerge and are deployed for testing and operations, sound emissions are a potential concern for environmental effects to marine life. Consistent acoustic measurement and data analysis methods can help promote comparisons of technologies and transferability between project sites. In 2022, acoustic emissions from a prototype scale wave energy converter (WEC) were characterized for a range of environmental conditions and power generation states in the coastal waters off southern California using a set of international technical specifications. Results from the international technical specification analyses were applied to United States regulatory threshold criteria for acoustic impacts to marine mammals and examined in the context of European underwater noise monitoring guidelines. Weighted 24 hour cumulative sound exposure levels SEL24h calculated from the highest power generation state WEC sound pressure levels were often more than 20 dB below threshold criteria for temporary threshold shifts in five relevant marine mammal hearing groups. Following European Union recommendations for analyses and reporting, WEC sound characterization in third octave bands centered at 63 Hz and 125 Hz show clear spatial decay of WEC-generated noise, with more pronounced attenuation at 63 Hz, and a less marked but still detectable gradient at 125 Hz, collectively suggesting a relatively confined acoustic footprint under the observed conditions. The value of the international technical specification approach is highlighted by the isolation of WEC sounds from the surrounding soundscape. This allows for a robust characterization of acoustic emissions through a range of device power generation and sea states. Furthermore, in threshold-based regulatory contexts like the U.S., this facilitates direct evaluation of source contributions, while in broader monitoring frameworks used in the E.U. it provides a reproducible foundation for assessing the contribution of emerging ocean energy technologies to the underwater acoustic environment.

Haxel, Joseph H. (ORCID:0000000273864761)↗

Defective internal allosteric network imparts dysfunctional ATP/substrate-binding cooperativity in oncogenic chimera of protein kinase A

An aberrant fusion of the DNAJB1 and PRKACA genes generates a chimeric protein kinase (PKA-C DNAJB1 ) in which the J-domain of the heat shock protein 40 is fused to the catalytic α subunit of cAMP-dependent protein kinase A (PKA-C). Deceivingly, this chimeric construct appears to be fully functional, as it phosphorylates canonical substrates, forms holoenzymes, responds to cAMP activation, and recognizes the endogenous inhibitor PKI. Nonetheless, PKA-C DNAJB1 has been recognized as the primary driver of fibrolamellar hepatocellular carcinoma and is implicated in other neoplasms for which the molecular mechanisms remain elusive. Here we determined the chimera’s allosteric response to nucleotide and pseudo-substrate binding. We found that the fusion of the dynamic J-domain to PKA-C disrupts the internal allosteric network, causing dramatic attenuation of the nucleotide/PKI binding cooperativity. Our findings suggest that the reduced allosteric cooperativity exhibited by PKA-C DNAJB1 alters specific recognitions and interactions between substrates and regulatory partners contributing to dysregulation.

59 BASIC BIOLOGICAL SCIENCES↗

Structural trends in atomic nuclei from laser spectroscopy of tin

Tin is the chemical element with the largest number of stable isotopes. Its complete proton shell, comparable with the closed electron shells in the chemically inert noble gases, is not a mere precursor to extended stability; since the protons carry the nuclear charge, their spatial arrangement also drives the nuclear electromagnetism. We report high-precision measurements of the electromagnetic moments and isomeric differences in charge radii between the lowest 1/2 + , 3/2 + , and 11/2 - states in 117–131 Sn, obtained by collinear laser spectroscopy. Supported by state-of-the-art atomic-structure calculations, the data accurately show a considerable attenuation of the quadrupole moments in the closed-shell tin isotopes relative to those of cadmium, with two protons less. Linear and quadratic mass-dependent trends are observed. While microscopic density functional theory explains the global behaviour of the measured quantities, interpretation of the local patterns demands higher-fidelity modelling.

74 ATOMIC AND MOLECULAR PHYSICS↗

Ionization by XFEL radiation produces distinct structure in liquid water

In the warm dense matter (WDM) regime, where condensed, gas, and plasma phases coexist, matter frequently exhibits unusual properties that cannot be described by contemporary theory. Experiments reporting phenomena in WDM are therefore of interest to advance our physical understanding of this regime, which is found in dwarf stars, giant planets, and fusion ignition experiments. Using 7.1 keV X-ray free electron laser radiation (nominally 5×10 5 J/cm 2 ), we produced and probed transient WDM in liquid water. Wide-angle X-ray scattering (WAXS) from the probe reveals a new ~9 Å structure that forms within 75 fs. By 100 fs, the WAXS peak corresponding to this new structure is of comparable magnitude to the ambient water peak, which is attenuated. Simulations suggest that the experiment probes a superposition of two regimes. In the first, fluences expected at the focus severely ionize the water, which becomes effectively transparent to the probe. In the second, out-of-focus pump radiation produces O 1+ and O 2+ ions, which rearrange due to Coulombic repulsion over 10 s of fs. Our simulations account for a decrease in ambient water signal and an increase in low-angle X-ray scattering but not the experimentally observed 9 Å feature, presenting a new challenge for theory.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Ion-specific phenomena limit energy recovery in forward-biased bipolar membranes

The ability for bipolar membranes (BPMs) to interconvert voltage and pH makes them attractive materials for use in energy conversion and storage. Reverse-biased BPMs, which use electrical voltage to dissociate water into acid and base, have become increasingly well studied. However, forward-biased BPMs (FB-BPMs), in which voltage is extracted from pH gradients through recombination, require further study. Here physics-based modeling elucidates how the complex coupling of transport and kinetics dictates the performance of FB-BPMs in electrochemical devices. Simulations reveal that the open-circuit potential of FB-BPMs is dictated by the balance of ion recombination and crossover, where recombination of buffering counter-ions attenuates the open-circuit potential. Counter-ion mass-transport limitations and uptake of ionic impurities limit achievable current densities by reducing the applied pH gradient or the available fixed-charge sites that mediate recombination. Further, the model highlights the importance of selective ion management in mitigating energy losses and provides insight into the rational material design of FB-BPMs for energy applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Platinum complexes of a boron-rich diphosphine ligand

Continuing herein, we describe the preparation, characterization, and reactivity of two Pt II bis-hydrocarbyl complexes containing the 1,2-bis(di(3-dicyclohexylboraneyl)propylphosphino)ethane (P 2 B Cy 4 ) ligand. These scaffolds are readily accessed from four-fold hydroboration of 1,2-bis(diallylphosphino)ethane Pt II precursors. The electrophilcity of such frameworks is showcased by facile coordination of the strong Lewis base, 4-N,N-dimethylaminopyridine (DMAP). Thermolysis reactions of [Pt(P 2 B Cy 4 )(R) 2 ] (R = CH 3 or Ph) show enhanced (and divergent) reactivity when compared to their “all-alkyl” diphosphine counterparts, implicating involvement of the pendant borane groups. This behaviour is attenuated by protection of these units with DMAP.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A combined SECM and electrochemical AFM approach to probe interfacial processes affecting molecular reactivity at redox flow battery electrodes

Redox flow batteries are attractive technologies for grid energy storage since they use solutions of redox-active molecules that enable a superior scalability and the decoupling of power and energy density. However, the reaction mechanisms of the redox active components at RFB electrodes are complex, and there is currently a pressing need to understand how interfacial processes impact the kinetics and operational reversibility of RFB systems. Here, we developed a combined electrochemical imaging methodology rooted in scanning electrochemical microscopy (SECM) and atomic force microscopy (AFM) for exploring the impact of electrode structure and conditioning on the electron transfer properties of model redox-active dialkoxybenzene derivatives, 2,5-di-tert-butyl-1,4-bis(2-methoxyethoxy)benzene (C1) and 2,3-dimethyl-1,4-dialkoxybenzene (C7). Using AFM and secondary-ion mass spectrometry (SIMS), we observed the formation of interfacial films with distinct mechanical properties compared to those of cleaved graphitic surfaces, and exclusively during reduction of electrogenerated radical cations. These films had an impact on the median rate and distribution of the electron transfer rate constant at the basal plane of multilayer and single layer graphene electrodes, displaying kinetically-limited values that did not yield the activation expected per the Butler–Volmer model with a transfer coefficient ~0.5. These changes were dependent on redoxmer structure: furthermore, SECM showed strong attenuation of C7 kinetics by a surface layer on MLG and SLG, while C1 kinetics were only affected by SLG. SECM and AFM results together show that these limiting films operate exclusively on the basal plane of graphite, with the edge plane showing a relative insensitivity to cycling and operation potential. Ultimately, this integrated electrochemical imaging methodology creates new opportunities to understand the unique role of interfacial processes on the heterogeneous reactivity of redoxmers at electrodes for RFBs, with a future role in elucidating phenomena at high active concentrations and spatiotemporal variations in electrode dynamics.

25 ENERGY STORAGE↗