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DOE OSTI2021

Computational and Experimental Validation of Fractal-Fin, Dimpled Solar Heat Collector

A 3 foot x 3 foot x 3 foot aluminum solar collector was manufactured using computer numerical control. The interior of the device included six triangular dimpled fins for enhanced heat transfer. The interior vertical wall on the south side was also dimpled. The solar collector working fluid was based on water, and the collector consisted solely of passive heat transfer mechanisms (no moving parts), making it ideal for off-the-grid and rural applications. Two types of heat transfer experiments were conducted. One experiment had external flat heaters attached on the top and the front side, while the other four sides were insulated. Except for the bottom surface, the second experiment had all its exterior surfaces sprayed with black solar paint to collect as much solar heat as possible. Temperature data as a function of time was collected using 14 thermocouples spread strategically throughout the solar collector. In addition, computational fluid dynamics (CFD) simulations were conducted using the dynamic Smagorinsky large eddy simulation turbulence model. The first simulation considered that both the top and front surfaces were exposed to a fixed temperature of 313.7 K (105 °F), while the remaining four surfaces were insulated. For the second simulation, all conditions were the same, except that the temperature for both heated surfaces was raised to 350 K (170.3 °F). The two temperatures are expected to bound the solar collector operational temperature during the late- Spring, Summer, and early-Fall months. The solar collector design, experimental data, CFD output, and a discussion of five manufacturing approaches and costs are documented in this report.

14 SOLAR ENERGY↗

DOE OSTI2022

EJFAT: Towards Intelligent Compute Destination Load Balancing

To handle increased data flow, Jefferson Lab (JLab) is partnering with ESnet for development of an AI/ML directed compute work Load Balancer (LB) of UDP streamed data. The LB is FPGA based featuring dynamically configurable, low latency and high throughput destination address switching. The LB provides integration of edge and core computing to support JLab experimental programs, the Electron-Ion Collider, as well as data centers of the future. In the ESnet/JLab FPGA Accelerated Transport (EJFAT) initiative, the function of the LB Data Plane (DP) is to redirect data streams to selectable (but unknown to sender) destination hosts based on current worload and within that host to destination ports as a function of sub- stream id. This effects hierarchical scaling, first across compute machines for processing over a series of events and second, across ports so different data source sub-streams may be assigned to different processors for further parallelization. The LB Control Plane (CP) programs the DP using compute farm telemetry to direct and balance workloads across a compute cluster as the operating conditions require. While Proportional/Integrative/Derivative (PID) controllers are often seen in similar applications, here we investigate the feasibility of a Reinforcement Learning (RL) based schedule manager running in the CP to provide dynamic updates to the DP scheduling policy.

Lawrence, David↗

DOE OSTI2022

Submersible Multistage Centrifugal Pump for Versatile Test Reactor Cartridge Test Loop

Submersible multistage centrifugal pumps are ideal for pumping in narrow confined spaces and achieving necessary head pressures and flow rates. Once a diameter is determined then manipulation of the number of stages and motor speed are all that are required to meet desired flow conditions. The Versatile Test Reactor (VTR) closed loop cartridge systems will need forced convection cooling independent of the main reactor. A multistage centrifugal pump can meet the necessary flow rates and pumping pressures while minimizing space taken. The pump considered for this work was based off a deep well submersible pump, a variation of a multistage centrifugal pump. We experimented with two pump sizes, 5 cm (2 inch) and 7.5 cm (3 inch) diameters. These diameters were chosen to fit into the inner diameter of standard 5 and 7.5 (2 and 3 inch) Schedule 40 pipe, respectively. This made the design for the test loop both simpler and less expensive as the need for an engineered pump housing was eliminated. Initial test cartridge planning indicated space for only a 5 cm (2 inch) diameter pump, though early testing of this size showed the need for an abnormally high-speed and high-power motor. Fine tuning of the cartridge design allowed a pump size increase to 7.5 cm (3 inches), which was the pump size most extensively tested in this work. The test loop is composed of various sizes of PVC and aluminum piping components in a loop configuration. The pump is driven by a Pittman 250 W (1/3 horsepower) electric motor with maximum speed of 3,450 RPM. Testing consisted of running the pump at a constant motor speed while varying a control valve to restrict flow through the loop, with differential pressure and flow rate recorded. This was done for one and two stage configurations for the 5 cm (2 inch) diameter impeller design and one, two, and three stage configurations for the 7.5 cm (3 inch diameter) impeller design, respectively. Due to pumping power requirements, two and three stage 7.5 cm (3 inch) diameter impeller testing at higher flowrates lowered the motor speed substantially. In regions where motor speed could not be maintained constant, the data were discarded. The test loop was also reconfigured to allow for the pump to be tested for pressure drop in a stalled or inoperable (0 RPM) flow condition. Demonstration of adequate natural convection cooling of the test cartridge fuel type is necessary under accident conditions, and this will depend upon the flow resistance through the impeller assembly when the pump is not operating. Thus, accurate knowledge of the effective impeller assembly loss coefficient is important for safety evaluations. The test loop was modified to provide water inlet and outlets on either side of the pump impeller stack, and a metered flow of lab water was provided in order to measure the pressure drop across the cartridges as a function of flowrate. Data from the pump head curve testing developed as part of this work and supported by analysis using pump head affinity laws indicates that a three stage 7.5 cm (3 inch) pump impeller design will meet target requirements for coolant flow within the VTR cartridge sodium cartridge at full power conditions [1] with margin; this corresponds to a flowrate of 45 l/min (12 gpm) at a pressure drop of 6.1 m (20 feet) of water head. The results of the pressure loss measurements across the impeller assembly when the pump is stationary (i.e., at 0 RPM) indicate that the pressure loss coefficient is 0.921 for a two impeller stack configuration; this value is calculated based on the flow velocity through the minimum available flow area within a single stage of the impeller which corresponds to 1.4 cm2.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2024

A road map to cosmological parameter analysis with third-order shear statistics: III. Efficient estimation of third-order shear correlation functions and an application to the KiDS-1000 data

Context. Third-order lensing statistics contain a wealth of cosmological information that is not captured by second-order statistics. However, the computational effort it takes to estimate such statistics in forthcoming stage IV surveys is prohibitively expensive. Aims. We derive and validate an efficient estimation procedure for the three-point correlation function (3PCF) of polar fields such as weak lensing shear. We then use our approach to measure the shear 3PCF and the third-order aperture mass statistics on the KiDS-1000 survey. Methods We constructed an efficient estimator for third-order shear statistics that builds on the multipole decomposition of the 3PCF. We then validated our estimator on mock ellipticity catalogs obtained from N -body simulations. Finally, we applied our estimator to the KiDS-1000 data and presented a measurement of the third-order aperture statistics in a tomographic setup. Results. Our estimator provides a speedup of a factor of ∼100–1000 compared to the state-of-the-art estimation procedures. It is also able to provide accurate measurements for squeezed and folded triangle configurations without additional computational effort. We report a significant detection of tomographic third-order aperture mass statistics in the KiDS-1000 data (S/N = 6.69). Conclusions. Our estimator will make it computationally feasible to measure third-order shear statistics in forthcoming stage IV surveys. Furthermore, it can be used to construct empirical covariance matrices for such statistics.

Astronomy & Astrophysics↗

DOE OSTI2021

Energy dependent calculations of fission product, prompt, and delayed neutron yields for neutron induced fission on 235 U, 238 U, and 239 Pu

In this article, we perform energy-dependent calculations of independent and cumulative fission product yields for 235 U, 238 U, and 239 Pu in the first chance fission region. Starting with the primary fission fragment distributions taken from available experimental data and analytical functions based on assumptions for the excitation energy and spin-parity distributions, the Hauser-Feshbach statistical decay treatment for fission fragment de-excitation is applied to more than 1,000 fission fragments for the incident neutron energies up to 5 MeV. The calculated independent yields are then used as an input of β-decay calculations to produce the cumulative yield, and summation calculations are performed. Model parameters in these procedures are adjusted by applying the Bayesian technique at the thermal energy for 235 U and 239 Pu and in the fast energy range for 238 U. The calculated fission observable quantities, such as the energy-dependent cumulative yields, and prompt and delayed neutron yields, are compared with available experimental data. We also study the possible impact of the second chance fission opening on the energy dependence of the delayed neutron yield by on the opening of second chance fission on the energy dependence calculation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Strong coupling from hadronic τ -decay data including τ → π − π 0 ν τ from Belle

In previous work we have combined the π − π 0 , 2 π − π + π 0 , and π − 3 π 0 spectral data obtained from hadronic τ decays measured by the ALEPH and OPAL experiments, together with electroproduction data for several of the subleading hadronic modes and data for the K K ¯ mode to construct an inclusive nonstrange vector spectral function entirely based on experimental data, with no Monte-Carlo generated input. In this paper, we include, for the first time, the Belle τ → π − π 0 ν τ high-statistics decay data to construct a new inclusive nonstrange vector spectral function that combines more of the world’s available data. As no Belle data are at present available for the two 4 π modes, this requires a revised data analysis in comparison with our previous work. From the resulting new spectral function, we obtain a new determination of the strong coupling, α s , using our previously developed strategy based on finite-energy sum rules. We find, at the Z mass scale, α s ( m Z 2 ) = 0.1159 ( 14 ) . We discuss the smaller central value and larger error of our new result compared to our previous result, showing the shifts to be due mainly to significant changes in updated HFLAV results for the π − 3 π 0 decay mode. Published by the American Physical Society 2025

Boito, Diogo (ORCID:0000000244267984)↗

DOE OSTI2025

SymbolFit: Automatic Parametric Modeling with Symbolic Regression

We introduce SymbolFit (API: https://github.com/hftsoi/symbolfit), a framework that automates parametric modeling by using symbolic regression to perform a machine-search for functions that fit the data while simultaneously providing uncertainty estimates in a single run. Traditionally, constructing a parametric model to accurately describe binned data has been a manual and iterative process, requiring an adequate functional form to be determined before the fit can be performed. The main challenge arises when the appropriate functional forms cannot be derived from first principles, especially when there is no underlying true closed-form function for the distribution. In this work, we develop a framework that automates and streamlines the process by utilizing symbolic regression, a machine learning technique that explores a vast space of candidate functions without requiring a predefined functional form because the functional form itself is treated as a trainable parameter, making the process far more efficient and effortless than traditional regression methods. We demonstrate the framework in high-energy physics experiments at the CERN Large Hadron Collider (LHC) using five real proton-proton collision datasets from new physics searches, including background modeling in resonance searches for high-mass dijet, trijet, paired-dijet, diphoton, and dimuon events. We show that our framework can flexibly and efficiently generate a wide range of candidate functions that fit a nontrivial distribution well using a simple fit configuration that varies only by random seed, and that the same fit configuration, which defines a vast function space, can also be applied to distributions of different shapes, whereas achieving a comparable result with traditional methods would have required extensive manual effort.

Tsoi, Ho Fung [Univ. of Pennsylvania, Philadelphia↗

DOE OSTI2021

Macroecological distributions of gene variants highlight the functional organization of soil microbial systems

Abstract The recent application of macroecological tools and concepts has made it possible to identify consistent patterns in the distribution of microbial biodiversity, which greatly improved our understanding of the microbial world at large scales. However, the distribution of microbial functions remains largely uncharted from the macroecological point of view. Here, we used macroecological models to examine how the genes encoding the functional capabilities of microorganisms are distributed within and across soil systems. Models built using functional gene array data from 818 soil microbial communities showed that the occupancy-frequency distributions of genes were bimodal in every studied site, and that their rank-abundance distributions were best described by a lognormal model. In addition, the relationships between gene occupancy and abundance were positive in all sites. This allowed us to identify genes with high abundance and ubiquitous distribution (core) and genes with low abundance and limited spatial distribution (satellites), and to show that they encode different sets of microbial traits. Common genes encode microbial traits related to the main biogeochemical cycles (C, N, P and S) while rare genes encode traits related to adaptation to environmental stresses, such as nutrient limitation, resistance to heavy metals and degradation of xenobiotics. Overall, this study characterized for the first time the distribution of microbial functional genes within soil systems, and highlight the interest of macroecological models for understanding the functional organization of microbial systems across spatial scales.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Influence of living grass Roots and endophytic fungal hyphae on soil hydraulic properties

Soil hydraulic properties are often estimated based on laboratory data or pedotransfer functions dependent on soil physical properties, which often do not consider potential impacts of soil roots or fungal hyphae. Here, we first review current knowledge of how these soil biotic components affect hydraulic properties, then we conducted laboratory experiments to specifically test if the presence of roots and mycorrhizal fungi had a significant effect on the hydraulic properties of two soils with contrasting textures: Flint sand and Hamblen silt loam. Soil cores were seeded with (Panicum virgatum) and grown in a greenhouse over three separate growth periods. The endophytic fungus Serendipita indica was injected as liquid inoculant into designated mycorrhizal cores. Saturated hydraulic conductivity (K sat ) measurements were made with a constant head permeameter, and soil water retention curves were obtained by the evaporation method, supplemented at the dry end for Hamblen silt loam with water activity meter data. Retention curve parameters were obtained by fitting the van Genuchten equation to the resulting measurements. Mean root volume ratios were higher in the mycorrhizal inoculated treatment than in the uninoculated treatment for both soils. For Flint sand, analysis of variance revealed that K sat was reduced by the presence of roots as compared to bare soil. This was likely due to roots clogging soil pores. Results also indicated the presence of roots changed the shape of the water retention curve for Flint sand by increasing water content at saturation and by reducing the slope of the curve. These changes suggested roots created additional porosity and broadened the pore-size distribution. The presence of mycorrhizal fungi accentuated the root effects. The influence of roots and mycorrhizal fungi on hydraulic properties was less obvious for the Hamblen silt loam, as none of the treatments differed from each other at p < 0.05. The results highlight the necessity to consider the impact of root and fungal structures on models of soil hydraulic properties.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

A simple method for floating graphene oxide films facilitates nanoscale investigations of ion and water adsorption

Graphene oxide (GO) is a promising material for separations. Nanoscale GO thin films at the air/water interface are excellent experimental models to understand molecular-scale interactions of ions and water with GO. However, the characteristics of GO, such as functional groups and flake size, also affect the thin film properties making it difficult to make systematic studies with GO thin films. This paper reports a simple, reliable, and quick method of preparing ultra-thin GO films, irrespective of their origin, and demonstrates the new opportunities possible with the utilization of this method. The total amount of GO used to form the thin film is significantly less compared to previous examples in the literature, minimizing the dissolved GO in the subphase. X-ray reflectivity (XR) studies show that the majority of the GO film has 1.5 nm thickness over a macroscopic area (~100 cm 2 ) with very small roughness. Sum frequency generation (SFG) spectroscopy measurements show that H 2 O and D 2 O interact differently with GO films, a property that was not observed before. SFG data show that functional groups vary significantly between different commercially available GO samples. The differences are also characterized with XR at high resolution. X-ray fluorescence near total reflection (XFNTR) measurements show that these differences strongly affect ion adsorption and interfacial water behavior near GO, which are vital properties in separation applications. The results pave the way for future studies to elucidate the complex separation mechanisms with GO.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

IRDFF-II: A New Neutron Metrology Library

High quality nuclear data is the most fundamental underpinning for all neutron metrology applications. This paper describes the release of version II of the International Reactor Dosimetry and Fusion File (IRDFF-II) that contains a consistent set of nuclear data for fission and fusion neutron metrology applications up to 60 MeV neutron energy. The library is intended to support: a) applications in research reactors; b) safety and regulatory applications in the nuclear power generation in commercial fission reactors; and c) material damage studies in support of the research and development of advanced fusion concepts. The paper describes the contents of the library, documents the thorough verification process used in its preparation, and provides an extensive set of validation data gathered from a wide range of neutron benchmark fields. The new IRDFF-II library includes 119 metrology reactions, four cover material reactions to support self-shielding corrections, five metrology metrics used by the dosimetry community, and cumulative fission products yields for seven fission products in three different neutron energy regions. In support of characterizing the measurement of the residual nuclei from the dosimetry reactions and the fission product decay modes, the present document lists the recommended decay data, particle emission energies and probabilities for 68 activation products. It also includes neutron spectral characterization data for 29 neutron benchmark fields for the validation of the library contents. Additional six reference fields were assessed (four from plutonium critical assemblies, two measured fields for thermal-neutron induced fission on 233U and 239Pu targets) but not used for validation due to systematic discrepancies in C/E reaction rate values or lack of reaction-rate experimental data. Another ten analytical functions are included that can be useful for calculating average cross sections, average energy, thermal spectrum average cross sections and resonance integrals. The IRDFF-II library and comprehensive documentation is available online at www-nds.iaea.org/IRDFF/. Evaluated cross sections can be compared with experimental data and other evaluations at www-nds.iaea.org/exfor/endf.htm. The new library is expected to become the international reference in neutron metrology for multiple applications.

IAEA IRDFF↗

DOE OSTI2023

Field Demonstration of the Brick Ontology to Scale up the Deployment of ASHRAE Guideline 36 Control Sequences

Many commercial buildings have a vast network of sensors as part of their building automation systems (BAS) that allows opportunities for energy consumption and cost savings by deploying advanced control sequences. However, this resource is often underutilized since BAS are typically programmed with simple control sequences with limited potential to deliver on these opportunities. The recent availability of ASHRAE Guideline 36 (G36) with advanced HVAC control sequences supports control retrofits in existing buildings to unlock much of the savings potential. However, barriers such as the lack of standard naming convention of building assets and data points, proprietary equipment and BAS, and the inherent uniqueness of buildings and their systems prevent building stakeholders from adopting any “plug-and-play” implementation of G36. Instead, control vendors must often undertake the manual and labor-intensive point mapping process to identify a data stream’s functional and spatial relationship within the HVAC system along with other relevant contexts and map it to the new control sequences. The vendor must carry out the point mapping process in each individual building since the mapping is unlikely to port over to another building. Even for the same building, the point mapping process can occur multiple times if various control vendors implement different control retrofits and/or multiple control retrofits happen over the lifecycle of the building. Then, there is the likelihood that G36 control sequences are programmed uniquely to the building, preventing the same implementation from being reused in another. Therefore, this paper presents a field demonstration of how we leveraged the Brick ontology with BACnet, OpenBuildingControl’s Control Description Language (CDL), and open-source support tools to implement scalable and portable advanced building controls. These tools provide standardized semantic descriptions and relationships of the building’s assets and data points (Brick), standardized communication protocol to read from and write to the building’s BAS (BACnet), and standardized code implementations (CDL) of standardized advanced control strategies (G36). We implemented G36’s hot water supply temperature setpoint reset in a Berkeley, CA building for this field demonstration. This field demonstration aims to show how integrating these tools may streamline the deployment of advanced control sequences such as G36 in a consistent manner regardless of differences found across buildings.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2022

Psilocybin: crystal structure solutions enable phase analysis of prior art and recently patented examples

Psilocybin {systematic name: 3-[2-(dimethylamino)ethyl]-1 H -indol-4-yl dihydrogen phosphate} is a zwitterionic tryptamine natural product found in numerous species of fungi known for their psychoactive properties. Following its structural elucidation and chemical synthesis in 1959, purified synthetic psilocybin has been evaluated in clinical trials and has shown promise in the treatment of various mental health disorders. In a recent process-scale crystallization investigation, three crystalline forms of psilocybin were repeatedly observed: Hydrate A, Polymorph A, and Polymorph B. The crystal structure for Hydrate A was solved previously by single-crystal X-ray diffraction. This article presents new crystal structure solutions for the two anhydrates, Polymorphs A and B, based on Rietveld refinement using laboratory and synchrotron X-ray diffraction data, and density functional theory (DFT) calculations. Utilizing the three solved structures, an investigation was conducted via Rietveld method (RM) based quantitative phase analysis (QPA) to estimate the contribution of the three different forms in powder X-ray diffraction (PXRD) patterns provided by different sources of bulk psilocybin produced between 1963 and 2021. Over the last 57 years, each of these samples quantitatively reflect one or more of the hydrate and anhydrate polymorphs. In addition to quantitatively evaluating the composition of each sample, this article evaluates correlations between the crystal forms present, corresponding process methods, sample age, and storage conditions. Furthermore, revision is recommended on characterizations in recently granted patents that include descriptions of crystalline psilocybin inappropriately reported as a single-phase `isostructural variant.' Rietveld refinement demonstrated that the claimed material was composed of approximately 81% Polymorph A and 19% Polymorph B, both of which have been identified in historical samples. In this article, we show conclusively that all published data can be explained in terms of three well-defined forms of psilocybin and that no additional forms are needed to explain the diffraction patterns.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Exploring the role of biotic factors in regulating the spatial variability in land surface phenology across four temperate forest sites

Here, land surface phenology (LSP), the characterization of plant phenology with satellite data, is essential for understanding the effects of climate change on ecosystem functions. Considerable LSP variation is observed within local landscapes, and the role of biotic factors in regulating such variation remains underexplored. In this study, we selected four National Ecological Observatory Network terrestrial sites with minor topographic relief to investigate how biotic factors regulate intra-site LSP variability. We utilized plant functional type (PFT) maps, functional traits, and LSP data to assess the explanatory power of biotic factors for the start and end of season (SOS and EOS) variability. Our results indicate that PFTs alone explain only 0.8–23.4% of intra-site SOS and EOS variation, whereas including functional traits significantly improves explanatory power, with cross-validation correlations ranging from 0.50 to 0.85. While functional traits exhibited diverse effects on SOS and EOS across different sites, traits related to competitive ability and productivity were important for explaining both SOS and EOS variation at these sites. These findings reveal that plants exhibit diverse phenological responses to comparable environmental conditions, and functional traits significantly contribute to intra-site LSP variability, highlighting the importance of intrinsic biotic properties in regulating plant phenology.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Topography and Functional Traits Control the Distribution of Key Shrub Plant Functional Types in Low-Arctic Tundra: Supporting Data

High-resolution classification maps derived from occupied aerial systems (UASs). The UAS data were collected in August 2021 using a Skydio 2+ drone equipped with a 4K resolution red-green-blue (RGB) camera (2024 Skydio Inc) and a 3DR SOLO Quadcopter carried a Parrot Sequoia+ Multispectral Sensor (2023 Parrot Drone SAS). This package includes vegetation classification maps at four locations around Next Generation Ecosystem Experiment Arctic (NGEE Arctic) Council watershed study site on the Seward Peninsula, Alaska. The classification maps were generated using a combination of RGB and canopy height information. The map data and metadata are provided as ENVI image (.dat) and text (.txt, *hdr) formats. Additional map quicklooks are provided as GIS *.kml files. These datasets are provided in support of Yang et al., (In review), “Topography and Functional Traits Control the Distribution of Key Shrub Plant Functional Types in Low-Arctic Tundra”.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a 15-year research effort (2012-2027) to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Quantitative proteomics reveals extensive lysine ubiquitination and transcription factor stability states in Arabidopsis

Abstract Protein activity, abundance, and stability can be regulated by post-translational modification including ubiquitination. Ubiquitination is conserved among eukaryotes and plays a central role in modulating cellular function; yet, we lack comprehensive catalogs of proteins that are modified by ubiquitin in plants. In this study, we describe an antibody-based approach to enrich ubiquitinated peptides coupled with isobaric labeling to enable quantification of up to 18-multiplexed samples. This approach identified 17,940 ubiquitinated lysine sites arising from 6,453 proteins from Arabidopsis (Arabidopsis thaliana) primary roots, seedlings, and rosette leaves. Gene ontology analysis indicated that ubiquitinated proteins are associated with numerous biological processes including hormone signaling, plant defense, protein homeostasis, and metabolism. We determined ubiquitinated lysine residues that directly regulate the stability of three transcription factors, CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1 (CIB1), CIB1 LIKE PROTEIN 2 (CIL2), and SENSITIVE TO PROTON RHIZOTOXICITY1 (STOP1) using in vivo degradation assays. Furthermore, codon mutation of CIB1 to create a K166R conversion to prevent ubiquitination, via CRISPR/Cas9-derived adenosine base editing, led to an early flowering phenotype and increased expression of FLOWERING LOCUS T (FT). These comprehensive site-level ubiquitinome profiles provide a wealth of data for future functional studies related to modulation of biological processes mediated by this post-translational modification in plants.

Biochemistry & Molecular Biology↗

DOE OSTI2021

The N-terminus of varicella-zoster virus glycoprotein B has a functional role in fusion

Varicella-zoster virus (VZV) is a medically important alphaherpesvirus that induces fusion of the virion envelope and the cell membrane during entry, and between cells to form polykaryocytes within infected tissues during pathogenesis. All members of the Herpesviridae , including VZV, have a conserved core fusion complex composed of glycoproteins, gB, gH and gL. The ectodomain of the primary fusogen, gB, has five domains, DI-V, of which DI contains the fusion loops needed for fusion function. We recently demonstrated that DIV is critical for fusion initiation, which was revealed by a 2.8Å structure of a VZV neutralizing mAb, 93k, bound to gB and mutagenesis of the gB-93k interface. To further assess the mechanism of mAb 93k neutralization, the binding site of a non-neutralizing mAb to gB, SG2, was compared to mAb 93k using single particle cryogenic electron microscopy (cryo-EM). The gB-SG2 interface partially overlapped with that of gB-93k but, unlike mAb 93k, mAb SG2 did not interact with the gB N-terminus, suggesting a potential role for the gB N-terminus in membrane fusion. The gB ectodomain structure in the absence of antibody was defined at near atomic resolution by single particle cryo-EM (3.9Å) of native, full-length gB purified from infected cells and by X-ray crystallography (2.4Å) of the transiently expressed ectodomain. Both structures revealed that the VZV gB N-terminus (aa72-114) was flexible based on the absence of visible structures in the cryo-EM or X-ray crystallography data but the presence of gB N-terminal peptides were confirmed by mass spectrometry. Notably, N-terminal residues 109 KSQD 112 were predicted to form a small α-helix and alanine substitution of these residues abolished cell-cell fusion in a virus-free assay. Importantly, transferring the 109 AAAA 112 mutation into the VZV genome significantly impaired viral propagation. These data establish a functional role for the gB N-terminus in membrane fusion broadly relevant to the Herpesviridae .

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Selection function of clusters in Dark Energy Survey year 3 data from cross-matching with South Pole Telescope detections

Context. Galaxy clusters selected based on overdensities of galaxies in photometric surveys provide the largest cluster samples. However, modeling the selection function of such samples is complicated by noncluster members projected along the line of sight (projection effects) and the potential detection of unvirialized objects (contamination). Aims. We empirically constrained the magnitude of these effects by cross-matching galaxy clusters selected in the Dark Energy Survey data with the redMaPPer algorithm with significant detections in three South Pole Telescope surveys (SZ, pol-ECS, pol-500d). Methods. For matched clusters, we augmented the redMaPPer catalog with the SPT detection significance. For unmatched objects we used the SPT detection threshold as an upper limit on the SZe signature. Using a Bayesian population model applied to the collected multiwavelength data, we explored various physically motivated models to describe the relationship between observed richness and halo mass. Results. Our analysis reveals a clear preference for models with an additional skewed scatter component associated with projection effects over a purely log-normal scatter model. We rule out significant contamination by unvirialized objects at the high-richness end of the sample. While dedicated simulations offer a well-fitting calibration of projection effects, our findings suggest the presence of redshift-dependent trends that these simulations may not have captured. Our findings highlight that modeling the selection function of optically detected clusters remains a complicated challenge that requires a combination of simulation and data-driven approaches.

79 ASTRONOMY AND ASTROPHYSICS↗