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At least 793 records · Page 44

Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community

BACKGROUND:It is well-known that global warming has effects on high-latitude tundra underlain with permafrost. This leads to a severe concern that decomposition of soil organic carbon (SOC) previously stored in this region, which accounts for about 50% of the world's SOC storage, will cause positive feedback that accelerates climate warming. We have previously shown that short-term warming (1.5 years) stimulates rapid, microbe-mediated decomposition of tundra soil carbon without affecting the composition of the soil microbial community (based on the depth of 42684 sequence reads of 16S rRNA gene amplicons per 3 g of soil sample). RESULTS:We show that longer-term (5 years) experimental winter warming at the same site altered microbial communities (p < 0.040). Thaw depth correlated the strongest with community assembly and interaction networks, implying that warming-accelerated tundra thaw fundamentally restructured the microbial communities. Both carbon decomposition and methanogenesis genes increased in relative abundance under warming, and their functional structures strongly correlated (R 2 > 0.725, p < 0.001) with ecosystem respiration or CH4 flux. CONCLUSIONS:Our results demonstrate that microbial responses associated with carbon cycling could lead to positive feedbacks that accelerate SOC decomposition in tundra regions, which is alarming because SOC loss is unlikely to subside owing to changes in microbial community composition. Video Abstract.

59 BASIC BIOLOGICAL SCIENCES↗

The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold

Exoribonuclease-resistant RNAs (xrRNAs) are discrete elements that block the progression of 5' to 3' exoribonucleases using specifically folded RNA structures. A recently discovered class of xrRNA is widespread in several genera of plant-infecting viruses, within both noncoding and protein-coding subgenomic RNAs. The structure of one such xrRNA from a dianthovirus revealed three-dimensional details of the resistant fold but did not answer all questions regarding the conservation and diversity of this xrRNA class. Here, we present the crystal structure of a representative polerovirus xrRNA that contains sequence elements that diverge from the previously solved structure. This new structure rationalizes previously unexplained sequence conservation patterns and shows interactions not present in the first structure. Together, the structures of these xrRNAs from dianthovirus and polerovirus genera support the idea that these plant virus xrRNAs fold through a defined pathway that includes a programmed intermediate conformation. This work deepens our knowledge of the structure-function relationship of xrRNAs and shows how evolution can craft similar RNA folds from divergent sequences.

59 BASIC BIOLOGICAL SCIENCES↗

The genotype-phenotype landscape of an allosteric protein

Allostery is a fundamental biophysical mechanism that underlies cellular sensing, signaling, and metabolism. Yet a quantitative understanding of allosteric genotype-phenotype relationships remains elusive. Here, we report the large-scale measurement of the genotype-phenotype landscape for an allosteric protein: the lac repressor from Escherichia coli , LacI. Using a method that combines long-read and short-read DNA sequencing, we quantitatively measure the dose-response curves for nearly 10 5 variants of the LacI genetic sensor. The resulting data provide a quantitative map of the effect of amino acid substitutions on LacI allostery and reveal systematic sequence-structure-function relationships. We find that in many cases, allosteric phenotypes can be quantitatively predicted with additive or neural-network models, but unpredictable changes also occur. For example, we were surprised to discover a new band-stop phenotype that challenges conventional models of allostery and that emerges from combinations of nearly silent amino acid substitutions.

59 BASIC BIOLOGICAL SCIENCES↗

Probing interspecies metabolic interactions within a synthetic binary microbiome using genome-scale modeling

Metabolic interactions within a microbial community play a key role in determining the structure, function, and composition of the community. However, due to the complexity and intractability of natural microbiomes, limited knowledge is available on interspecies interactions within a community. In this work, using a binary synthetic microbiome, a methanotroph-photoautotroph (M-P) coculture, as the model system, we examined different genome-scale metabolic modeling (GEM) approaches to gain a better understanding of the metabolic interactions within the coculture, how they contribute to the enhanced growth observed in the coculture, and how they evolve over time. Using batch growth data of the model M-P coculture, we compared three GEM approaches for microbial communities. Two of the methods are existing approaches: SteadyCom, a steady state GEM, and dynamic flux balance analysis (DFBA) Lab, a dynamic GEM. We also proposed an improved dynamic GEM approach, DynamiCom, for the M-P coculture. SteadyCom can predict the metabolic interactions within the coculture but not their dynamic evolutions; DFBA Lab can predict the dynamics of the coculture but cannot identify interspecies interactions. DynamiCom was able to identify the cross-fed metabolite within the coculture, as well as predict the evolution of the interspecies interactions over time. A new dynamic GEM approach, DynamiCom, was developed for a model M-P coculture. Constrained by the predictions from a validated kinetic model, DynamiCom consistently predicted the top metabolites being exchanged in the M-P coculture, as well as the establishment of the mutualistic N-exchange between the methanotroph and cyanobacteria. The interspecies interactions and their dynamic evolution predicted by DynamiCom are supported by ample evidence in the literature on methanotroph, cyanobacteria, and other cyanobacteria-heterotroph cocultures.

59 BASIC BIOLOGICAL SCIENCES↗

Opportunities for inclusive diffraction at EIC

The possibilities for inclusive diffraction in the Electron Ion Collider, EIC, in the US, are analyzed. We find that thanks to the excellent forward proton tagging, the EIC will be able to access a wider kinematical range of longitudinal momentum fraction and momentum transfer of the leading proton than at HERA. This opens up the possibility to measure subleading diffractive exchanges. The extended t-range would allow the precise extraction of 4-dimensional reduced cross section in diffraction. In addition, the varying beam energy setups at the EIC would allow for precise measurements of the longitudinal diffractive structure function.

Slominski, Wojtek↗

Multidimensional, high precision beam spin asymmetry measurements of semi-inclusive pion production off the proton with CLAS12

High precision measurements of the polarized electron beam-spin asymmetry in SIDIS from the proton have been performed using a 10.6 GeV incident electron beam and the CLAS12 spectrometer at Jefferson Lab. The proceeding reports a multidimensional study of the structure function ratio F^{sin\phi}_{LU}/F_{UU} F L U s i n ϕ / F U U extracted from single pion ( \pi^{+} π + , \pi^{-} π − , \pi^{0} π 0 ) SIDIS data over a large kinematic range in z z , x_{B} x B , P_{T} P T and virtualities Q^{2} Q 2 ranging from 1~GeV ^2 2 up to 7~GeV ^2 2 . F^{sin\phi}_{LU} F L U s i n ϕ is a twist-3 quantity that can reveal novel properties of quark-gluon correlations within the nucleon.

Diehl, Stefan↗

Mechanistic Studies to Enable Aerobic Oxidation of C-H Bonds by Manganese Catalysts (Final Report)

The project Mechanistic Studies to Enable Aerobic Oxidation of C-H Bonds by Manganese Catalysts provided fundamental new insight into the factors affecting hydrocarbon oxidation reactions by manganese-oxo complexes. These insights stem from the development of a structure-function relationship, whereby particular molecular properties of manganese(IV)-oxo complexes were shown to correlate to their efficacy in hydrocarbon oxidation reactions. This work is important, as manganese oxidation catalysts have seen increasing use in synthetic transformations, including reactions relevant to the synthesis of pharmaceuticals and other value-added chemicals. The desirability of developing new manganese catalysts stems from the inexpensive nature and low toxicity of the metal manganese, which contrasts with the high cost and toxicity of many other metals. The work carried out by this project was disseminated to the scientific community in the form of 14 peer-reviewed publications and over twenty presentations. In addition, the research results were incorporated into graduate and undergraduate courses at the University of Kansas, providing additional means of dissemination.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Present and future of JLab CLAS12 physics program

The CLAS12 detector at Jefferson Lab produced the first results in SIDIS and DI-HADRON reactions. Making use of the CEBAF high energy (up to 11 GeV) and highly longitudinal polartized (up to 90%) electron beam will cover unexplored territories in electron-scattering physics. Exclusive reactions on nuclons and nuclei will be measured with high precision in high luminosity (up to 10e35 cm-2s-1) experiments. Mapping out a new class of structure functions, GPDs and TMDs, detecting and reconstructing exotic meson and baryon states and accessing nucleons correlations in nuclei, in the next decade, the CLAS12 rich physics program will provide insight in the complex dynamics of the QCD paving the road to the EIC physics. In this talk, the CLAS12 detector and JLab Hall-B physics program will be described reporting some preliminary results for flag-ship reactions and plans for future upgrades of the detector.

Battaglieri, Marco↗

Spin Structure Program at Jefferson Lab

High performance polarized beam and targets at JLab enabled an extensive program to measure nucleon spin structure functions with high precision. This talk will highlight the recent JLab spin experiments, including the measurement of the neutron spin asymmetry (A1n) in the valance quark (high-x) region and the measurement of the neutron spin moment d2 in medium-high Q2 region to study quark-gluon correlations. Recent results on spin moments at low Q2 (spin sum rules and spin polarizabilities) for both the proton and neutron will also be presented

Chen, Jian-Ping↗

Complete Initial Evaluation of Novel Complexants for Tc Holdback for Simplified Single Cycle Separations.

Management of technetium at the back end of nuclear fuel cycle is complicated by its unique physico-chemical character, but must be addressed to due to the environmental, storage and reprocessing challenges of this fission product. In a single-cycle scenario, the recovery and purification of uranium is particularly challenging due to the tendency of a pertechnetate anion to follow uranyl cation. This report summarizes initial studies directed towards finding the solution for technetium management. Two options for controlling technetium’s chemistry in solvent extraction scenarios were studied. Molecular recognition of pertechnetate by aqueous complexants based on guanidinium moieties was compared to redox manipulation of technetium using dihydrazide reagents. Solvent extraction, potentiometric and nuclear magnetic resonance spectroscopy studies were performed. The influence of guanidinium reagents on the liquid-liquid partitioning of technetium is less pronounced, relative to dihydrazides. Strong impact exerted by dihydrazides originates from the technetium-catalyzed decomposition of such compounds which reduces technetium to a tetravalent, non-extractable state. Although this route of technetium management is very effective the destruction of dihydrazides is undesirable. Guanidinium complexants show a more tempered influence on technetium. The effect on the liquid-liquid partitioning of pertechnetate is evident and likely guided by anion recognition due to ion-pair and hydrogen bond formation. Guanidiniums are stable in presence of technetium as evidenced by nuclear magnetic resonance studies. The steady state chemistry of guanidiniums identify this class of aqueous complexants as solid candidates for structure-function pertechnetate recognition studies.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Optimization of the artificial viscosity in Lagrangian staggered discretization codes. Modeling 1D stand-alone shock - case study

We have developed new measures of errors for numerical shock. The new approach is based on analysis of the structure function, and separation of the errors related to oscillations and shock width, which also include error in the position of the ”center” of the numerical shock. We have demonstrated that those measures correctly characterize the numerical solution. We introduced an objective function in, which both types of errors are weighted, and presented optimal values of the coefficients of the linear and quadratic viscosity for different weights and different Mach numbers.

97 MATHEMATICS AND COMPUTING↗

Common occupational classification system amendments for Accelerator Science and Engineering workforce

A common system to classify occupations and skills is essential to support accelerator workforce planning between the Department of Energy (DOE) National Laboratories. In 2025, ten DOE laboratories conducted a census of their accelerator science and engineering workforce and projected their accelerator workforce needs for the next ten years. To support this, revision 3 of the “Common Occupational Classification System” (COCS) was used as a common taxonomy. Modifications were made to include accelerator-specific skills and specialisms. COCS was originally developed for DOE Office of Environmental Restoration and Waste Management in 1996. The framework provides a high-level functional structure that can be expanded with further occupations and specialisms and remains well aligned to DOE laboratory roles nearly 30 years later. Accelerator occupations and specialisms were added to the framework for the 2025 effort to quantify the accelerator workforce. This document is a companion document to COCS and provides a definition for these new occupations and specialisms that do not appear in COCS. Proceeding with a stable taxonomy is seen as essential such that its use becomes easier each year; the taxonomy as used for the 2025 effort is recommended to be continued.

43 PARTICLE ACCELERATORS↗

Proton Spin from Small-x With Constraints from the Valence Quark Model

We apply the valence quark model to constrain the non-perturbative initial condition for the small-x helicity evolution. The remaining free parameters are constrained by performing a global analysis to the available polarized small-x deep inelastic scattering data. A good description of the world data is obtained with only 8 free parameters. The model parameters are tightly constrained by the data, allowing us to predict the proton polarized structure-function to be negative at small x. Furthermore, we obtain the small-x quark and gluon spins, depending on the applied running coupling prescription.

Adamiak, Daniel [Thomas Jefferson National Acceler↗

Tailored Silicone Network Architecture for Ultimate Mechanical Reinforcement

Hydrosilylation cured silicone elastomers are subject to reaction inefficiency, leading to incomplete and non-uniform crosslink networks, restricting the potential of mechanical reinforcement. This work investigates pre-synthesized, functional PDMS architectures as additives to improve ultimate mechanical performance relative to conventional single-step curing. Three custom, functional structures were prepared: a partially crosslinked PDMS scaffold (Structure A), a bottle-brush PDMS (Structure B), and a star-shaped PDMS derived from an MQ resin (Structure C). Rheological characterization was used to identify the ultimate design space and proper stoichiometric ratio for Structure A, and confirm successful formation of all structures for suitable incorporation into a base silicone formulation at 30wt%. Mechanical tests indicated that all three structures increased in ultimate tensile strength relative to their single-step counterparts, with Structure A providing additional improvements to toughness (432 vs. 258 kJ/m3) and ultimate elongation (158 vs. 115%). Furthermore, Structure B remained very soft in the unfilled state, while Structure C provided hardness (23 vs. 18 Shore A) and stiffness (780 vs. 420 kPa Young’s modulus) increases. In silica filled systems, Structure A retained increased strength but reduced elongation, while Structure B indicated strong reinforcement in terms of strength, toughness, and stiffness. Thermal analysis on the cure profiles of these materials suggested that pre-formation of network architectures enable a more complete reaction than a single-step process (15.9 vs. 15.1 J/g). Ultimately, these results indicate that tailoring PDMS architecture before the final cure can improve ultimate mechanical properties via improved network development in silicone elastomers. Furthermore, this work offers a promising strategy for designing higher-performance, more tunable silicone formulations.

36 MATERIALS SCIENCE↗

Quantum fluctuations of quarks and gluons in nuclei

Acceptance talk for the 2024 Kenneth G. Wilson Award for Excellence in Lattice Field Theory: For key contributions to lattice QCD studies of noise reduction in nuclear systems, the structure of nuclei, and transverse-momentum dependent hadronic structure functions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Using Particle Image Velocimetry to Determine Turbulence Model Parameters

The primary parameter of a standard k-ϵ model, C μ , was calculated from stereoscopic particle image velocimetry (PIV) data for a supersonic jet exhausting into a transonic crossflow. This required the determination of turbulent kinetic energy, turbulent eddy viscosity, and turbulent energy dissipation rate. Image interrogation was optimized, with different procedures used for mean strain rates and Reynolds stresses, to produce useful turbulent eddy viscosity fields. The eddy viscosity was calculated by a least-squares fit to all components of the three-dimensional strain-rate tensor that were available from the PIV data. This eliminated artifacts and noise observed when using a single strain component. Local dissipation rates were determined via Kolmogorov’s similarity hypotheses and the second-order structure function. The eddy viscosity and dissipation rates were then combined to determine C μ . Considerable spatial variation was observed in C μ , with the highest values found in regions where turbulent kinetic energy was relatively low but where turbulent mixing was important, e.g., along the high-strain jet edges and in the wake region. This suggests that use of a constant C μ in modeling may lead to poor Reynolds stress predictions at mixing interfaces. A data-driven modeling approach that can predict this spatial variation of C μ based on known state variables may lead to improved simulation results without the need for calibration.

42 ENGINEERING↗

Proteome-wide characterization of PTMs reveals host cell responses to viral infection and identifies putative antiviral drug targets

Post-translational modifications (PTMs) are biochemical modifications that can significantly alter protein structure, function, stability, localization, and interactions with other molecules, thereby activating or inactivating intracellular processes. A growing body of research has begun to highlight the role of PTMs, including phosphorylation, ubiquitination, acetylation, and redox modifications, during virus-host interactions. Collectively, these PTMs regulate key steps in mounting the host immune response and control critical host pathways required for productive viral replication. This has led to the conception of antiviral therapeutics that focus on controlling host protein PTMs, potentially offering pathogen-agnostic treatment options and revolutionizing our capacity to prevent virus transmission. On the other hand, viruses can hijack the host cellular PTM machinery to modify viral proteins in promoting viral replication and evading immune surveillance. PTM regulation during virus-host interactions is complex and poorly mapped, and the development of effective PTM-targeted antiviral drugs will require a more comprehensive understanding of the cellular pathways essential for virus replication. In this review, we discuss the roles of PTMs in virus infection and how technological advances in mass spectrometry-based proteomics can capture systems-level PTM changes during viral infection. Additionally, we explore how such knowledge is leveraged to identify PTM-targeted candidates for developing antiviral drugs. Looking ahead, studies focusing on the discovery and functional elucidation of PTMs, either on the host or viral proteins, will not only deepen our understanding of molecular pathology but also pave the way for developing better drugs to fight emerging viruses.

Immunology↗

Fe-Exchanged Small-Pore Zeolites as Ammonia Selective Catalytic Reduction (NH 3 -SCR) Catalysts

Cu-exchanged small-pore zeolites have been extensively studied in the past decade as state-of-the-art selective catalytic reduction (SCR) catalysts for diesel engine exhaust NOx abatement for the transportation industry. During this time, Fe-exchanged small-pore zeolites, e.g., Fe/SSZ-13, Fe/SAPO-34, Fe/SSZ-39 and high-silica Fe/LTA, have also been investigated but much less extensively. In comparison to their Cu-exchanged counterparts, such Fe/zeolite catalysts display inferior low-temperature activities, but improved stability and high-temperature SCR selectivities. Such characteristics entitle these catalysts to be considered as key components of highly efficient emission control systems to improve the overall catalyst performance. In this short review, recent studies on Fe-exchanged small-pore zeolite SCR catalysts are summarized, including (1) the synthesis of small-pore Fe/zeolites; (2) nature of the SCR active Fe species in these catalysts as determined by experimental and theoretical approaches, including Fe species transformation during hydrothermal aging; (3) SCR reactions and structure-function correlations; and (4) a few aspects on industrial applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗