23 Search Results

Target of rapamycin (TOR) and sucrose non-fermenting 1–related protein kinase 1 (SnRK1) are conserved regulators of plant growth and metabolism and are often portrayed as functionally antagonistic under nutrient limitation. However, how this relationship operates across different nutrient contexts remains poorly defined. Here, we generated an Arabidopsis dual-reporter line that enables simultaneous monitoring of TOR and SnRK1 activities and profiled their dynamics under carbon and nitrogen perturbations. We found that TOR and SnRK1 activities\r\noverall exhibit a negative relationship during the transition from carbon starvation to carbon abundance; however, their temporal dynamics during that transition do not support a strictly inversemore » correlation. Under dark conditions, TOR activity is gradually repressed, while SnRK1 is initially repressed in the early hours and subsequently activated during extended darkness. During nitrogen starvation, TOR activity is progressively repressed, whereas SnRK1 is activated during early hours and then becomes repressed. In vitro, recombinant SnRK1a1 directly\r\ninhibits the activity of immunoprecipitated TOR (IP-TOR), whereas IP-TOR does not directly affect SnRK1a1 activity. Together, these results support a nutrient dependent model in which TOR and SnRK1 are coordinated primarily by cellular metabolic status.\r\n« less

Most virus infection assays have indirect readout such as virus number following entry (e.g., PCR, cell lysis). While effective, these technologies are labor‐intensive, require specialized environments (e.g., sterile or RNA‐free), and detect later‐stage viral events like lysis or cell death, lacking sensitivity to early fusion events. To address these limitations, we present biologically relevant 2D membrane materials, host‐cell‐derived supported lipid bilayers (hcd‐SLBs), integrated with organic microelectrode arrays (OMEAs) for detection of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) fusion. By overexpressing angiotensin‐converting enzyme 2 (ACE2) receptors on the native membranes, the platform functions as a viral sensor capable of detectingmore » virus pseudo particles (VPPs) through the late pathway. Additionally, hcd‐SLBs extracted from human lung epithelium expressing native ACE2 detect fusion events through the early pathway. The platform's utility as a drug‐screening tool is demonstrated by testing antibodies targeting either the ACE2 on the host membrane or the viral spike (S) proteins. To enhance the throughput, microfluidics are integrated for automation and OMEAs are incorporated within each channel, miniaturizing the testing units. This system supports high‐throughput data generation, automation, and scalability, providing an efficient platform for viral fusion detection that advances the study of pathogen‐host interactions and accelerates antiviral drug discovery.« less

REBCO coated conductors have a strong potential for high-field magnet applications. The REBCO technology, however, is still in its infancy for accelerator magnet applications. As part of the U.S. Magnet Development Program (MDP), we developed a six-layer canted cos θ dipole magnet, C3a, using CORC® wires developed by Advanced Conductor Technologies LLC. All the layers were wound using a semi-automated winding machine. Three layers of the magnet used CORC® wires containing the SuperPower “AP” REBCO tapes and the remaining layers used the wires containing the “HM” tapes. At 77 K, both kinds of CORC® wires showed 5% to 10% degradation,more » after bending to a minimum bend radius of 30 or 35 mm, with respect to the self-field critical current measured before winding. At 4.2 K, the magnet reached 9.5 kA at a ramp rate of 9 A s^-1 and generated a dipole field of 1.4 T. Further, the critical current of one layer degraded by 4% after a current transient up to 10.5 kA ramped in an averaged rate of 175 kA s^-1 or 20 T s^-1. We confirmed the HM CORC® wire can carry a higher current than the AP CORC® wire at 4.2 K. The test results of the C3a magnet showed that the fabrication and assembly procedure can be used for the upcoming full-scale C3 magnet.« less

Protein-Protein Interactions (PPIs) are a key interface between virus and host, and these interactions are important to both viral reprogramming of the host and to host restriction of viral infection. In particular, viral-host PPI networks can be used to further our understanding of the molecular mechanisms of tissue specificity, host range, and virulence. At higher scales, viral-host PPI screening could also be used to screen for small-molecule antivirals that interfere with essential viral-host interactions, or to explore how the PPI networks between interacting viral and host genomes co-evolve. Current high-throughput PPI assays have screened entire viral-host PPI networks. However, thesemore » studies are time consuming, often require specialized equipment, and are difficult to further scale. Here, we develop methods that make larger-scale viral-host PPI screening more accessible. This approach combines the mDHFR split-tag reporter with the iSeq2 interaction-barcoding system to permit massively-multiplexed PPI quantification by simple pooled engineering of barcoded constructs, integration of these constructs into budding yeast, and fitness measurements by pooled cell competitions and barcode-sequencing. We applied this method to screen for PPIs between SARS-CoV-2 proteins and human proteins, screening in triplicate >180,000 ORF-ORF combinations represented by >1,000,000 barcoded lineages. Our results complement previous screens by identifying 74 putative PPIs, including interactions between ORF7A with the taste receptors TAS2R41 and TAS2R7, and between NSP4 with the transmembrane KDELR2 and KDELR3. We show that this PPI screening method is highly scalable, enabling larger studies aimed at generating a broad understanding of how viral effector proteins converge on cellular targets to effect replication.« less

The Exabiome project seeks to improve the understanding of microbiomes through the development of methods for accelerating metagenomic science using exascale computing. This article gives an overview of scientific impact of the three components of the project: metagenome assembly, protein family detection, and comparative analysis of metagenomes. Exabiome developed MetaHipMer, the only metagenome assembler capable of scaling to full exascale systems. MetaHipMer has enabled ground-breaking assemblies on the Frontier supercomputer, with many scientific benefits, such as the discovery of rare species and viral genomes. To investigate protein families, Exabiome developed two exascale tools, PASTIS and HipMCL. Together, these can utilizemore » exascale resources to understand the functional diversity of billions of dark matter proteins and novel protein families. For comparative analysis, Exabiome developed kmerprof, a tool that can be used to compare huge metagenomes for many different scientific purposes, for example, grouping human microbiomes according to body location.« less

Ligands are the key to almost any strategy in the assembly of programmable nanocrystals (or nanoparticles) and must be accurately considered in any predictive model. Hard Spheres (or Shapes) provide the simplest and yet quite successful approach to assembly, with remarkable sophisticated predictions verified in experiments. There are, however, many situations where hard spheres/shapes predictions fail. This prompts three important questions: In what situations should hard spheres/shapes models be expected to work? and when they do not work, Is there a general model that successfully corrects hard sphere/shape predictions? and given other successful models where ligands are included explicitly, andmore » of course, numerical simulations, can we unify hard sphere/shape models, explicit ligand models and all atom simulations?. Further, the Orbifold Topological Model (OTM) provides a positive answer to these three questions. In this paper, I give a detailed review of OTM, describing the concept of ligand vortices and how it leads to spontaneous valence and nanoparticle “eigenshapes” while providing a prediction of the lattice structure, without fitting parameters, which accounts for many body effects not captured by (two-body) potentials. I present a thorough survey of experiments and simulations and show that, to this date, they are in full agreement with the OTM predictions. I conclude with a discussion on whether NC superlattices are equilibrium structures and some significant challenges in structure prediction.« less

This Festschrift Virtual Special Issue in The Journal of Physical Chemistry B is dedicated to the scientific contributions of Prof. José Nelson Onuchic. It serves as a celebration of his years of service, mentorship, and leadership to the biological physics, theoretical chemistry, and computational biology communities. This collection of more than 60 articles has been compiled from an extensive network of scientists that have, in distinct ways, been impacted by the scientific legacy of Prof. Onuchic. It is a written testament to how his work has influenced many areas related to the physics and chemistry of biological systems. In conclusion,more » this Festschrift provides a good sample of the areas in that Professor Onuchic has had a direct impact via collaboration, mentorship, and scientific dissemination of his research.« less

Zeolite nanosheets (ZNs) offer improved micropore accessibilities and transport properties for enhanced molecular catalysis and separations. However, practical application of the ZN materials is hampered by the lack of efficient synthesis methods. Here, in this work, a ZN self-seeded method is demonstrated for single-step reproduction of flower-like assemblies of very large MFI ZN plates. The ZN plates are ~60 nm-thick stacks of 4-nm-thick single-crystal sheets. The ZN flower growth involves terrace nucleation on the seed surfaces and subsequent ZN epitaxial growth in [010] orientation directed by a diquaternary agent. The open architecture of the assemblies prevented collapse and agglomeration ofmore » ZNs during thermal activation that effectively preserved the interconnected intra-sheet and inter-sheet micropore system. Thus, the ZN assemblies exhibited markedly enhanced molecular adsorption capacity and transport diffusivity for the probing xylene molecules as compared to the conventional crystals. The ZN assembly and its harvestable very large-sized ZNs have the potential for developing high-performance ZN adsorbents, catalysts, and molecular-sieve membranes.« less

The Mn₄Ca oxygen-evolving complex (OEC) in Photosystem II (PSII) is assembled in situ from free Mn²⁺, Ca²⁺, and water. In an early light-driven step, Mn²⁺ in a protein high-affinity site is oxidized to Mn³⁺. Using dual-mode electron paramagnetic resonance spectroscopy, we observed that Mn³⁺ accumulation increases as chloride concentration increases in spinach PSII membranes depleted of all extrinsic subunits. At physiologically relevant pH values, this effect requires the presence of calcium. Here, when combined with pH studies, we conclude that the first Mn²⁺ oxidation event in OEC assembly requires a deprotonation that is facilitated by chloride.

In order to assess the efficacy of novel HIV-1 treatments leading to a functional cure, the time to viral rebound is frequently used as a surrogate endpoint. The longer the time to viral rebound, the more efficacious the therapy. In support of such an approach, mathematical models serve as a connection between the size of the latent reservoir and the time to HIV-1 rebound after treatment interruption. The simplest of such models assumes that a single successful latent cell reactivation event leads to observable viremia after a period of exponential viral growth. Here we consider a generalization developed by Pinkevychmore » et al. and Hill et al. of this simple model in which multiple reactivation events can occur, each contributing to the exponential growth of the viral load. We formalize and improve the previous derivation of the dynamics predicted by this model, and use the model to estimate relevant biological parameters from SIV rebound data. We confirm a previously described effect of very early antiretroviral therapy (ART) initiation on the rate of recrudescence and the viral load growth rate after treatment interruption. We find that every day ART initiation is delayed results in a 39% increase in the recrudescence rate (95% credible interval: [18%, 62%]), and a 11% decrease of the viral growth rate (95% credible interval: [4%, 20%]). We show that when viral rebound occurs early relative to the viral load doubling time, a model with multiple successful reactivation events fits the data better than a model with only a single successful reactivation event.« less