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DOE OSTI2023

ADP enhances the allosteric activation of eukaryotic elongation factor 2 kinase by calmodulin

Protein translation, one of the most energy-consumptive processes in a eukaryotic cell, requires robust regulation, especially under energy-deprived conditions. A critical component of this regulation is the suppression of translational elongation through reduced ribosome association of the GTPase eukaryotic elongation factor 2 (eEF-2) resulting from its specific phosphorylation by the calmodulin (CaM)-activated α–kinase eEF-2 kinase (eEF-2K). It has been suggested that the eEF-2K response to reduced cellular energy levels is indirect and mediated by the universal energy sensor AMP-activated protein kinase (AMPK) through direct stimulatory phosphorylation and/or downregulation of the eEF-2K-inhibitory nutrient-sensing mTOR pathway. Here, we provide structural, biochemical, and cell-biological evidence of a direct energy-sensing role of eEF-2K through its stimulation by ADP. A crystal structure of the nucleotide-bound complex between CaM and the functional core of eEF-2K phosphorylated at its primary stimulatory site (T348) reveals ADP bound at a unique pocket located on the face opposite that housing the kinase active site. Within this basic pocket (BP), created at the CaM/eEF-2K interface upon complex formation, ADP is stabilized through numerous interactions with both interacting partners. Biochemical analyses using wild-type eEF-2K and specific BP mutants indicate that ADP stabilizes CaM within the active complex, increasing the sensitivity of the kinase to CaM. Induction of energy stress through glycolysis inhibition results in significantly reduced enhancement of phosphorylated eEF-2 levels in cells expressing ADP-binding compromised BP mutants compared to cells expressing wild-type eEF-2K. These results suggest a direct energy-sensing role for eEF-2K through its cooperative interaction with CaM and ADP.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Loads on a Jacket-Supported Wind Turbine During Hurricane Sandy Simulation

Abstract The dynamic response of a jacket-supported offshore wind turbine under coupled wind, wave, and current fields during Hurricane Sandy is the subject of this study. To illustrate the detailed procedure related to the response evaluation of a 5-MW offshore wind turbine with a jacket support structure, we consider a single site where the water depth is 50 m. Loads are computed using two simulation tools, fast and abaqus, with partial coupling. Aerodynamic loads on the turbine rotor are first evaluated using a wind turbine model in fast with a fixed base; then, these rotor aerodynamic loads are applied as point loads at the top of a model of a tower that is supported by a jacket structure in abaqus. On the basis of stochastic simulations, we discuss the applicability of the abaqus jacket modeling and describe the characteristics and comparisons of the aerodynamic and hydrodynamic effects on loads on the jacket members. Details related to the structural model and soil–pile interaction model employed in the analyses are also discussed.

Engineering↗

DOE OSTI2022

Design Guidelines for Deployable Wind Turbines for Defense and Disaster Response Missions

Access to on-site electrical energy is critical to ensuring a successful military or humanitarian response to conflicts and disasters. These missions typically rely on access to liquid fuel that could be vulnerable to disruption or attack during transport. Generating power on location with wind technology can reduce this risk and enhance mission reach by diversifying energy sources. Common characteristics of these missions are short planning and execution time horizons and a global scope of potential locations. Compared to conventional wind turbine applications, defense and disaster response applications place a premium on rapid shipping and installation, short-duration operation (days to months), and quick teardown upon mission completion. These design drivers depart from features found in conventional distributed wind turbines, thus necessitating unique design guidance. The supporting information for this guidance comes from available relevant references, technical analyses, and input from industry and military stakeholders. This poster serves as a summary of project publications which presents the best currently available design guidance for deployable wind turbines to facilitate the effective development and acquisition of technology solutions to support mission success. This Defense and Disaster Deployable Turbine Project (D3T) is a multi-laboratory effort led by Sandia National Laboratories and funded by the U.S. Department of Energy Office of Energy Efficiency and Renewable Energy Wind Energy Technologies Office.

deployable wind↗

DOE OSTI2022

Quantitatively Monitoring Bubble-Flow at a Seep Site Offshore Oregon: Field Trials and Methodological Advances for Parallel Optical and Hydroacoustical Measurements

Two lander-based devices, the Bubble-Box and GasQuant-II, were used to investigate the spatial and temporal variability and total gas flow rates of a seep area offshore Oregon, United States. The Bubble-Box is a stereo camera–equipped lander that records bubbles inside a rising corridor with 80 Hz, allowing for automated image analyses of bubble size distributions and rising speeds. GasQuant is a hydroacoustic lander using a horizontally oriented multibeam swath to record the backscatter intensity of bubble streams passing the swath plain. The experimental set up at the Astoria Canyon site at a water depth of about 500 m aimed at calibrating the hydroacoustic GasQuant data with the visual Bubble-Box data for a spatial and temporal flow rate quantification of the site. For about 90 h in total, both systems were deployed simultaneously and pressure and temperature data were recorded using a CTD as well. Detailed image analyses show a Gaussian-like bubble size distribution of bubbles with a radius of 0.6–6 mm (mean 2.5 mm, std. dev. 0.25 mm); this is very similar to other measurements reported in the literature. Rising speeds ranged from 15 to 37 cm/s between 1- and 5-mm bubble sizes and are thus, in parts, slightly faster than reported elsewhere. Bubble sizes and calculated flow rates are rather constant over time at the two monitored bubble streams. Flow rates of these individual bubble streams are in the range of 544–1,278 mm 3 /s. One Bubble-Box data set was used to calibrate the acoustic backscatter response of the GasQuant data, enabling us to calculate a flow rate of the ensonified seep area (~1,700 m 2 ) that ranged from 4.98 to 8.33 L/min (5.38 × 10 6 to 9.01 × 10 6 CH 4 mol/year). Such flow rates are common for seep areas of similar size, and as such, this location is classified as a normally active seep area. For deriving these acoustically based flow rates, the detailed data pre-processing considered echogram gridding methods of the swath data and bubble responses at the respective water depth. The described method uses the inverse gas flow quantification approach and gives an in-depth example of the benefits of using acoustic and optical methods in tandem.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Specificity determinants revealed by the structure of glycosyltransferase Campylobacter concisus PglA

Abstract In selected Campylobacter species, the biosynthesis of N‐linked glycoconjugates via the pgl pathway is essential for pathogenicity and survival. However, most of the membrane‐associated GT‐B fold glycosyltransferases responsible for diversifying glycans in this pathway have not been structurally characterized which hinders the understanding of the structural factors that govern substrate specificity and prediction of resulting glycan composition. Herein, we report the 1.8 Å resolution structure of Campylobacter concisus PglA, the glycosyltransferase responsible for the transfer of N ‐acetylgalatosamine (GalNAc) from uridine 5′‐diphospho‐ N ‐acetylgalactosamine (UDP‐GalNAc) to undecaprenyl‐diphospho‐ N , N ′‐diacetylbacillosamine (UndPP‐diNAcBac) in complex with the sugar donor GalNAc. This study identifies distinguishing characteristics that set PglA apart within the GT4 enzyme family. Computational docking of the structure in the membrane in comparison to homologs points to differences in interactions with the membrane‐embedded acceptor and the structural analysis of the complex together with bioinformatics and site‐directed mutagenesis identifies donor sugar binding motifs. Notably, E113, conserved solely among PglA enzymes, forms a hydrogen bond with the GalNAc C6″‐OH. Mutagenesis of E113 reveals activity consistent with this role in substrate binding, rather than stabilization of the oxocarbenium ion transition state, a function sometimes ascribed to the corresponding residue in GT4 homologs. The bioinformatic analyses reveal a substrate‐specificity motif, showing that Pro281 in a substrate binding loop of PglA directs configurational preference for GalNAc over GlcNAc. This proline is replaced by a conformationally flexible glycine, even in distant homologs, which favor substrates with the same stereochemistry at C4, such as glucose. The signature loop is conserved across all Campylobacter PglA enzymes, emphasizing its importance in substrate specificity.

Vuksanovic, Nemanja↗

DOE OSTI2025

Response of Subsurface Nitrogen-Cycling Microbial Communities to Environmental Fluctuations (Final Technical Report)

Riparian floodplains are dynamic ecosystems linking terrestrial and riverine systems. These floodplains experience hydrological shifts such as changes in water table height, flooding, and drought and can be ‘hotspots’ of biogeochemical cycling due to shifting sediment moisture (and saturation) and subsurface exchanges of water, nutrients, and other compounds across different sediment layers. Subsurface microbial communities are the primary drivers of biogeochemical processes in floodplains, and thus their structure and function can directly influence both surface and groundwater quality. The microbial nitrogen (N) cycle is particularly important in floodplains as it affects nutrient availability and removal. Two functional guilds of chemoautotrophic (i.e. CO2-fixing) microorganisms are responsible for the first oxidative step of the N cycle, nitrification: ammonia-oxidizing archaea (AOA) and bacteria (AOB) catalyze the oxidation of ammonia to nitrite, while nitrite-oxidizing bacteria (NOB) oxidize nitrite to nitrate. Despite the critical role nitrification plays in N-cycling in both terrestrial and aquatic ecosystems, our understanding of the diversity, ecophysiology, and activity of nitrifying organisms in subsurface floodplain soils/sediments is extremely limited. To help address this critical knowledge gap, the overarching goal of this project was to determine how shifts in key environmental parameters and gradients impact microbial N-cycling communities/processes, with particular emphasis on nitrification, within hydrologically-variable floodplain sediments in the Wind River Basin near Riverton, Wyoming. The three specific objectives of this project were to: (1) to associate in situ environmental drivers of N cycling with distinct functional guilds; (2) determine the guild response to variation in key ecosystem drivers; and (3) develop a dynamic ecosystem model of the microbial N cycle with the Riverton subsurface using community genomic and biogeochemical data collected in the first two objectives. Over the course of this project, we employed both 16S rRNA gene amplicon sequencing and genome-resolved metagenomics to examine the phylogenetic diversity and metabolic potential of subsurface nitrifier communities within 68 samples collected across multiple sites, depths, and time points within the Riverton floodplain, allowing for both spatial and temporal investigations at different scales. This project benefitted tremendously from recent advances in high-throughput sequencing technologies coupled with dramatic improvements in the computational tools and algorithms available for analyzing such large, complex genomic datasets. By pairing these cutting-edge genomic approaches with depth-resolved sampling and detailed geochemical analyses of the Riverton floodplain, we have gained novel insights into the structure and function of subsurface nitrifier communities in relation to both hydrology and biogeochemistry. This project resulted in the most detailed and comprehensive characterization of N-cycling floodplain microbial communities to date and will hopefully inspire and pave the way for future studies using similar approaches in other floodplains. Indeed, such information is critical for understanding subsurface biogeochemical cycling and how elemental stores are altered from perturbations initiated by the water cycle within floodplains. Finally, because of the terrestrial-aquatic nature of the Riverton floodplain, results from this project are also of relevance to disciplines such as soil science, estuarine science, limnology & oceanography, biogeochemistry, geobiology, environmental engineering, as well as genomics and data science.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Analysis of Microbial Communities as Indicators of Microbially Induced Corrosion Potential in Stainless Steel Piping

The 200 West Area Pump-and-Treat (200W P&T) facility is part of the final remedy decision for the 200 ZP-1 Operable Unit (OU) and is the interim remedial action for 200-UP-1 OU at the Hanford Site. The facility also treats water from other sources across the site, including 200-DV-1 OU perched water, groundwater from the 200-BP-5 OU, and leachate from the Environmental Restoration Disposal Facility. The facility originally operated a biological treatment process for nitrate that resulted in systemic biofouling and loss of injection well capacity, requiring frequent and costly well rehabilitation. Biofouling has also contributed to corrosion of welds and pitting of stainless-steel piping at the facility. The biological treatment for nitrate was suspended at the end of 2019 calendar year to eliminate negative impacts from biological treatments which improve facility operations and treatment of carbon tetrachloride. Evaluation of the 200W P&T facility’s response to operational improvements, specifically the suspension of the biological treatment, provides information on the potential for continued microbially induced corrosion (MIC). To this end, historical data sets (2015-2017) were compared with molecular biological analyses of 200W P&T water samples from 2018-2020 to quantify trends in total microbial biomass and specific microbial indicator species (iron, sulfate, nitrate, and manganese reducing bacteria) known to cause and enhance metal corrosion. Results showed unequivocal reductions (in excess of 90%) in all microbiological indicators measured following the suspension of the biological treatment. Although abundance measurements for all corrosive MIC populations initially declined after removal of the treatment system, nitrate-reducing bacteria (nirK) and sulfate-reducing bacteria remain highly abundant in the system, an order of magnitude higher than the number of cells present prior to the removal of the biological treatment system [5.14e (1.4) cells/L, vs. 1.14e (0.07) cells/L, reported as average (±SD) for n=3]. In addition, there was an unexpected inflection point in 2019 where all microbial indicators increased unexpectedly in abundance in 2020 by as much as two orders of magnitude compared to 2019 samples. Given the limited number of water samples available for this analysis, the cause of the increase in microbial indicators post-biological treatment has not yet been determined. Systematic sampling of the facility for continued monitoring is recommended so that the responses of MIC populations can be evaluated to ensure that further corrosion is avoided, allowing the 200W P&T facility to operate safely and efficiently at design capacity.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

Unusual water-assisted NO adsorption over Pd/FER calcined at high temperatures: The effect of cation migration

Moisture contained in vehicle exhaust gas normally degrades the capacity and efficiency of Pd ion-exchanged zeolites as NO x adsorbents by competitive adsorption on active sites. Here, we report a counterexample to this general proposition, in which moisture facilitates the storage of NO as a nitrosyl complex on hydrated Pd ions in high temperature calcined FER-type zeolites. The divalent Pd 2+ cations upon elevated temperature (>800 °C) calcination occupy cationic position that render them fully coordinated by oxygen ions of the zeolite framework, and become inactive for the adsorption of probe molecules such as NO or CO. These ‘hidden’ Pd ions, however, are accessible by NO when the zeolite is hydrated, but readily release NO at around 200°C as dehydration proceeds. Herein, by combining systematic in situ infra-red data with X-ray diffraction Rietveld analyses, we revealed that the high temperature-induced relocation of Pd ions to more stable cationic positions located near 6-membered ring of the ferrierite cage is responsible for this anomalous behavior. This discovery constitutes a notable advance in understanding coordination chemistry of cations in zeolites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Airborne Wind Energy

Airborne wind energy (AWE) is “the conversion of wind energy into electricity using tethered flying devices”. Pursuit of AWE and airborne wind energy systems began in 1980. Interest and investment in AWE have grown substantially in the last decade, with approximately 70 active research entities including over 20 technology developers globally. This report describes technical analyses of various aspects of AWE and insight gained from dedicated outreach provided to the U.S. Department of Energy’s Wind Energy Technologies Office to underpin its response to the congressional request in the Energy Act of 2020 for a report on the “potential for, and technical viability of, airborne wind energy systems to provide a significant source of energy in the United States.”

17 WIND ENERGY↗

DOE OSTI2020

Quantification of the Radiative Effect of Aerosol–Cloud Interactions in Shallow Continental Cumulus Clouds

The indirect radiative effect of aerosol variability on shallow cumulus clouds is realized in nature with considerable concurrent meteorological variability. Large-eddy simulations constrained by observations at a continental site in Oklahoma are performed to represent the variability of different meteorological states on days with different aerosol conditions. The total radiative effect of this natural covariation between aerosol and other meteorological drivers of total cloud amount and albedo is quantified. The changes to these bulk quantities are used to understand the response of the cloud radiative effect to aerosol–cloud interactions (ACI) in the context of concurrent processes, as opposed to attempting to untangle the effect of individual processes on a case-by-case basis. Mutual information (MI) analysis suggests that meteorological variability masks the strength of the relationship between cloud drop number concentration and the cloud radiative effect. This is shown to be mostly due to variation in solar zenith angle and cloud field horizontal heterogeneity masking the relationship between cloud drop number and cloud albedo. By combining MI and more traditional differential analyses, a framework to identify important modes of covariation between aerosol, clouds, and meteorological conditions is developed. This shows that accounting for solar zenith angle variation and implementing an albedo bias correction increases the detectability of the radiative effects of ACI in simulations of shallow cumulus.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

DCFC + Hydrogen Station Design Optimization [Slides]

Both direct current fast charging (DCFC) and Hydrogen stations are working to create successful long-term business models; however, analyses for DCFC and hydrogen fueling infrastructure are almost always performed separately. This work provides a detailed exploration of the benefit of integrating DCFC and hydrogen stations to lower the total system cost from load balancing and equipment cost sharing. To achieve this we have adapted the REopt optimization framework to simultaneously optimize the design and operation of integrated DCFC and H2 fueling station. Results indicate that 1) combining hydrogen fueling and DCFC stations can significantly reduce lifetime costs compared to separated stations. 2) Co-location with additional site load reduces DCFC costs, however, integration of DCFC with hydrogen provides an even greater cost reduction. 3) Adding PV to combined stations further reduces the lifetime station cost. 4) Capital investments in station combination today can help reduce the cost of operating DCFC tomorrow and 5) product diversification acts as a hedge against variability and enables a more dynamic response to market changes.

08 HYDROGEN↗

DOE OSTI2020

Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease

DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a key member of the phosphatidylinositol-3 kinase-like (PIKK) family of protein kinases with critical roles in DNA-double strand break repair, transcription, metastasis, mitosis, RNA processing, and innate and adaptive immunity. The absence of DNA-PKcs from many model organisms has led to the assumption that DNA-PKcs is a vertebrate-specific PIKK. Here, we find that DNA-PKcs is widely distributed in invertebrates, fungi, plants, and protists, and that threonines 2609, 2638, and 2647 of the ABCDE cluster of phosphorylation sites are highly conserved amongst most Eukaryotes. Furthermore, we identify highly conserved amino acid sequence motifs and domains that are characteristic of DNA-PKcs relative to other PIKKs. These include residues in the Forehead domain and a novel motif we have termed YRPD, located in an α helix C-terminal to the ABCDE phosphorylation site loop. Combining sequence with biochemistry plus structural data on human DNA-PKcs unveils conserved sequence and conformational features with functional insights and implications. The defined generally progressive DNA-PKcs sequence diversification uncovers conserved functionality supported by Evolutionary Trace analysis, suggesting that for many organisms both functional sites and evolutionary pressures remain identical due to fundamental cell biology. The mining of cancer genomic data and germline mutations causing human inherited disease reveal that robust DNA-PKcs activity in tumors is detrimental to patient survival, whereas germline mutations compromising function are linked to severe immunodeficiency and neuronal degeneration. We anticipate that these collective results will enable ongoing DNA-PKcs functional analyses with biological and medical implications.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

All the light we cannot see: Climate manipulations leave short and long‐term imprints in spectral reflectance of trees

Abstract Anthropogenic climate change, particularly changes in temperature and precipitation, affects plants in multiple ways. Because plants respond dynamically to stress and acclimate to changes in growing conditions, diagnosing quantitative plant‐environment relationships is a major challenge. One approach to this problem is to quantify leaf responses using spectral reflectance, which provides rapid, inexpensive, and nondestructive measurements that capture a wealth of information about genotype as well as phenotypic responses to the environment. However, it is unclear how warming and drought affect spectra. To address this gap, we used an open‐air field experiment that manipulates temperature and rainfall in 36 plots at two sites in the boreal‐temperate ecotone of northern Minnesota, USA. We collected leaf spectral reflectance (400–2400 nm) at the peak of the growing season for three consecutive years on juveniles (two to six years old) of five tree species planted within the experiment. We hypothesized that these mid‐season measurements of spectral reflectance capture a snapshot of the leaf phenotype encompassing a suite of physiological, structural, and biochemical responses to both long‐ and short‐time scale environmental conditions. We show that the imprint of environmental conditions experienced by plants hours to weeks before spectral measurements is linked to regions in the spectrum associated with stress, namely the water absorption regions of the near‐infrared and short‐wave infrared. In contrast, the environmental conditions plants experience during leaf development leave lasting imprints on the spectral profiles of leaves, attributable to leaf structure and chemistry (e.g., pigment content and associated ratios). Our analyses show that after accounting for baseline species spectral differences, spectral responses to the environment do not differ among the species. This suggests that building a general framework for understanding forest responses to climate change through spectral metrics may be possible, likely having broader implications if the common responses among species detected here represent a widespread phenomenon. Consequently, these results demonstrate that examining the entire spectrum of leaf reflectance for environmental imprints in contrast to single features (e.g., indices and traits) improves inferences about plant‐environment relationships, which is particularly important in times of unprecedented climate change.

Stefanski, Artur [Department of Forest Resources U↗

DOE OSTI2020

Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2

To investigate the evolutionary history of the recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China, a total of 70 genomes of virus strains from China and elsewhere with sampling dates between 24 December 2019 and 3 February 2020 were analyzed. To explore the potential intermediate animal host of the SARS-CoV-2 virus, we reanalyzed virome data sets from pangolins and representative SARS-related coronaviruses isolates from bats, with particular attention paid to the spike glycoprotein gene. We performed phylogenetic, split network, transmission network, likelihood-mapping, and comparative analyses of the genomes. Additionally, based on Bayesian time-scaled phylogenetic analysis using the tip-dating method, we estimated the time to the most recent common ancestor and evolutionary rate of SARS-CoV-2, which ranged from 22 to 24 November 2019 and 1.19 to 1.31 × 10 -3 substitutions per site per year, respectively. Our results also revealed that the BetaCoV/bat/Yunnan/RaTG13/2013 virus was more similar to the SARS-CoV-2 virus than the coronavirus obtained from the two pangolin samples (SRR10168377 and SRR10168378). We also identified a unique peptide (PRRA) insertion in the human SARS-CoV-2 virus, which may be involved in the proteolytic cleavage of the spike protein by cellular proteases, and thus could impact host range and transmissibility. Interestingly, the coronavirus carried by pangolins did not have the RRAR motif. Therefore, we concluded that the human SARS-CoV-2 virus, which is responsible for the recent outbreak of COVID-19, did not come directly from pangolins.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Patchy burn severity explains heterogeneous soil viral and prokaryotic responses to fire in a mixed conifer forest

ABSTRACT Effects of fire on soil viruses and virus–host dynamics are largely unexplored, despite known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we assessed how viral and prokaryotic communities responded to a prescribed burn in a mixed conifer forest. We sequenced 91 viral-size fraction metagenomes (viromes) and 115 16S rRNA gene amplicon libraries from 120 samples: four samples at five timepoints (two before fire and three after fire) at six sites (four treatment, two control). We hypothesized that compositional differences would be most significant between burned and unburned soils, but instead, plot location best distinguished viral communities, more than treatment (burned or not), depth (0–3 or 3–6 cm), or timepoint. For both viruses and prokaryotes, some burned communities resembled unburned controls, while others were significantly different, revealing heterogeneous responses to fire. These patterns were explained by burn severity, here defined by soil chemistry. Viral but not prokaryotic richness decreased significantly with burn severity, and low viromic DNA yields indicated substantial loss of viral biomass at higher severity. The relative abundances of Firmicutes, Actinobacteriota, and the viruses predicted to infect them increased significantly with burn severity, suggesting survival and viral infection of these fire-responsive and potentially spore-forming taxa. The degree of burn severity experienced by each patch of soil, rather than burn status alone, differed over mere meters in the same fire. Therefore, our analyses highlight the importance of high-resolution, paired biogeochemical data to explain soil community responses to fire. IMPORTANCE The impact of fire on the soil microbiome, particularly on understudied soil viral communities, warrants investigation, given known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we collected 120 soil samples before and after a prescribed burn in a mixed conifer forest to assess the impacts of this disturbance on soil viral and prokaryotic communities. We show that simple categorical comparisons of burned and unburned areas were insufficient to reveal the underlying community response patterns. The patchy nature of the fire (indicated by soil chemistry data) led to significant changes in viral and prokaryotic community composition in areas of high burn severity, while communities that experienced lower burn severity were indistinguishable from those in unburned controls. Our results highlight the importance of considering highly resolved burn severity and biogeochemical measurements, even in nearby soils after the same fire, in order to understand soil microbial responses to prescribed burns.

Microbiology↗

DOE OSTI2023

Structure and functional determinants of Rad6–Bre1 subunits in the histone H2B ubiquitin-conjugating complex

The conserved complex of the Rad6 E2 ubiquitin-conjugating enzyme and the Bre1 E3 ubiquitin ligase catalyzes histone H2B monoubiquitination (H2Bub1), which regulates chromatin dynamics during transcription and other nuclear processes. Here, we report a crystal structure of Rad6 and the non-RING domain N-terminal region of Bre1, which shows an asymmetric homodimer of Bre1 contacting a conserved loop on the Rad6 ‘backside’. This contact is distant from the Rad6 catalytic site and is the location of mutations that impair telomeric silencing in yeast. Mutational analyses validated the importance of this contact for the Rad6–Bre1 interaction, chromatin-binding dynamics, H2Bub1 formation and gene expression. Moreover, the non-RING N-terminal region of Bre1 is sufficient to confer nucleosome binding ability to Rad6 in vitro. Interestingly, Rad6 P43L protein, an interaction interface mutant and equivalent to a cancer mutation in the human homolog, bound Bre1 5-fold more tightly than native Rad6 in vitro, but showed reduced chromatin association of Bre1 and reduced levels of H2Bub1 in vivo. These surprising observations imply conformational transitions of the Rad6–Bre1 complex during its chromatin-associated functional cycle, and reveal the differential effects of specific disease-relevant mutations on the chromatin-bound and unbound states. Overall, our study provides structural insights into Rad6–Bre1 interaction through a novel interface that is important for their biochemical and biological responses.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Structure-based group A streptococcal vaccine design: Helical wheel homology predicts antibody cross-reactivity among streptococcal M protein–derived peptides

Group A streptococcus (Strep A) surface M protein, an α-helical coiled-coil dimer, is a vaccine target and a major determinant of streptococcal virulence. The sequence-variable N-terminal region of the M protein defines the M type and also contains epitopes that promote opsonophagocytic killing of streptococci. Recent reports have reported considerable cross-reactivity among different M types, suggesting the prospect of identifying cross-protective epitopes that would constitute a broadly protective multivalent vaccine against Strep A isolates. In this work, we have used a combination of immunological assays, structural biology, and cheminformatics to construct a recombinant M protein–based vaccine that included six Strep A M peptides that were predicted to elicit antisera that would cross-react with an additional 15 nonvaccine M types of Strep A. Rabbit antisera against this recombinant vaccine cross-reacted with 10 of the 15 nonvaccine M peptides. Two of the five nonvaccine M peptides that did not cross-react shared high sequence identity (≥50%) with the vaccine peptides, implying that high sequence identity alone was insufficient for cross-reactivity among the M peptides. Additional structural analyses revealed that the sequence identity at corresponding polar helical-wheel heptad sites between vaccine and nonvaccine peptides accurately distinguishes cross-reactive from non–cross-reactive peptides. On the basis of these observations, we developed a scoring algorithm based on the sequence identity at polar heptad sites. When applied to all epidemiologically important M types, this algorithm should enable the selection of a minimal number of M peptide–based vaccine candidates that elicit broadly protective immunity against Strep A.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

2024 Update of Comprehensive Review of Multi-arm Caliper Data for the Big Hill SPR Site

The Big Hill SPR site has a rich data set consisting of multi-arm caliper (MAC) logs collected from the cavern wells. This data set provides insight into the on-going casing deformation at the Big Hill site. This report summarizes the MAC surveys for each well and presents well longevity estimates where possible. Included in the report is an examination of the well twins for each cavern and a discussion on what may or may not be responsible for the different levels of deformation between some of the well twins. The report also takes a systematic view of the MAC data presenting spatial patterns of casing deformation and deformation orientation in an effort to better understand the underlying causes. The conclusions present a hypothesis suggesting the small-scale variations in casing deformation are attributable to similar scale variations in the character of the salt-caprock interface. These variations do not appear directly related to shear zones or faults. In addition, the deformation orientation shows no preferred directionality. This 2024 edition of this report represents an update to the original, 2023 edition. The updates primarily focus on the inclusion of MAC log data run since the December 2021 threshold date for the original report, but some new analyses are also included.

58 GEOSCIENCES↗