14 Search Results

SNAP is a neutron time-of-flight diffractometer at the Spallation Neutron Source operated by Oak Ridge National Laboratory. It generates large arrays of neutron detection events that encode the crystalline atomic structure of materials under study. SNAPRed is an application that makes these datasets accessible to end users by orchestrating the process of data reduction while automatically managing the variable neutron instrumentation configuration. It supports arbitrary grouping and masking of individual detector pixels and includes custom-developed data compression approaches to accommodate the large volumes of data generated by the SNAP instrument.

Active matter demonstrates complex spatiotemporal self-organization not accessible at equilibrium and the emergence of collective behavior. Fluids comprised of microscopic Quincke rollers represent a popular realization of synthetic active matter. Temporal activity modulations, realized by modulated external electric fields, represent an effective tool to expand the variety of accessible dynamic states in active ensembles. Here, we report on the emergence of shockwave patterns composed of coherently moving particles energized by a pulsed electric field. The shockwaves emerge spontaneously and move faster than the average particle speed. Combining experiments, theory, and simulations, we demonstrate that the shockwaves originate from intermittent spontaneousmore » vortex cores due to a vortex meandering instability. They occur when the rollers’ translational and rotational decoherence times, regulated by the electric pulse durations, become comparable. The phenomenon does not rely on the presence of confinement, and multiple shock waves continuously arise and vanish in the system.« less

Cationic homo-polyamino acid (CHPA) peptides containing isopeptide bonds of diamino acids have been identified from Actinomycetes strains. However, none has been reported from other bacteria. Here, we report a δ-poly-L-ornithine synthetase from Acinetobacter baumannii, which we name PosA. Surprisingly, structural analysis of the adenylation domain and biochemical assay shows L-ornithine as the substrate for PosA. The product from the enzymatic reaction was purified and identified as poly-L-ornithine composed of 7-12 amino acid units. Chemical labeling of the polymer confirmed the isopeptide linkage of δ-poly-L-ornithine. We examine the biological activity of chemically synthesized 12-mer δ-poly-L-ornithine, illustrating that the polymer may actmore » as an anti-fungal agent. Structures of the isolated adenylation domain from PosA are presented with several diamino acids and biochemical assays identify important substrate binding residues. Structurally-guided genome-mining led to the identification of homologs with different substrate binding residues that could activate additional substrates. A homolog from Bdellovibrionales sp. shows modest activity with L-arginine but not with any diamino acids observed to be substrates for previously examined CHPA synthetases. Our study indicates the possibility that additional CHPAs may be produced by various microbes, supporting the further exploration of uncharacterized natural products.« less

Skeletal muscle is more resilient to ischemia-reperfusion injury than other organs. Tissue specific post-translational modifications of cytochrome c (Cytc) are involved in ischemia-reperfusion injury by regulating mitochondrial respiration and apoptosis. Here, we describe an acetylation site of Cytc, lysine 39 (K39), which was mapped in ischemic porcine skeletal muscle and removed by sirtuin5 in vitro. Using purified protein and cellular double knockout models, we show that K39 acetylation and acetylmimetic K39Q replacement increases cytochrome c oxidase (COX) activity and ROS scavenging while inhibiting apoptosis via decreased binding to Apaf-1, caspase cleavage and activity, and cardiolipin peroxidase activity. These results aremore » discussed with X-ray crystallography structures of K39 acetylated (1.50 Å) and acetylmimetic K39Q Cytc (1.36 Å) and NMR dynamics. We propose that K39 acetylation is an adaptive response that controls electron transport chain flux, allowing skeletal muscle to meet heightened energy demand while simultaneously providing the tissue with robust resilience to ischemia-reperfusion injury.« less

Compared to most ATP-site kinase inhibitors, small molecules that target an allosteric pocket have the potential for improved selectivity due to the often observed lower structural similarity at these distal sites. Despite their promise, relatively few examples of structurally confirmed, high-affinity allosteric kinase inhibitors exist. Cyclin-dependent kinase 2 (CDK2) is a target for many therapeutic indications, including non-hormonal contraception. However, an inhibitor against this kinase with exquisite selectivity has not reached the market because of the structural similarity between CDKs. In this paper, we describe the development and mechanism of action of type III inhibitors that bind CDK2 with nanomolarmore » affinity. Notably, these anthranilic acid inhibitors exhibit a strong negative cooperative relationship with cyclin binding, which remains an underexplored mechanism for CDK2 inhibition. Furthermore, the binding profile of these compounds in both biophysical and cellular assays demonstrate the promise of this series for further development into a therapeutic selective for CDK2 over highly similar kinases like CDK1. The potential of these inhibitors as contraceptive agents is seen by incubation with spermatocyte chromosome spreads from mouse testicular explants, where they recapitulate Cdk2^-/- and Spdya^-/- phenotypes.« less

The holographic principle, theorized to be a property of quantum gravity, postulates that the description of a volume of space can be encoded on a lower-dimensional boundary. The anti-de Sitter (AdS)/conformal field theory correspondence or duality is the principal example of holography. The Sachdev–Ye–Kitaev (SYK) model of N >> 1 Majorana fermions has features suggesting the existence of a gravitational dual in AdS₂, and is a new realization of holography. Here, we invoke the holographic correspondence of the SYK many-body system and gravity to probe the conjectured ER=EPR relation between entanglement and spacetime geometry through the traversable wormhole mechanism asmore » implemented in the SYK model. A qubit can be used to probe the SYK traversable wormhole dynamics through the corresponding teleportation protocol. This can be realized as a quantum circuit, equivalent to the gravitational picture in the semiclassical limit of an infinite number of qubits. Here we use learning techniques to construct a sparsified SYK model that we experimentally realize with 164 two-qubit gates on a nine-qubit circuit and observe the corresponding traversable wormhole dynamics. Despite its approximate nature, the sparsified SYK model preserves key properties of the traversable wormhole physics: perfect size winding, coupling on either side of the wormhole that is consistent with a negative energy shockwave, a Shapiro time delay, causal time-order of signals emerging from the wormhole, and scrambling and thermalization dynamics. Our experiment was run on the Google Sycamore processor. By interrogating a two-dimensional gravity dual system, our work represents a step towards a program for studying quantum gravity in the laboratory. Future developments will require improved hardware scalability and performance as well as theoretical developments including higher-dimensional quantum gravity duals and other SYK-like models.« less

Performance on auditory change detection tasks can be improved by training. We examined the stimulus specificity of these training effects in behavior and ERPs. A flicker change detection task was employed in which spatialized auditory scenes were alternated until a "change" or "same" response was made. For half of the trials, scenes were identical. The other half contained changes in the spatial locations of objects from scene to scene. On Day 1, participants were either trained on this auditory change detection task (trained group), or trained on a non-auditory change detection task (control group). On Day 2, all participants weremore » tested on the flicker task while EEG was recorded. The trained group showed greater change detection accuracy than the control group. They were less biased to respond "same" and showed full generalization of learning from trained to novel auditory objects. ERPs for "change" compared to "same" trials showed more negative going P1, N1, and P2 amplitudes, as well as a larger P3b amplitude. The P3b amplitude also differed between the trained and control group, with larger amplitudes for the trained group. Analysis of ERPs to scenes viewed prior to a decision revealed build-up of a difference between "change" and "same" trials in N1 and P2. Results demonstrate that training has an impact early in the "same" versus "change" decision-making process, and that the flicker paradigm combined with the ERP method can be used to study the build-up of change detection in auditory scenes.« less

Catalyzing life-sustaining reactions, proteins are composed by 20 different amino acids that fold into a compact yet flexible three-dimensional architecture, which dictates what their function(s) might be. Determining the spatial arrangement of the atoms, the protein’s 3D structure, enables key advances in fundamental and applied research. Protein crystallization is a powerful technique to achieve this. Unlike Earth’s crystallization experiments, biomolecular crystallization in space in the absence of gravitational force is actively sought to improve crystal growth techniques. However, the effects of changing gravitational vectors on a protein solution reaching supersaturation remain largely unknown. Here, we have developed a low-cost crystallizationmore » cell within a CubeSat payload module to exploit the unique experimental conditions set aboard a sounding rocket. We designed a biaxial gimbal to house the crystallization experiments and take measurements on the protein solution in-flight with a spectrophotometry system. After flight, we used X-ray diffraction analysis to determine that flown protein has a structural rearrangement marked by loss of the protein’s water and sodium in a manner that differs from crystals grown on the ground. We finally show that our gimbal payload module design is a portable experimental setup to take laboratory research investigations into exploratory space flights.« less