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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Vegetation heterogeneity reflects soil thermal state and surface soil displacement in a thawing permafrost landscape

Thawing permafrost has the potential to dramatically alter the physical and ecological structure of northern landscapes. Warming of the Arctic and subsequent degradation of permafrost have created a need to assess the stability and movement of soils on hillslopes and the potential impacts on ecosystem structure. In this work, we explore the relationships among vegetation heterogeneity, soil temperature, and soil surface displacements observed from 2019 to 2022 in a watershed in the discontinuous permafrost region on the Seward Peninsula of Alaska. Vegetation heterogeneity was measured as the standard deviation (SD) of the normalized difference vegetation index (NDVI) from 3 m PlanetScope satellite imagery around each soil temperature and active layer thickness observation. Locations of observations were clustered into three soil thermal groups, warm, intermediate, and cold, based on soil temperature and active layer thickness. Average annual horizontal surface displacements were significantly lower for soils within the warm thermal group (median = 0.033 m yr −1 ) compared to soils within the cold thermal group (median = 0.090 m yr −1 ; p < 0.001). Conversely, vegetation heterogeneity was significantly higher in the warm (median = 0.014 SD NDVI; p = 0.002) and intermediate (median = 0.015 SD NDVI; p = 0.002) groups compared with the cold thermal group (median = 0.012 SD NDVI), suggesting a warming-induced shift in vegetation community complexity. Because of the observed associations of ground surface displacement rates and vegetation heterogeneity with soil thermal state, we hypothesize that warming soil conditions induce changes in the rates and patterns of hillslope erosion due to an increase in surface movement as near-surface permafrost thaws, followed by a decrease as the permafrost table deepens and excess ice content diminishes. The transition to warm soils promotes surface ecosystem transformation, shifting the dominant vegetation at the site, given the warming climatic conditions of the region. We integrated our observations of soil temperature, vegetation heterogeneity, and soil surface displacements into a conceptual model that describes the co-evolution of hillslopes and vegetation in warming permafrost environments, which is currently unrepresented in earth system models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Landscape analysis of environmental data sources for linkage with SEER cancer patients database

Abstract One of the challenges associated with understanding environmental impacts on cancer risk and outcomes is estimating potential exposures of individuals diagnosed with cancer to adverse environmental conditions over the life course. Historically, this has been partly due to the lack of reliable measures of cancer patients’ potential environmental exposures before a cancer diagnosis. The emerging sources of cancer-related spatiotemporal environmental data and residential history information, coupled with novel technologies for data extraction and linkage, present an opportunity to integrate these data into the existing cancer surveillance data infrastructure, thereby facilitating more comprehensive assessment of cancer risk and outcomes. In this paper, we performed a landscape analysis of the available environmental data sources that could be linked to historical residential address information of cancer patients’ records collected by the National Cancer Institute’s Surveillance, Epidemiology, and End Results Program. The objective is to enable researchers to use these data to assess potential exposures at the time of cancer initiation through the time of diagnosis and even after diagnosis. The paper addresses the challenges associated with data collection and completeness at various spatial and temporal scales, as well as opportunities and directions for future research.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

High-throughput mapping of the phage resistance landscape in E. coli

Bacteriophages (phages) are critical players in the dynamics and function of microbial communities and drive processes as diverse as global biogeochemical cycles and human health. Phages tend to be predators finely tuned to attack specific hosts, even down to the strain level, which in turn defend themselves using an array of mechanisms. However, to date, efforts to rapidly and comprehensively identify bacterial host factors important in phage infection and resistance have yet to be fully realized. Here, we globally map the host genetic determinants involved in resistance to 14 phylogenetically diverse double-stranded DNA phages using two model Escherichia coli strains (K-12 and BL21) with known sequence divergence to demonstrate strain-specific differences. Using genome-wide loss-of-function and gain-of-function genetic technologies, we are able to confirm previously described phage receptors as well as uncover a number of previously unknown host factors that confer resistance to one or more of these phages. We uncover differences in resistance factors that strongly align with the susceptibility of K-12 and BL21 to specific phage. We also identify both phage specific mechanisms, such as the unexpected role of cyclic-di-GMP in host sensitivity to phage N4, and more generic defenses, such as the overproduction of colanic acid capsular polysaccharide that defends against a wide array of phages. Our results indicate that host responses to phages can occur via diverse cellular mechanisms. Our systematic and high-throughput genetic workflow to characterize phage-host interaction determinants can be extended to diverse bacteria to generate datasets that allow predictive models of how phage-mediated selection will shape bacterial phenotype and evolution. The results of this study and future efforts to map the phage resistance landscape will lead to new insights into the coevolution of hosts and their phage, which can ultimately be used to design better phage therapeutic treatments and tools for precision microbiome engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Landscape of pear-shaped even-even nuclei

The phenomenon of reflection-asymmetric nuclear shapes is relevant to nuclear stability, nuclear spectroscopy, nuclear decays and fission, and the search for new physics beyond the standard model. Global surveys of ground-state octupole deformation, performed with a limited number of models, suggest that the number of pear-shaped isotopes is fairly limited across the nuclear landscape. Here, we carry out a global analysis of ground-state octupole deformations for particle-bound even-even nuclei with Z ≤ 110 and N ≤ 210 using nuclear density functional theory (DFT) with several nonrelativistic and covariant energy density functionals. In this way, we can identify the best candidates for reflection-asymmetric shapes. The calculations are performed in the frameworks of axial reflection-asymmetric Hartree-Fock-Bogoliubov theory and relativistic Hartree-Bogoliubov theory using DFT solvers employing harmonic oscillator basis expansion. We consider five Skyrme and four covariant energy density functionals. We predict several regions of ground-state octupole deformation. In addition to the “traditional” regions of neutron-deficient actinide nuclei around 224 Ra and neutron-rich lanthanides around 146 Ba, we identified vast regions of reflection-asymmetric shapes in very neutron-rich nuclei around 200 Gd and 288 Pu, as well as in several nuclei around 112 Ba. Our analysis suggests several promising candidates with stable ground-state octupole deformation, primarily in the neutron-deficient actinide region, that can be reached experimentally. Detailed comparison between Skyrme and covariant models is performed. Octupole shapes predicted in this study are consistent with the current experimental information. This work can serve as the starting point of a systematic search for parity doublets in odd-mass and odd-odd nuclei, which will be of interest in the context of new physics searches.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Natural anomaly mediation from the landscape with implications for LHC SUSY searches

Supersymmetric models with the anomaly-mediated supersymmetry (SUSY) breaking (AMSB) form for soft SUSY breaking terms arise in two different settings: (1) extra-dimensional models where SUSY breaking occurs in a sequestered sector, and (2) 4 − d models with dynamical SUSY breaking in a hidden sector where scalars gain masses of order the gravitino mass m 3 / 2 , but gaugino masses and trilinear soft terms are assumed to be of the AMSB form. Both models run into serious conflicts with (1) LHC sparticle and Higgs mass constraints, (2) constraints from winolike weakly interacting massive particle dark matter searches, and (3) bounds from naturalness. These conflicts may be avoided by introducing minor changes to the underlying phenomenological models consisting of nonuniversal bulk scalar Higgs masses and A terms, providing a setting for natural anomaly mediation (nAMSB). In nAMSB, the wino is still expected to be the lightest of the gauginos, but the Higgsinos are expected to be the lightest electroweakinos (EWinos) in accord with naturalness. We examine what sorts of spectra are expected to emerge when nAMSB arises from a string landscape setting: While model 2 can only be natural for a Higgs mass m h ≲ 123 GeV , model 1 can accommodate naturalness along with m h ∼ 125 GeV while still respecting LHC bounds on sparticle masses. We explore the LHC phenomenology of nAMSB models where we find that for Higgsino pair production, typically larger dilepton mass gaps arise from the soft dilepton-plus-jets signature than in models with gaugino mass unification. For wino-pair production, the higher m 3 / 2 portion of nAMSB parameter space is excluded by recent LHC bounds from gaugino pair production searches. We characterize the dominant LHC signatures arising from the remaining lower m 3 / 2 ∼ 90 – 200 TeV range of parameter space, which should be fully testable at high-luminosity LHC via EWino pair production searches. Published by the American Physical Society 2024

Astronomy & Astrophysics↗
DOE OSTI2020

From canyons to valleys: Numerically continuing sticky-hard-sphere clusters to the landscapes of smoother potentials

Here, we study the energy landscapes of particles with short-range attractive interactions as the range of the interactions increases. Starting with the set of local minima for 6 ≤ $\textit{N}$ ≤ 12 hard spheres that are “sticky,” i.e., they interact only when their surfaces are exactly in contact, we use numerical continuation to evolve the local minima (clusters) as the range of the potential increases, using both the Lennard-Jones and Morse families of interaction potentials. As the range increases, clusters merge, until at long ranges only one or two clusters are left. We compare clusters obtained by continuation with different potentials and find that for short and medium ranges, up to about 30% of particle diameter, the continued clusters are nearly identical, both within and across families of potentials. For longer ranges, the clusters vary significantly, with more variation between families of potentials than within a family. We analyze the mechanisms behind the merge events and find that most rearrangements occur when a pair of nonbonded particles comes within the range of the potential. An exception occurs for nonharmonic clusters, i.e., those that have a zero eigenvalue in their Hessian, which undergo a more global rearrangement.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

A Radiative Transfer Model for Patchy Landscapes Based on Stochastic Radiative Transfer Theory

The availability of global high-resolution land cover maps provides promising a priori knowledge for characterizing subpixel heterogeneity and improving predictions of directional reflectance of coarse-resolution pixels. Due to mutual shadowing and sheltering effects between the adjacent forest and cropland patches, the spectral nonlinear mixing of patchy ecotones is significant, especially when the sun illuminates the ecotone from the forest side with high solar zenith angle. The spectral linear mixture (SLM) approach leads to overestimation of the bidirectional reflectance factor (BRF) in the red band in the principal plane (PP), with a maximum absolute error (MAE) of 0.0063 and a maximum relative error (MRE) of 52.5%, and to underestimation in the near-infrared band in PP with an MAE of 0.0940 and an MRE of 14.5%. In a scenario with randomly distributed boundary orientations, the overestimation of SLM increases with the degree of fragmentation and the view zenith angle. We propose a Radiative Transfer model for patchy ECotones (RTEC). which improves R² from 0.61 to 0.94 in the red band of Landsat-8 directional reflectance at the validation site. The RTEC model provides an efficient and analytical approach for directional reflectance predictions over heterogeneous patchy landscapes at coarse resolution and will be used for biophysical parameter retrievals [e.g., the leaf area index (LAI)] in future applications.

Zeng, Yelu↗
DOE OSTI2020

Bioenergy landscapes drive trophic shifts in generalist ants

Changes in trophic niche—the pathways through which an organism obtains energy and nutrients—are a fundamental way in which organisms respond to environmental conditions. But the capacity for species to alter their trophic niches in response to global change, and the ways they do so when able, remain largely unknown. Here we examine food webs in three long–term and large–scale experiments to test how resource availability and nutritional requirements interact to determine an organism's trophic niche in the context of one of the largest global trends in land use—the rise in bioenergy production. Here, we use carbon and nitrogen stable isotope analyses to characterize arthropod food webs across three biofuel crops representing a gradient in plant resource richness (corn monocultures, fields dominated by native switchgrass and restored prairie), and to quantify changes in the trophic niche of a widespread generalist ant species across habitats. In doing so, we measure the effects of basal resource richness on food chain length, niche breadth and trophic position. We frame our results in the context of two hypotheses that explain variation in trophic niche—the niche variation hypothesis which emphasizes the importance of resource diversity and ecological opportunity, and the optimal diet hypothesis which emphasizes dietary constraints and the availability of optimal resources. Increasing plant richness lengthened food chains by 10%–20% compared to monocultures. Niche breadths of generalist ants did not vary with resource richness, suggesting they were limited by optimal diet requirements and constraints rather than by ecological opportunity. The ants instead responded to changes in plant richness by shifting their estimated trophic position. In resource–poor monocultures, the ants were top predators, sharing a trophic position with predatory spiders. In resource–rich environments, in contrast, the ants were omnivores, relying on a mix of animal prey and plant–based resources. In addition to highlighting novel ecosystem impacts of alternate bioenergy landscapes, our results suggest that niche breadth and trophic diversification depend more on the presence of optimal resources than on ecological opportunity alone.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Landscape responses to intraplate deformation in the Kalahari constrained by sediment provenance and chronology in the Okavango Basin

The structural depression that occupies the Okavango Basin in southern Africa comprises a depo-centre within the intracratonic Kalahari Basin where sediments of the Cenozoic Kalahari Group have accumulated. The Okavango Basin has been formed due to stretching and subsidence at an area of diffused deformation, southwestwards to the main East African Rift System (EARS). Sediments from two full Kalahari Group sequences, located on opposite sides of the Gumare Fault that forms a major fault within the Okavango Basin, were studied to determine their provenance and chronology. Terrestrial Cosmogenic Nuclide (TCN) 26 Al/ 10 Be burial dating was used to constrain a chronostratigraphical framework, and Pb, Sr, and Nd isotopic ratios combined with geochemical and sedimentological analyses were applied to track the source areas of the sediments.Results indicate the following sequence of basin filling: (a) Accumulation between ca. 4–3 Ma during which the currently downthrown (southern) block received a mixture of sediments mostly from the Choma-Kalomo, Ghanzi-Chobe, and Damara terranes, and possibly from the Lufilian Belt and/or Karoo basalts during earlier stages of deposition. Simultaneously, the upthrown (northern) block received sediments from more distant Archean sources in the Zimbabwe and/or Kasai cratons, (b) Hiatus in sedimentation occurred at both sites between ca. 3–2 Ma, (c) Sediments on both sides of the Gumare Fault share a similar source (Angolan Shield) with minor distinct contributions to the downthrown block from the Kasai Craton and local sources input to the upthrown block, and (d) Regional distribution of aeolian sand since at least 1 Ma. The change in source areas is attributed to rearrangements of the drainage systems that were probably linked to vertical crustal movements on the margins of the Okavango Basin. The tectonically induced morphodynamics controlled the landscape evolution of the endorheic basin where vast lakes, wetlands and salt pans have developed through time.

58 GEOSCIENCES↗
DOE OSTI2025

The Carbon Budget of Land Conversion: Sugarcane Expansion and Implications for a Sustainable Bioenergy Landscape in Southeastern United States

The expansion of sugarcane onto land currently occupied by improved (IMP) and semi-native (SN) pastures will reshape the U.S. bioenergy landscape. We combined biometric, ground-based and eddy covariance methods to investigate the impact of sugarcane expansion across subtropical Florida on the carbon (C) budget over a 3-year rotation. With 2.3- and 5.1-fold increase in productivity over IMP and SN pastures, sugarcane displayed a C use efficiency (CUE; i.e., fraction of gross C uptake allocated to plant growth) of 0.59, well above that of pastures (0.31–0.23). Sugarcane also had greater C allocation to aboveground productivity and hence, harvestable biomass relative to IMP and SN. Cane heterotrophic respiration over the 3-year rotation (903 ± 335 gC m −2 year −1 ) was 1% and 14% higher than IMP and SN pastures, respectively. These soil C losses responded largely to disturbance over the first year after conversion (1510 ± 227 gC m −2 year −1 ) but declined in subsequent years to an average 599 ± 90 gC m −2 year −1 —well below those of IMP (933 ± 140 gC m −2 year −1 ) and SN (759 ± 114 gC m −2 year −1 ) pastures—despite a significant 40%–61% increase in soil C inputs. Soil C inputs, however, shifted from root-dominated in pastures to litter-dominated in sugarcane, with only 5% C allocation to roots. Reduced decomposition rates in sugarcane were likely driven by changes in the recalcitrance and distribution rather than the size of the newly incorporated soil C pool. As a result, we observed a rapid shift in the net ecosystem C balance (NECB) of sugarcane from a large source immediately following conversion to approaching the net C losses of IMP pastures only 2 years after conversion. The environmental cost of converting pasture to sugarcane underscores the importance of implementing management practices to harness the soil C storage potential of sugarcane in advancing a sustainable bioeconomy in Southeastern United States.

09 BIOMASS FUELS↗
DOE OSTI2025

Integrated Modeling Driven Evaluation of Opportunities for Climate‐Resilient Perennial Biomass Crop Plantings in Flood‐Prone Agricultural Landscapes

Adapting to future climate change in flood-prone landscapes will require climate-resilient agricultural systems. Planting perennial crops, like switchgrass and willow, along river corridors can mitigate future flooding while supporting bioenergy markets. We developed an integrated assessment linking climate, hydrologic, and inundation model results to assess future flood risk to river-adjacent agricultural lands in the Mid-Atlantic Region (MAR) and explore this opportunity. We produced ensemble streamflow projections for every MAR stream using a hydrologic model driven by a suite of downscaled and bias-corrected Coupled Model Intercomparison Project Phase 6 climate projections. We then conducted high-resolution inundation mapping based on projected flood frequencies for baseline and future periods. Results show that in the near-term future, at least two-thirds of the streams will experience 100-year floods more severe than the baseline 200-year floods. Riparian zones are projected to face a median rise of inundation by 9.5%–24.1%. Results show that there is an opportunity to mitigate flooding in over half of MAR's counties with the quantities of switchgrass and willow plantings anticipated for mature bioenergy markets, even under the most extreme (200-year) flood events. Our integrated modeling framework can guide similar regions to evaluate opportunities for flood-resilient agricultural systems under climate change.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Reestablishing larval connectivity in an estuarine landscape: the importance of shoreline and subtidal oysters ( Crassostrea virginica ) in a comprehensive oyster restoration program

The decline of oyster reefs in estuaries has resulted from a combination of chronic and acute disturbances. The loss has resulted in decreased yield for the oyster fishery as well as a decline in ecological benefits that has led to increased efforts to restore oyster reefs. The need for scientific guidance in accomplishing these restoration goals has become even more pressing in the northcentral Gulf of Mexico in the wake of injury to oyster reefs resulting from the Deepwater Horizon oil spill. Restoration of both the shallow, marsh-fringing oyster aggregations and the deeper subtidal oyster reefs is necessary. Historically, fringing oysters have been overlooked in the oyster habitat landscape because of their limited commercial value. Here, we use a biophysical transport model to examine the transport and settlement of oyster larvae in known oyster reefs along the coast of the northcentral Gulf of Mexico. The modeling demonstrated that the majority of oyster larvae settle within the embayment (>98%) or sub-basin (>65%) of their origin. Additionally, the model demonstrated the importance of fringing oysters as a source of larvae to re-seed other fringing oysters along marsh edges as well as subtidal oyster reefs. We conclude that networks of reefs, including both fringing oyster habitat and subtidal oyster reefs within sub-basins, are necessary to provide resilience to the population at the sub-basin level. Finally, we conclude that fringing oyster habitat may serve as an archipelago-like network to enhance larval supply and connectivity for oysters throughout the mesosaline portions of estuaries.

ADCIRC↗
DOE OSTI2023

Holistic energy landscape management in 2D/3D heterojunction via molecular engineering for efficient perovskite solar cells

Constructing two-dimensional (2D) perovskite atop of 3D with energy landscape management is still a challenge in perovskite photovoltaics. Here, we report a strategy through designing a series of π-conjugated organic cations to construct stable 2D perovskites and to realize delicate energy level tunability at 2D/3D heterojunctions. As a result, the hole transfer energy barriers can be reduced both at heterojunctions and within 2D structures, and the preferable work function shift reduces charge accumulation at interface. Leveraging these insights and also benefitted from the superior interface contact between conjugated cations and poly(triarylamine) (PTAA) hole transporting layer, a solar cell with power conversion efficiency of 24.6% has been achieved, which is the highest among PTAA-based n-i-p devices to the best of our knowledge. The devices exhibit greatly enhanced stability and reproducibility. This approach is generic to several hole transporting materials, offering opportunities to realize high efficiency without using the unstable Spiro-OMeTAD.

14 SOLAR ENERGY↗
DOE OSTI2026

Unraveling design principles of protein landscapes in photosynthetic membranes in plant chloroplasts

The supramolecular organization of proteins within photosynthetic membranes is crucial for energy conversion in plants. Here, we introduce an analytical and computational pipeline that integrates high-resolution cryo–scanning electron microscopy, biochemical quantification, advanced Monte Carlo computer simulations, and statistical methods to elucidate the elusive protein landscapes of grana membranes in intact Arabidopsis leaves. Our integrated analysis challenges the prevailing view that particles on the exoplasmic fracture faces in freeze-fracture samples represent photosystem II exclusively. Instead, these particles also include cytochrome b 6 f complexes. Furthermore, our steric clash analysis demonstrates that stacked membranes contain a mixture of larger PSII supercomplexes (C 2 S 2 M 2 and C 2 S 2 ) in addition to a smaller complex (C 2 ). This suggests that in vivo PSII supercomplexes exist in an equilibrium distribution of differing sizes. Furthermore, we discovered that, although size exclusion effects govern the global protein arrangement, local packing exhibits orientational order indicative of lateral attractive protein-protein interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

SOX2-driven enhancer landscape defines the transcriptional architecture of retinogenesis

Retinal neurogenesis is mediated by the coordinated activities of a complex gene regulatory network (GRN) of transcription factors (TFs) in multipotent retinal progenitor cells (RPCs). How this GRN mechanistically guides neural competence remains poorly understood. In this study, we present integrated transcriptional, genetic and genomic analyses to uncover the regulatory mechanisms of SOX2, a key factor in establishing neural identity in RPCs. We show that SOX2 is preferentially enriched in the RPC-specific enhancer landscape associated with essential regulators of retinogenesis. Disruption of SOX2 expression impairs retinogenesis, marked by a selective loss of enhancer activity near genes essential for RPC proliferation and lineage specification. We identified the RPC transcription factor VSX2 as a binding partner for SOX2 and, together, SOX2 and VSX2 co-target a core, retina-specific chromatin repertoire characterized by enhanced TF binding and robust chromatin accessibility. This cooperative binding establishes a shared SOX2-VSX2 transcriptional code that promotes the expression of crucial regulators of neurogenesis while repressing the acquisition of alternative lineage cell fate. Our data illuminate fundamental biological insights on how transcription factors act in concert to drive chromatin-based genetic programs underlying retinal neural identity.

Chromatin↗
DOE OSTI2022

Land-use intensity of electricity production and tomorrow’s energy landscape

The global energy system has a relatively small land footprint at present, comprising just 0.4% of ice-free land. This pales in comparison to agricultural land use– 30–38% of ice-free land–yet future low-carbon energy systems that shift to more extensive technologies could dramatically alter landscapes around the globe. The challenge is more acute given the projected doubling of global energy consumption by 2050 and widespread electrification of transportation and industry. Yet unlike greenhouse gas emissions, land use intensity of energy has been rarely studied in a rigorous way. Here we calculate land-use intensity of energy (LUIE) for real-world sites across all major sources of electricity, integrating data from published literature, databases, and original data collection. We find a range of LUIE that span four orders of magnitude, from nuclear with 7.1 ha/TWh/y to dedicated biomass at 58,000 ha/TWh/y. By applying these LUIE results to the future electricity portfolios of ten energy scenarios, we conclude that land use could become a significant constraint on deep decarbonization of the power system, yet low-carbon, land-efficient options are available.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2020

Mapping the immunogenic landscape of near-native HIV-1 envelope trimers in non-human primates

The induction of broad and potent immunity by vaccines is the key focus of research efforts aimed at protecting against HIV-1 infection. Soluble native-like HIV-1 envelope glycoproteins have shown promise as vaccine candidates as they can induce potent autologous neutralizing responses in rabbits and non-human primates. In this study, monoclonal antibodies were isolated and characterized from rhesus macaques immunized with the BG505 SOSIP.664 trimer to better understand vaccine-induced antibody responses. Our studies reveal a diverse landscape of antibodies recognizing immunodominant strain-specific epitopes and non-neutralizing neo-epitopes. Additionally, we isolated a subset of mAbs against an epitope cluster at the gp120-gp41 interface that recognize the highly conserved fusion peptide and the glycan at position 88 and have characteristics akin to several human-derived broadly neutralizing antibodies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The genotype-phenotype landscape of an allosteric protein

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

59 BASIC BIOLOGICAL SCIENCES↗