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At least 685 records · Page 38

Impacts of Pasture Conversion to Sugarcane on Water Fluxes and Water Use Efficiency in the Southeastern US

The expansion of sugarcane (cane), a high-yielding perennial crop, will likely reshape the bioenergy landscape in the Southeastern US. However, its ecohydrological implications, particularly following conversion from grazed pastures, a dominant land use in the region, remain highly uncertain. We investigated the impact of cane expansion on evapotranspiration (ET) and its partitioning, and the mechanisms influencing both ET components and water use efficiency (WUE) across multiple scales and growth cycles in subtropical Florida. We combined eddy covariance, biometric measurements, and process-based stomatal conductance (g s ) models. ET was 1.7% lower in cane than in improved pasture (IMP) but exceeded that in semi-native pasture (SN) by 21%. Transpiration (T) followed a similar pattern, consistent with lower g s in cane relative to IMP. Cane had more conservative water use and greater sensitivity of g s to vapor pressure deficit (VPD) compared to IMP pasture, suggesting cane may be more tolerant of increasing atmospheric water demand. In contrast, SN showed lower g s and weaker stomatal sensitivity to VPD compared to cane, resulting in lower T. In cane, stomatal regulation and T varied across growth cycles, with stomata becoming less water conservative as stands matured, highlighting the importance of incorporating stand age-dependent stomatal regulation into hydrological models. Evaporation (E) was higher in cane than pastures (19%–26%), partially offsetting WUE gains. Cane exhibited higher intrinsic WUE (GPP/g s ; Gross Primary Productivity), ecosystem WUE (GPP/ET), and harvest WUE (harvest/ET) than both pasture types. Large-scale pasture-to-cane conversion could produce widely contrasting hydrological outcomes. The net regional impact will depend on the proportion of each pasture type converted and on cane's high g s sensitivity to VPD, which triggers tight stomatal regulation and conservative water use, both of which will become increasingly consequential under intensifying atmospheric water demand.

bioenergy↗

Benefits and Cautions in Data Assimilation Strategies: An Example of Modeling Groundwater Recharge

Assimilating recent observations improves model outcomes for real-time assessments of groundwater processes. This is demonstrated in estimating time-varying recharge to a shallow fractured-rock aquifer in response to precipitation. Results from estimating the time-varying water-table altitude (h) and recharge, and their error covariances, are compared for forecasting, filtering, and fixed-lag smoothing (FLS), which are implemented using the Kalman Filter as applied to a data-driven, mechanistic model of recharge. Forecasting uses past observations to predict future states and is the current paradigm in most groundwater modeling investigations; filtering assimilates observations up to the current time to estimate current states; and FLS estimates states following a time lag over which additional observations are collected. Results for forecasting yield a large error covariance relative to the magnitude of the expected recharge. With assimilating recent observations of h, filtering and FLS produce estimates of recharge that better represent time-varying observations of h and reduce uncertainty in comparison to forecasting. Although model outcomes from applying data assimilation through filtering or FLS reduce model uncertainty, they are not necessarily mass conservative, whereas forecasting outcomes are mass conservative. Mass conservative outcomes from forecasting are not necessarily more accurate, because process errors are inherent in any model. Improvements in estimating real-time groundwater conditions that better represent observations need to be weighed for the model application against outcomes with inherent process deficiencies. In conclusion, results from data assimilation strategies discussed in this investigation are anticipated to be relevant to other groundwater processes models where system states are sensitive to system inputs.

aquifer recharge↗

Genome-wide DNA methylation patterns harbour signatures of hatchling sex and past incubation temperature in a species with environmental sex determination

Conservation of thermally sensitive species depends on monitoring organismal and population-level responses to environmental change in real time. Epigenetic processes are increasingly recognized as key integrators of environmental conditions into developmentally plastic responses, and attendant epigenomic data sets hold potential for revealing cryptic phenotypes relevant to conservation efforts. Here, we demonstrate the utility of genome-wide DNA methylation (DNAm) patterns in the face of climate change for a group of especially vulnerable species, those with temperature-dependent sex determination (TSD). Due to their reliance on thermal cues during development to determine sexual fate, contemporary shifts in temperature are predicted to skew offspring sex ratios and ultimately destabilize sensitive populations. Using reduced-representation bisulphite sequencing, we profiled the DNA methylome in blood cells of hatchling American alligators (Alligator mississippiensis), a TSD species lacking reliable markers of sexual dimorphism in early life stages. We identified 120 sex-associated differentially methylated cytosines (DMCs; FDR < 0.1) in hatchlings incubated under a range of temperatures, as well as 707 unique temperature-associated DMCs. We further developed DNAm-based models capable of predicting hatchling sex with 100% accuracy (in 20 training samples and four test samples) and past incubation temperature with a mean absolute error of 1.2°C (in four test samples) based on the methylation status of 20 and 24 loci, respectively. Though largely independent of epigenomic patterning occurring in the embryonic gonad during TSD, DNAm patterns in blood cells may serve as nonlethal markers of hatchling sex and past incubation conditions in conservation applications. These findings also raise intriguing questions regarding tissue-specific epigenomic patterning in the context of developmental plasticity.

59 BASIC BIOLOGICAL SCIENCES↗

Cis-regulatory evolution shapes facial diversity in birds and mammals

Birds and mammals exhibit extraordinary facial diversity, reflecting adaptations to distinct ecological niches and feeding strategies. While core face-building developmental programs are conserved and orchestrated by interactions between ectodermal organizers and the underlying mesenchyme, mechanisms driving facial shape variation remain poorly understood. Here, we integrate single-cell transcriptomic and chromatin accessibility profiling of mouse and chicken developing face to construct a comparative regulatory map. Although both ectodermal and mesenchymal populations display distinct regulatory features in each species, the mesenchyme exhibits markedly greater divergence, pointing to its central role in shaping facial morphology. We further reveal unexpected molecular complexity in the main face-shaping organizer, including a mouse-specific Shh/Wnt5a expression domain. At key morphogen loci (Bmp4, Fgf8, and Wnt5a), conserved and lineage-specific enhancers exhibit spatially restricted activity patterns that mirror divergent signaling domains. These findings demonstrate how cis-regulatory evolution modulates conserved developmental programs to generate morphological novelty, providing a valuable resource for studying vertebrate facial evolution.

Kyomen, Stella [Max Planck Institute for Evolution↗

A protective and broadly binding antibody class engages the influenza virus hemagglutinin head at its stem interface

ABSTRACT Influenza infection and vaccination impart strain-specific immunity that protects against neither seasonal antigenic variants nor the next pandemic. However, antibodies directed to conserved sites can confer broad protection. Here, we identify and characterize a class of human antibodies that engage a previously undescribed, conserved epitope on the influenza hemagglutinin (HA) protein. Prototype antibody S8V1-157 binds at the normally occluded interface between the HA head and stem. Antibodies to this HA head–stem interface epitope are non-neutralizingin vitrobut protect against lethal influenza infection in mice. These antibodies bind to most influenza A subtypes and seasonal human variants, and are present at low frequencies in the memory B cell populations of multiple human donors. Vaccines designed to elicit these antibodies might contribute to “universal” influenza immunity. IMPORTANCE Antibodies to the influenza virus hemagglutinin (HA) protein confer the strongest protection against infection. Human antibodies elicited by infection and/or vaccination fail to protect against antigenically novel animal, pandemic, or human seasonal viruses. Improved vaccines are needed. We identify a novel class of antibodies that bind most divergent HA subtypes and all seasonal human HA antigenic variants tested. These antibodies confer protection from lethal influenza challenge in animal models. The corresponding epitope on the HA head is occluded by its interaction with the stem and is inaccessible in the well-resolved prefusion state. The immunogenicity of this head–stem interface indicates that poorly understood conformations of HA presenting widely conserved surfaces are explored in biochemical, cell-based, andin vivoassays. Head–stem interface antibodies warrant further investigation as an avenue to improve influenza vaccines and therapeutics.

Microbiology↗

Structure of the Core Postfusion Porcine Endogenous Retrovirus Fusion Protein

Retroviral elements from endogenous retroviruses have functions in mammalian physiology. The best-known examples are the envelope proteins that function in placenta development and immune suppression. Porcine endogenous retroviruses (PERVs) are an understudied class of endogenous retroviruses that infect cultured human cells, raising concern regarding porcine xenografts. The PERV envelope glycoprotein has also been proposed as a possible swine syncytin with a role in placental development. Despite the growing interest in PERVs, their envelope glycoproteins remain poorly characterized. Here, we successfully determined the postfusion crystal structure of the PERV core fusion ectodomain. The PERV fusion protein structure reveals a conserved class I viral fusion protein six-helix bundle. Biophysical experiments demonstrated that the thermodynamic stability of the PERV fusion protein secondary structure was the same at physiological and acidic pHs. A conserved surface analysis highlights the high degree of sequence conservation among retroviral fusogens in the chain reversal region that facilitates the large-scale conformational change required for membrane fusion. Further structural alignment of class I viral fusogens revealed a phylogenetic clustering that shows evolution into various lineages that correlate with virus mechanisms of cell entry. Our work indicates that structural dendrograms can be used to qualitatively infer insights into the fusion mechanisms of newly discovered class I viral fusogen structures.

59 BASIC BIOLOGICAL SCIENCES↗

Identification of hidden N4-like viruses and their interactions with hosts

The N4-like viruses, which were recently assigned to the novel viral family Schitoviridae in 2021, belong to a podoviral-like viral lineage and possess conserved genomic characteristics and a unique replication mechanism. Despite their significance, our understanding of N4-like viruses is primarily based on viral isolates. To address this knowledge gap, this study has established a comprehensive N4-like viral data sets comprising 342 high-quality N4-like viruses/proviruses (144 viral isolates, 158 uncultured viruses, and 40 integrated N4-like proviruses). These viruses were classified into 97 subfamilies (89 of which are newly identified), 148 genera (100 of which are newly identified), and 253 species (177 of which are newly identified). The study reveals that N4-like viruses inhibit the polar region, oligotrophic open oceans, and the human gut, where they infect various bacterial lineages, such as Alpha/Beta/Gamma/Epsilon-proteobacteria in the Proteobacteria phylum. Although N4-like viral endogenization appears to be prevalent in Proteobacteria, it has also been observed in Firmicutes. Additionally, the phylogenetic analysis has identified evolutionary divergence within the hallmark genes of N4-like viruses, indicating a complex origin of the different conserved parts of viral genomes. Moreover, 1,101 putative auxiliary metabolic genes (AMGs) were identified in the N4-like viral pan-proteome, which mainly participate in nucleotide and cofactor/vitamin metabolisms. Of these AMGs, 27 were found to be associated with virulence, suggesting their potential involvement in the spread of bacterial pathogenicity. The findings of this study are significant, as N4-like viruses represent a unique viral lineage with a distinct replication mechanism and a conserved core genome. This work has resulted in a comprehensive global map of the entire N4-like viral lineage, including information on their distribution in different biomes, evolutionary divergence, genomic diversity, and the potential for viral-mediated host metabolic reprogramming. As such, this work significantly contributes to our understanding of the ecological function and viral-host interactions of bacteriophages.

60 APPLIED LIFE SCIENCES↗

Salt supplementation-induced metabolic reprogramming in Streptomyces coelicolor

Members of the genus Streptomyces are major producers of a wide variety of secondary metabolites that serve as bioactive compounds. Many secondary metabolites are produced in response to environmental signals such as biotic and abiotic stresses. In this study, we identified salt supplementation as one of the stimuli activating secondary metabolism in the model Streptomyces species, Streptomyces coelicolor. Comparative metabolomics revealed overproduction of several known secondary metabolites, most notably undecylprodigiosin and coelimycin P1, in addition to their biosynthetic intermediates and derivatives, as well as many unknown metabolites. Transcriptomic analysis revealed activation of diverse biological processes including cation uptake, compatible solute production, and the phosphate limitation stress response through conserved and species-specific mechanisms, presumably to overcome the increased salinity. This response leads to activation of a variety of regulatory and metabolic pathways required for production of secondary metabolites including activation of conserved metabolic pathways for energy and substrate supply and species-specific secondary metabolite biosynthetic gene clusters. Furthermore, several promoter sequences contributing to upregulation of secondary metabolism induced by salt supplementation were identified. Overall, our data show how S. coelicolor copes with the increased salinity and tailors the cellular metabolism toward secondary metabolism in a conserved and species-specific manner.

Otani, Hiroshi [USDOE Joint Genome Institute (JGI)↗

A Constrained Data Assimilation Algorithm Based on GSI Hybrid 3D-EnVar and Its Application

Abstract Data assimilation (DA) at mesoscales is important for severe weather forecasts, yet the techniques of data assimilation at this scale remain a challenge. This study introduces dynamical constraints in the Gridpoint Statistical Interpolation (GSI) three-dimensional ensemble variational (3D-EnVar) data assimilation algorithm to enable the use of high-resolution surface observations of precipitation to improve atmospheric analysis at mesoscales. The constraints use the conservations of mass and moisture. Mass constraint suppresses the unphysical high-frequency oscillation, while moisture conservation constrains the atmospheric states to conform with the observed high-resolution precipitation. We show that the constrained data assimilation (CDA) algorithm significantly reduced the spurious residuals of the mass and moisture budgets compared to the original data assimilation (ODA). A case study is presented for a squall line over the Southern Great Plains on 20 May 2011 during Midlatitude Continental Convective Clouds Experiment (MC3E) of the Atmospheric Radiation Measurement (ARM) program by using ODA or CDA analysis as initial condition of forecasts. The state variables, and the location and intensity of the squall line are better simulated in the CDA experiment. Results show how surface observation of precipitation can be used to improve atmospheric analysis through data assimilation by using the dynamical constraints of mass and moisture conservations.

Wang, Jia↗

A willow sex chromosome reveals convergent evolution of complex palindromic repeats

Background: Sex chromosomes have arisen independently in a wide variety of species, yet they share common characteristics, including the presence of suppressed recombination surrounding sex determination loci. Mammalian sex chromosomes contain multiple palindromic repeats across the non-recombining region that show sequence conservation through gene conversion and contain genes that are crucial for sexual reproduction. In plants, it is not clear if palindromic repeats play a role in maintaining sequence conservation in the absence of homologous recombination. Results: Here we present the first evidence of large palindromic structures in a plant sex chromosome, based on a highly contiguous assembly of the W chromosome of the dioecious shrub Salix purpurea . The W chromosome has an expanded number of genes due to transpositions from autosomes. It also contains two consecutive palindromes that span a region of 200 kb, with conspicuous 20-kb stretches of highly conserved sequences among the four arms that show evidence of gene conversion. Four genes in the palindrome are homologous to genes in the sex determination regions of the closely related genus Populus , which is located on a different chromosome. These genes show distinct, floral-biased expression patterns compared to paralogous copies on autosomes. Conclusion: The presence of palindromes in sex chromosomes of mammals and plants highlights the intrinsic importance of these features in adaptive evolution in the absence of recombination. Convergent evolution is driving both the independent establishment of sex chromosomes as well as their fine-scale sequence structure.

59 BASIC BIOLOGICAL SCIENCES↗

Constellation's best estimate alternate source term methodology overview

Safety analyses for a nuclear power plants need to consider postulated accidents that results in at risk of accidental release of radiation. The regulations require plant specific safety analysis reports to include an evaluation of the requirements of 10CFR50.67. Such a safety analysis report mandates limits such that calculated radiological consequences relative to certain dose locations do not exceed a total effective dose equivalent (TEDE) limits following a postulated release of radioactivity. Calculations are performed to estimate the radiological consequences, in terms of dose, to people and equipment to ensure the estimated doses are within the prescribed limits. Analysis should demonstrate, with reasonable assurance, that these prescribed limits are complied with. Conventional methodologies utilize conservative approaches to address lack of uncertainty quantification in the utilized approaches, methods, and/or inputs. These built-in excess conservatisms often result in compounding effects and hence overly conservative results in the estimated radiological consequences, which leads to inaccurate margin evaluation for operation and accident mitigation. Therefore, evaluating accurate dose consequences is needed for both operational and safety reasons. The research documented in this paper provides an overview of Constellation's Best Estimate Alternate Source Term (BEAST) Methodology. BEAST methodology relies upon the use of realistic yet bounding input distributions for key analysis parameters, which replaces use of conservative deterministic singular inputs that bound overall analysis domain. This approach enables evaluating a more accurate accident analysis response, while enabling a bounding licensing basis envelope via more accurate quantification of uncertainty in the application. Therefore, built-in margin for a given scenario is more accurately evaluated.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

New technology for an ancient fish: A lamprey life cycle modeling tool with an R Shiny application

Lampreys (Petromyzontiformes) are an ancient group of fishes with complex life histories. We created a life cycle model that includes an R Shiny interactive web application interface to simulate abundance by life stage. This will allow scientists and managers to connect available demographic information in a framework that can be applied to questions regarding lamprey biology and conservation. We used Pacific lamprey ( Entosphenus tridentatus ) as a case study to highlight the utility of this model. We applied a global sensitivity analysis to explore the importance of individual life stage parameters to overall population size, and to better understand the implications of existing gaps in knowledge. We also provided example analyses of selected management scenarios (dam passage, fish translocations, and hatchery additions) influencing Pacific lamprey in fresh water. These applications illustrate how the model can be applied to inform conservation efforts. This tool will provide new capabilities for users to explore their own questions about lamprey biology and conservation. Simulations can hone hypotheses and predictions, which can then be empirically tested in the real world.

Gomes, Dylan G. E. (ORCID:0000000226423728)↗

Viral Nuclease Inhibitors: Small molecule disruptors of the UL12 alkaline nuclease display broad anti-herpes virus activity

Herpes simplex virus 1 (HSV-1) UL12 encodes a highly conserved 5′ → 3′ alkaline exonuclease that is essential for the production of infectious virus. Together with the viral single-stranded DNA-binding/annealing protein ICP8, UL12 functions as a two-component recombinase that mediates recombination-dependent viral DNA replication. Here, we present the crystal structure of the catalytic domain of the HSV alkaline nuclease (UL12), which provides the first view of an α-herpesvirus alkaline nuclease. Using this structure, we optimized a series of small-molecule viral nuclease inhibitors (VNIs) that target the UL12 active site and potently inhibit UL12 exonuclease activity in vitro. We have thus established a robust platform for structure-based docking, SAR analysis and rational inhibitor design. Because UL12 orthologs are conserved across all human herpesviruses, we examined the activity of these compounds against the β- and γ-herpesvirus alkaline nucleases UL98 and SOX and found that they inhibit all three enzymes. The VNIs also exhibit antiviral activity against HSV-1 and HCMV in cell culture. EC 50 and IC 50 values were in the nanomolar to low micromolar range. Together, these findings establish herpesvirus alkaline nucleases as conserved, druggable antiviral targets and provide a foundation for the development of broad-spectrum anti-herpesvirus therapeutics, either as standalone agents or in combination with existing nucleoside analogs.

Sharma, Nidhi↗

Protecting Biodiversity through Forest Management: Lessons Learned and Strategies for Success

The strong links among biodiversity, forests, and climate change require that forces affecting them be addressed simultaneously. Here we summarize findings and lessons learned from decades of field work exploring ways to balance conservation with development, while effectively addressing drivers of deforestation and biodiversity loss. Examples are provided for approaches to forest management that support both biodiversity conservation and greenhouse gas mitigation. Causes of deforestation are reviewed and recommendations provided for specific steps that would slow the loss of high conservation-value forests.

54 ENVIRONMENTAL SCIENCES↗

Hilbert space fragmentation in a 2D quantum spin system with subsystem symmetries

We consider a 2D quantum spin model with ring-exchange interaction that has subsystem symmetries associated to conserved magnetization along rows and columns of a square lattice, which implies the conservation of the global dipole moment. The model is not integrable, but violates the eigenstate thermalization hypothesis through an extensive Hilbert space fragmentation, including an exponential number of inert subsectors with trivial dynamics, arising from kinetic constraints. While subsystem symmetries are quite restrictive for the dynamics, we show that they alone cannot account for such a number of inert states, even with infinite-range interactions. We present a procedure for constructing shielding structures that can separate and disentangle dynamically active regions from each other. Notably, subsystem symmetries allow the thickness of the shields to be dependent only on the interaction range rather than on the size of the active regions, unlike in the case of generic dipole-conserving systems.

Khudorozhkov, Alexey↗

Hamiltonian structure of 2D fluid dynamics with broken parity

Isotropic fluids in two spatial dimensions can break parity symmetry and sustain transverse stresses which do not lead to dissipation. Corresponding transport coefficients include odd viscosity, odd torque, and odd pressure. We consider an isotropic Galilean invariant fluid dynamics in the adiabatic regime with momentum and particle density conservation. We find conditions on transport coefficients that correspond to dissipationless and separately to Hamiltonian fluid dynamics. The restriction on the transport coefficients will help identify what kind of hydrodynamics can be obtained by coarse-graining a microscopic Hamiltonian system. Interestingly, not all parity-breaking transport coefficients lead to energy conservation and, generally, the fluid dynamics is energy conserving but not Hamiltonian. We show how this dynamics can be realized by imposing a nonholonomic constraint on the Hamiltonian system.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

FY20 Verification of BISON Using Analytic and Manufactured Solutions

In 2010, the U.S. Department of Energy created its first Energy Innovation Hub, which is focused on developing high-fidelity and high-resolution Modeling and Simulation (M&S) tools for modeling of Light Water Reactors (LWRs). This hub, Consortium for Advanced Simulation of LWRs (CASL), has developed an LWR simulation tool called Virtual Environment for Reactor Applications (VERA). The multi-physics capability of VERA is achieved through the coupling of single-physics codes, including BISON, CTF, MPACT, and MAMBA. BISON is a fuel performance code which models the thermo-mechanical behavior of nuclear fuel using high performance M&S. It is capable of modeling traditional LWR fuel rods, fuel plates, and TRi-structural ISOtropic (TRISO) fuel particles. It can employ three-dimensional Cartesian, two-dimensional axisymmetric cylindrical, or one-dimensional radial spherical geometry. It includes empirical models for a large variety of fuel physics: temperature- and burnup-dependent thermal properties, fuel swelling and densification, fission gas production, cladding creep, fracture, cladding plasticity, and gap/plenum models. This document details a series of code verification test problems that are used to test BISON. These problems add confidence that the BISON code is a faithful representation of its underlying mathematical model. The suite of verification tests are mapped to the underlying conservation equations solved by the code: heat conduction, mechanics, and species conservation. Twenty-two problems are added for the heat conduction solution, two for the mechanics solution, and none for species conservation. Method of Manufactured Solutions (MMS) capability is demonstrated with three problems, and temperature drops across the fuel gap are tested.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

PNNL Measurement Results for the 2018 FlatTop Criticality Nuclear Accident Dosimetry Exercise at the Nevada National Security Site (IER-253)

The Pacific Northwest National Laboratory (PNNL) participated in the FlatTop exercise IER-253 at the National Nuclear Security Site (NNSS) during the week of May 21, 2018. This report summarizes the measurements of the personal nuclear accident dosimeters (PNAD). Additionally, portable survey instrument readings and measurements of the simulated biological samples are included. The FlatTop exercise (IER-253) tested only PNADs and did not include fixed nuclear accident dosimeters (FNAD). Previous PNAD results obtained in 2016 at the Godiva-IV exercise IER-148 were summarized in PNNL Measurement Results for the 2016 Criticality Accident Dosimetry Exercise at the Nevada National Security Site IER-148 (PNNL-26497). The results clearly indicated that the previous dose conversions were a historical legacy of the Hanford Site and corresponded closer to kerma dose (or first collision dose, and not to Hp(10) dose). The technical basis for PNAD dose was based on the Godiva-IV exercise and documented in A New Dose Calculation Methodology for New PNAD and FNAD Designs at PNNL (PNNL-27023). The configuration of the PNAD was described in these two documents. The FlatTop exercise was the first time PNNL tested this new dose calculation methodology. Results were generally favorable with some results conservatively over reported that fell above the performance criteria. The reported gamma dose results fell non-conservatively low because only the default parameters obtained from the Godiva-IV exercise were used, and because the OSL gamma dosimeter has an energy dependency. The results from the simulated biological samples were also favorable, and in several cases conservatively over reported.

61 RADIATION PROTECTION AND DOSIMETRY↗