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DOE OSTI2021

Winter roosting ecology of tricolored bats ( Perimyotis subflavus ) in trees and bridges

Abstract Tricolored bats (Perimyotis subflavus) that roost in subterranean hibernacula have experienced precipitous declines from white-nose syndrome (WNS); however, understudied populations also use during winter non-subterranean roosts such as tree cavities, bridges, and foliage. Our objectives were to determine winter roost use by tricolored bats in an area devoid of subterranean roosts, determine roost microclimates to relate them to growth requirements of the fungal causal agent of WNS, and determine habitat factors influencing winter tree selection. From November to March 2017–2019, we used radiotelemetry to track 15 bats to their day roosts in the upper Coastal Plain of South Carolina and recorded microclimates in accessible tree cavities and bridges. We also characterized habitat and tree characteristics of 24 used trees and 153 random, available trees and used discrete choice models to determine selection. Roost structures included I-beam bridges, cavities in live trees, and foliage. Bridges were warmer and less humid than cavities. Roost temperatures often were amenable to fungal growth (< 19.5°C) but fluctuated widely depending on ambient temperatures. Bats used bridges on colder days (8.7°C ± 5.0 SD) and trees on warmer days (11.3°C ± 5.4). Bats selected low-decay trees closer to streams in areas with high canopy closure and cavity abundance. Bats also appeared to favor hardwood forests and avoid pine forests. Our results suggest that access to multiple roost microclimates might be important for tricolored bats during winter, and forest management practices that retain live trees near streams and foster cavity formation in hardwood forests likely will benefit this species. Our results also suggest tricolored bats using bridge and tree roosts might be less susceptible to WNS than bats using subterranean hibernaculum roosts. Thus, forests in areas without subterranean hibernacula in the southeastern United States that support bats during winter might represent important refugia from WNS for multiple species.

Zoology↗

DOE OSTI2023

Investigation of Cu Species in Dealuminated Beta Zeolite Studied by Operando Closed-Cell Gas Reaction STEM

Direct conversion of ethanol to C3+ olefins is an attractive pathway to produce sustainable aviation fuels [1]. We recently reported a copper-containing catalyst supported on dealuminated (DeAl) beta zeolite that is capable of catalyzing cascade ethanol to olefins reactions with high olefins selectivity (88% C3+ olefin selectivity at 100% ethanol conversion). However, one of the deactivation mechanisms of the catalyst is copper sintering [2]. It was found that copper agglomerates can be redispersed through a simple oxidative treatment. To better understand the kinetics and process conditions conducive to redispersion, we studied the atmosphere and temperature dependent Cu species in Cu/DeAl-Beta catalyst under conditions matching those of the working catalyst.

beta zeolite↗

DOE OSTI2023

Asteroseismological analysis of the polluted ZZ Ceti star G 29 – 38 with TESS

G29 – 38 (TIC 422526868) is one of the brightest (V = 13.1) and closest (d = 17.51 pc) pulsating white dwarfs with a hydrogen-rich atmosphere (DAV/ZZ Ceti class). It was observed by the TESS spacecraft in sectors 42 and 56. The atmosphere of G 29 – 38 is polluted by heavy elements that are expected to sink out of visible layers on short time-scales. Here, the photometric TESS data set spans ~51 d in total, and from this, we identified 56 significant pulsation frequencies, that include rotational frequency multiplets. In addition, we identified 30 combination frequencies in each sector. The oscillation frequencies that we found are associated with g-mode pulsations, with periods spanning from ~ 260 to ~ 1400 s. We identified rotational frequency triplets with a mean separation δν ℓ = 1 of 4.67 μHz and a quintuplet with a mean separation δν ℓ = 2 of 6.67 μHz, from which we estimated a rotation period of about 1.35 ± 0.1 d. We determined a constant period spacing of 41.20 s for ℓ = 1 modes and 22.58 s for ℓ = 2 modes. We performed period-to-period fit analyses and found an asteroseismological model with M * /M ⊙ = 0.632 ± 0.03, K, and log g = 8.048 ± 0.005 (with a hydrogen envelope mass of M H ~ 5.6 × 10 –5 M * ), in good agreement with the values derived from spectroscopy. We obtained an asteroseismic distance of 17.54 pc, which is in excellent agreement with that provided by Gaia (17.51 pc).

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Mechanism of efficient double-strand break repair by a long non-coding RNA

The Authors wish to correct an error in Figure 6. In Figure 6B the panel label should read ‘Ku + DNA-PKcs + LINP1, 6 kbp bridge’ instead of ‘Ku + DNA-PKcs + PAXX, 6 kbp bridge’. The published article has been updated. This error does not affect the conclusions of the article.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Mechanism of efficient double-strand break repair by a long non-coding RNA

Mechanistic studies in DNA repair have focused on roles of multi-protein DNA complexes, so how long non-coding RNAs (lncRNAs) regulate DNA repair is less well understood. Yet, lncRNA LINP1 is over-expressed in multiple cancers and confers resistance to ionizing radiation and chemotherapeutic drugs. Here, we unveil structural and mechanistic insights into LINP1’s ability to facilitate non-homologous end joining (NHEJ). We characterized LINP1 structure and flexibility and analyzed interactions with the NHEJ factor Ku70/Ku80 (Ku) and Ku complexes that direct NHEJ. LINP1 self-assembles into phase-separated condensates via RNA–RNA interactions that reorganize to form filamentous Ku-containing aggregates. Structured motifs in LINP1 bind Ku, promoting Ku multimerization and stabilization of the initial synaptic event for NHEJ. Significantly, LINP1 acts as an effective proxy for PAXX. Collective results reveal how lncRNA effectively replaces a DNA repair protein for efficient NHEJ with implications for development of resistance to cancer therapy.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Caught in motion: human NTHL1 undergoes interdomain rearrangement necessary for catalysis

Abstract Base excision repair (BER) is the main pathway protecting cells from the continuous damage to DNA inflicted by reactive oxygen species. BER is initiated by DNA glycosylases, each of which repairs a particular class of base damage. NTHL1, a bifunctional DNA glycosylase, possesses both glycolytic and β-lytic activities with a preference for oxidized pyrimidine substrates. Defects in human NTHL1 drive a class of polyposis colorectal cancer. We report the first X-ray crystal structure of hNTHL1, revealing an open conformation not previously observed in the bacterial orthologs. In this conformation, the six-helical barrel domain comprising the helix-hairpin-helix (HhH) DNA binding motif is tipped away from the iron sulphur cluster-containing domain, requiring a conformational change to assemble a catalytic site upon DNA binding. We found that the flexibility of hNTHL1 and its ability to adopt an open configuration can be attributed to an interdomain linker. Swapping the human linker sequence for that of Escherichia coli yielded a protein chimera that crystallized in a closed conformation and had a reduced activity on lesion-containing DNA. This large scale interdomain rearrangement during catalysis is unprecedented for a HhH superfamily DNA glycosylase and provides important insight into the molecular mechanism of hNTHL1.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters

Abstract With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

A scanning-to-incision switch in TFIIH-XPG induced by DNA damage licenses nucleotide excision repair

Nucleotide excision repair (NER) is critical for removing bulky DNA base lesions and avoiding diseases. NER couples lesion recognition by XPC to strand separation by XPB and XPD ATPases, followed by lesion excision by XPF and XPG nucleases. Here, we describe key regulatory mechanisms and roles of XPG for and beyond its cleavage activity. Strikingly, by combing single-molecule imaging and bulk cleavage assays, we found that XPG binding to the 7-subunit TFIIH core (coreTFIIH) stimulates coreTFIIH-dependent double-strand (ds)DNA unwinding 10-fold, and XPG-dependent DNA cleavage by up to 700-fold. Simultaneous monitoring of rates for coreTFIIH single-stranded (ss)DNA translocation and dsDNA unwinding showed XPG acts by switching ssDNA translocation to dsDNA unwinding as a likely committed step. Pertinent to the NER pathway regulation, XPG incision activity is suppressed during coreTFIIH translocation on DNA but is licensed when coreTFIIH stalls at the lesion or when ATP hydrolysis is blocked. Moreover, ≥15 nucleotides of 5'-ssDNA is a prerequisite for efficient translocation and incision. Our results unveil a paired coordination mechanism in which key lesion scanning and DNA incision steps are sequentially coordinated, and damaged patch removal is only licensed after generation of ≥15 nucleotides of 5'-ssDNA, ensuring the correct ssDNA bubble size before cleavage.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

The Human Phenotype Ontology in 2024: phenotypes around the world

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

EEPD1 evolved a unique DNA clamping dimer protecting reversed replication forks

Exonuclease/endonuclease/phosphatase (EEP)-fold hydrolases are canonically monomeric phosphodiesterases exemplified by APE1, DNase I, and TDP2 nucleases. While EEP family domain containing protein 1 (EEPD1) acts in DNA stress responses, its proposed nuclease activities are enigmatic. Here, we integrate hybrid structural methods, evolution, biochemistry, cancer genomics, plus molecular and cell biology to define EEPD1 structure, assembly, and function at stalled DNA replication forks. Results imply EEPD1 surprisingly requires both unique EEP domain dimer and distinctive tandem Helix-hairpin-Helix [(HhH) 2 ] domains to clamp double-stranded (ds) DNA at reversed DNA replication forks for fork protection. Small-angle X-ray Scattering (SAXS), crystal, and cryo-EM structures unveil an unprecedented tryptophan handshake dimer, conserved interface di-Trp-Pro pocket, and adjustable “wrist” enabling an open-closed conformational switch. EEPD1 dimer cooperatively binds complex dsDNA replication fork intermediates but alone lacks nuclease activity due to loss of key EEP catalytic residues during Metazoan evolution and atmospheric oxygen buildup. Instead, EEPD1 prevents nucleolytic degradation of reversed replication forks by MRE11. Furthermore, cancer bioinformatics support oxidative damage-dependent EEPD1 association as a significant modulator of overall patient survival. Collective findings uncover unexpected EEP dimer and fork protection function in clamping, not cleaving, reversed replication forks for metazoan oxidative stress responses controlling genome stability and cancer outcomes.

Shen, Runze [Univ. of Texas, Houston, TX (United S↗

DOE OSTI2022

Altered properties and structures of root exudate polysaccharides in a root hairless mutant of barley

Root exudates and rhizosheaths of attached soil are important features of growing roots. To elucidate factors involved in rhizosheath formation, wild-type (WT) barley (Hordeum vulgare L. cv. Pallas) and a root hairless mutant, bald root barley (brb), were investigated with a combination of physiological, biochemical, and immunochemical assays. When grown in soil, WT barley roots bound ~5-fold more soil than brb per unit root length. High molecular weight (HMW) polysaccharide exudates of brb roots had less soil-binding capacity than those of WT root exudates. Carbohydrate and glycan monoclonal antibody analyses of HMW polysaccharide exudates indicated differing glycan profiles. Relative to WT plants, root exudates of brb had reduced signals for arabinogalactan-protein (AGP), extensin, and heteroxylan epitopes. In contrast, the root exudate of 2-week-old brb plants contained ~25-fold more detectable xyloglucan epitope relative to WT. Root system immunoprints confirmed the higher levels of release of the xyloglucan epitope from brb root apices and root axes relative to WT. Epitope detection with anion-exchange chromatography indicated that the increased detection of xyloglucan in brb exudates was due to enhanced abundance of a neutral polymer. Conversely, brb root exudates contained decreased amounts of an acidic polymer, with soil-binding properties, containing the xyloglucan epitope and glycoprotein and heteroxylan epitopes relative to WT. We, therefore, propose that, in addition to physically structuring soil particles, root hairs facilitate rhizosheath formation by releasing a soil-binding polysaccharide complex.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

DNA Sequence-Based Identification of Fusarium : A Work in Progress

Accurate species-level identification of an etiological agent is crucial for disease diagnosis and management because knowing the agent’s identity connects it with what is known about its host range, geographic distribution, and toxin production potential. This is particularly true in publishing peer-reviewed disease reports, where imprecise and/or incorrect identifications weaken the public knowledge base. This can be a daunting task for phytopathologists and other applied biologists that need to identify Fusarium in particular, because published and ongoing multilocus molecular systematic studies have highlighted several confounding issues. Paramount among these are: (i) this agriculturally and clinically important genus is currently estimated to comprise more than 400 phylogenetically distinct species (i.e., phylospecies), with more than 80% of these discovered within the past 25 years; (ii) approximately one-third of the phylospecies have not been formally described; (iii) morphology alone is inadequate to distinguish most of these species from one another; and (iv) the current rapid discovery of novel fusaria from pathogen surveys and accompanying impact on the taxonomic landscape is expected to continue well into the foreseeable future. To address the critical need for accurate pathogen identification, our research groups are focused on populating two web-accessible databases (FUSARIUM-ID v.3.0 and the nonredundant National Center for Biotechnology Information nucleotide collection that includes GenBank) with portions of three phylogenetically informative genes (i.e., TEF1, RPB1, and RPB2) that resolve at or near the species level in every Fusarium species. The objectives of this Special Report, and its companion in this issue ( Torres-Cruz et al. 2022 ), are to provide a progress report on our efforts to populate these databases and to outline a set of best practices for DNA sequence-based identification of fusaria.

Plant Sciences↗

DOE OSTI2024

A Metabolomics Assay to Diagnose Citrus Huanglongbing Disease and to Aid in Assessment of Treatments to Prevent or Cure Infection

Citrus greening disease, or Huanglongbing (HLB), has devastated citrus crops globally in recent years. The causal bacterium, ‘ Candidatus Liberibacter asiaticus’, presents a sampling issue for qPCR diagnostics and results in a high false negative rate. In this work, we compared six metabolomics assays to identify HLB-infected citrus trees from leaf tissue extracted from 30 control and 30 HLB-infected trees. A liquid chromatography-mass spectrometry-based assay was most accurate. A final partial least squares-discriminant analysis (PLS-DA) model was trained and validated on 690 leaf samples with corresponding qPCR measures from three citrus varieties (Rio Red grapefruit, Hamlin sweet orange, and Valencia sweet orange) from orchards in Florida and Texas. Trees were naturally infected with HLB transmitted by the insect vector Diaphorina citri. In a randomized validation set, the assay was 99.9% accurate to classify diseased from nondiseased samples. This model was applied to samples from trees receiving plant defense-inducer compounds or biological treatments to prevent or cure HLB infection. From two trials, HLB-related metabolite abundances and PLS-DA scores were tracked longitudinally and compared with those of control trees. We demonstrate how our assay can assess tree health and the efficacy of HLB treatments and conclude that no trialed treatment was efficacious.

Plant Sciences↗

DOE OSTI2022

The local wavenumber model for computation of turbulent mixing

We present an overview of the current status in the development of a two-point spectral closure model for turbulent flows, known as the local wavenumber (LWN) model. The model is envisioned as a practical option for applications requiring multi-physics simulations in which statistical hydrodynamics quantities such as Reynolds stresses, turbulent kinetic energy, and measures of mixing such as density-correlations and mix-width evolution, need to be captured with relatively high fidelity. In this review, we present the capabilities of the LWN model since it was first formulated in the early 1990s, for computations of increasing levels of complexity ranging from homogeneous isotropic turbulence, inhomogeneous and anisotropic single-fluid turbulence, to two-species mixing driven by buoyancy forces. The review concludes with a discussion of some of the more theoretical considerations that remain in the development of this model.

42 ENGINEERING↗

DOE OSTI2024

Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships

A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here, we present the culmination of the efforts of the modENCODE (model organism Encyclopedia of DNA Elements) and modERN (model organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms,Drosophila melanogaster(fly) andCaenorhabditis elegans(worm). These data sets comprise 605 TFs identifying 3.6 M sites in the fly and 356 TFs identifying 0.9 M sites in the worm, and represent the majority of the regulatory space in each genome. We demonstrate that TFs associate with chromatin in clusters termed “metapeaks,” that larger metapeaks have characteristics of high-occupancy target (HOT) regions, and that the importance of consensus sequence motifs bound by TFs depends on metapeak size and complexity. Combining ChIP-seq data with single-cell RNA-seq data in a machine-learning model identifies TFs with a prominent role in promoting target gene expression in specific cell types, even differentiating between parent–daughter cells during embryogenesis. These data are a rich resource for the community that should fuel and guide future investigations into TF function. To facilitate data accessibility and utility, all strains expressing green fluorescent protein (GFP)-tagged TFs are available at the stock centers for each organism. The chromatin immunoprecipitation sequencing data are available through the ENCODE Data Coordinating Center, GEO, and through a direct interface that provides rapid access to processed data sets and summary analyses, as well as widgets to probe the cell-type-specific TF–target relationships.

Biochemistry & Molecular Biology↗

DOE OSTI2025

Noise-aware circuit compilations for a continuously parameterized two-qubit gateset

State-of-the-art noisy-intermediate-scale quantum processors are currently implemented across a variety of hardware platforms, each with their own distinct gatesets. As such, circuit compilation should not only be aware of but also deeply connect to the native gateset and noise properties of each. Trapped-ion processors are one such platform that provides a gateset that can be continuously parameterized across both one- and two-qubit gates. Here we use the Quantum Scientific Computing Open User Testbed to study noise-aware compilations focused on continuously parameterized two-qubit 𝑍⁢𝑍 gates (based on the Mølmer-Sørensen interaction) using $\scriptsize{SUPERSTAQ}$, a quantum software platform for hardware-aware circuit compiler optimizations. We discuss the realization of 𝑍⁢𝑍 gates with arbitrary angle on the all-to-all connected trapped-ion system. Then we discuss a variety of different compiler optimizations that innately target these 𝑍⁢𝑍 gates and their noise properties. These optimizations include moving from a restricted maximally entangling gateset to a continuously parameterized one, swap mirroring to further reduce the total entangling angle of the operations, focusing the heaviest 𝑍⁢𝑍 angle participation on the best-performing gate pairs, and circuit approximation to remove the least impactful 𝑍⁢𝑍 gates. We demonstrate these compilation approaches on the hardware with randomized quantum volume circuits, observing the potential to realize a larger quantum volume as a result of these optimizations. Using differing yet complementary analysis techniques, we observe the distinct improvements in system performance provided by these noise-aware compilations and study the role of stochastic and coherent error channels for each compilation choice.

Noise↗

DOE OSTI2026

Indirect tunneling enabled spontaneous time-reversal symmetry breaking and Josephson diode effect in TiN/Al 2 ⁢O 3 /Hf 0.8 ⁢Zr 0.2 ⁢O 2 /Nb tunnel junctions

Josephson diode (JD) effect in Josephson tunnel junctions (JTJs) has attracted a great deal of attention due to its importance for developing superconducting-circuitry-based quantum technologies. Even though the preparation of high-quality JTJs by techniques employed in the semiconductor industry has been demonstrated, which was an important milestone because JTJs are the building blocks of superconducting electronics even before the quantum era, the JD effect has not been accomplished in them, nor has the highly desirable electrical control of the effect. We report here the fabrication of JTJs featuring a composite tunnel barrier of Al 2 ⁢O 3 and Hf 0.8 ⁢Zr 0.2 ⁢O 2 using complementary-metal-oxide-semiconductor compatible atomic layer deposition. These JTJs were found to show the JD effect in nominally zero magnetic fields with nonreciprocity controllable via an electric training current, yielding a surprisingly large diode efficiency. The quasiparticle tunneling, through which the Josephson coupling in a JTJ is established, was found to show theoretically expected gap features but no nonreciprocity. We attribute these observations to the simultaneous presence of positive and negative local Josephson couplings in the JTJs, with the negative Josephson coupling originating from indirect tunneling, which results in spontaneous time-reversal symmetry breaking. Finally, the double-minima washboard potential for the ensemble-averaged phase difference in the resistively and capacitively shunted junction model is shown to fully account for the experimentally observed JD effect.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2026

Solovay-Kitaev algorithm and randomized compilation

This paper discusses a technique for randomizing over synthesized one-qubit gate sequences in order to mitigate coherent errors in fault-tolerant circuits. We present simulated and experimental data showing that randomization can reduce the trace distance to the target state.

Widzowski Maupin, Oliver Gabriel [Sandia National ↗