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DOE OSTI2015

An adaptable multiple power source for mass spectrometry and other scientific instruments

Power supplies are commonly used in the operation of many types of scientific equipment, including mass spectrometers and ancillary instrumentation. A generic modern mass spectrometer comprises an ionization source, such as electrospray ionization (ESI), ion transfer devices such as ion funnels and multipole ion guides, and ion signal detection apparatus. Very often such platforms include, or are interfaced with ancillary elements in order to manipulate samples before or after ionization. In order to operate such scientific instruments, numerous direct current (DC) channels and radio frequency (RF) signals are required, along with other controls such as temperature regulation. In particular, DC voltages in the range of ±400 V, along with MHz range RF signals with peak-to-peak amplitudes in the hundreds of volts range are commonly used to transfer ionized samples under vacuum. Additionally, an ESI source requires a high voltage (HV) DC source capable of producing several thousand volts and heaters capable of generating temperatures up to 300°C. All of these signals must be properly synchronized and managed in order to carry out ion trapping, accumulation and detection.

47 OTHER INSTRUMENTATION↗

DOE OSTI2014

A nonvoxel-based dose convolution/superposition algorithm optimized for scalable GPU architectures

Purpose: Real-time adaptive planning and treatment has been infeasible due in part to its high computational complexity. There have been many recent efforts to utilize graphics processing units (GPUs) to accelerate the computational performance and dose accuracy in radiation therapy. Data structure and memory access patterns are the key GPU factors that determine the computational performance and accuracy. In this paper, the authors present a nonvoxel-based (NVB) approach to maximize computational and memory access efficiency and throughput on the GPU. Methods: The proposed algorithm employs a ray-tracing mechanism to restructure the 3D data sets computed from the CT anatomy into a nonvoxel-based framework. In a process that takes only a few milliseconds of computing time, the algorithm restructured the data sets by ray-tracing through precalculated CT volumes to realign the coordinate system along the convolution direction, as defined by zenithal and azimuthal angles. During the ray-tracing step, the data were resampled according to radial sampling and parallel ray-spacing parameters making the algorithm independent of the original CT resolution. The nonvoxel-based algorithm presented in this paper also demonstrated a trade-off in computational performance and dose accuracy for different coordinate system configurations. In order to find the best balance between the computed speedup and the accuracy, the authors employed an exhaustive parameter search on all sampling parameters that defined the coordinate system configuration: zenithal, azimuthal, and radial sampling of the convolution algorithm, as well as the parallel ray spacing during ray tracing. The angular sampling parameters were varied between 4 and 48 discrete angles, while both radial sampling and parallel ray spacing were varied from 0.5 to 10 mm. The gamma distribution analysis method (γ) was used to compare the dose distributions using 2% and 2 mm dose difference and distance-to-agreement criteria, respectively. Accuracy was investigated using three distinct phantoms with varied geometries and heterogeneities and on a series of 14 segmented lung CT data sets. Performance gains were calculated using three 256 mm cube homogenous water phantoms, with isotropic voxel dimensions of 1, 2, and 4 mm. Results: The nonvoxel-based GPU algorithm was independent of the data size and provided significant computational gains over the CPU algorithm for large CT data sizes. The parameter search analysis also showed that the ray combination of 8 zenithal and 8 azimuthal angles along with 1 mm radial sampling and 2 mm parallel ray spacing maintained dose accuracy with greater than 99% of voxels passing the γ test. Combining the acceleration obtained from GPU parallelization with the sampling optimization, the authors achieved a total performance improvement factor of >175 000 when compared to our voxel-based ground truth CPU benchmark and a factor of 20 compared with a voxel-based GPU dose convolution method. Conclusions: The nonvoxel-based convolution method yielded substantial performance improvements over a generic GPU implementation, while maintaining accuracy as compared to a CPU computed ground truth dose distribution. Such an algorithm can be a key contribution toward developing tools for adaptive radiation therapy systems.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Validating the Use of Gaussian Process Regression for Adaptive Mapping of Residual Stress Fields

Probing the stress state using a high density of measurement points is time intensive and presents a limitation for what is experimentally feasible. Alternatively, individual strain fields used for determining stresses can be reconstructed from a subset of points using a Gaussian process regression (GPR). Results presented in this paper evidence that determining stresses from reconstructed strain fields is a viable approach for reducing the number of measurements needed to fully sample a component’s stress state. The approach was demonstrated by reconstructing the stress fields in wire-arc additively manufactured walls fabricated using either a mild steel or low-temperature transition feedstock. Effects of errors in individual GP reconstructed strain maps and how these errors propagate to the final stress maps were assessed. Implications of the initial sampling approach and how localized strains affect convergence are explored to give guidance on how best to implement a dynamic sampling experiment.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Divergent selection and climate adaptation fuel genomic differentiation between sister species of Sphagnum (peat moss)

Abstract Background and Aims New plant species can evolve through the reinforcement of reproductive isolation via local adaptation along habitat gradients. Peat mosses (Sphagnaceae) are an emerging model system for the study of evolutionary genomics and have well-documented niche differentiation among species. Recent molecular studies have demonstrated that the globally distributed species Sphagnum magellanicum is a complex of morphologically cryptic lineages that are phylogenetically and ecologically distinct. Here, we describe the architecture of genomic differentiation between two sister species in this complex known from eastern North America: the northern S. diabolicum and the largely southern S. magniae. Methods We sampled plant populations from across a latitudinal gradient in eastern North America and performed whole genome and restriction-site associated DNA sequencing. These sequencing data were then analyzed computationally. Key Results Using sliding-window population genetic analyses we find that differentiation is concentrated within ‘islands’ of the genome spanning up to 400 kb that are characterized by elevated genetic divergence, suppressed recombination, reduced nucleotide diversity and increased rates of non-synonymous substitution. Sequence variants that are significantly associated with genetic structure and bioclimatic variables occur within genes that have functional enrichment for biological processes including abiotic stress response, photoperiodism and hormone-mediated signalling. Demographic modelling demonstrates that these two species diverged no more than 225 000 generations ago with secondary contact occurring where their ranges overlap. Conclusions We suggest that this heterogeneity of genomic differentiation is a result of linked selection and reflects the role of local adaptation to contrasting climatic zones in driving speciation. This research provides insight into the process of speciation in a group of ecologically important plants and strengthens our predictive understanding of how plant populations will respond as Earth’s climate rapidly changes.

58 GEOSCIENCES↗

DOE OSTI2016

Nanoparticle standards

We will purchase a COTS materials printer and adapt it for solution printing of known elemental concentration solutions. A methodology will be developed to create deposits of known mass in known locations on selected substrates. The deposits will be characterized for deposited mass, physical morphology, thickness and uniformity. Once an acceptable methodology has been developed and validated, we will create round robin samples to be characterized by LGSIMS instruments at LANL, PNNL and NIST. We will demonstrate the feasibility of depositing nanoparticles in known masses with the goal of creating separated nanoparticles in known locations.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2025

LDRD Abbreviated report: High-Order General-Discrete-Ordinates Method Enabling Efficient Deterministic Transport in Hydrodynamic Simulations

Deterministic transport simulations for national-security and energy applications often operate in high-dimensional phase-space, where accuracy and cost both become major challenges. A common numerical artifact in such problems is the “ray-effect,” which appears as unphysical streaks. Beyond misinterpretation, these artifacts can contaminate tightly coupled physics, such as fluid dynamics, radiation-hydrodynamics, and laser-plasma interactions, eroding the predictive capability of entire multiphysics workflows. Our objective was to make high-dimension studies practical on modern hardware while mitigating the ray-effect without relying on prohibitively expensive sampling approaches such as Monte Carlo methods. We developed the Generic Discretization Library (GenDiL), a Graphics Processing Unit (GPU)-first framework that uses high-order Discontinuous Galerkin (DG) methods and matrix-free algorithms to reduce memory usage and improve computational efficiency, critical for phase-space simulations. GenDiL supports phase-space adaptivity in both mesh size and polynomial order (hp-adaptivity) to place resolution only where it is needed. A central capability is Local Dimensional Refinement (LDR), which couples lower-dimension continuum models to higher-dimension kinetic models through stable and conservative interfaces, so that high-fidelity physics is applied only in regions where it is essential. Building on the GenDiL framework, we developed the General SN (GSN) family of algorithms as a true generalization of the polar SN approach (discrete ordinates, often denoted SN). Rather than tying discrete ordinates to a specific polar change of coordinates, GSN formulates transport on an arbitrary change of coordinates chosen to reduce ray-effect. We studied two complementary variants: an analytic variant, where the coordinate map is prescribed in advance by a closed-form function; and a data-driven variant, where a quantity of interest, such as the net flux, guides the coordinate system. GenDiL provides the library infrastructure for efficient GPU execution, but the GSN concept is algorithmic and independent of any one library. Across representative high-dimension tests, including non-symmetric solutions, both variants delivered strong ray-effect mitigation at practical cost, moving four- to six-dimensional analysis toward repeatable, routine studies.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS1976

Electrical conductivity cell and method for fabricating the same

A flask having a threaded neck and a cap adapted for threaded engagement on the neck are used. A laminated disc between the cap and the neck forms a gas tight seal and the cap has a central opening that exposes a medial region of the disc. Piercing the disc through the opening are two electrodes, the inner ends of which contact the sample within the flask and the outer ends of which can be connected to test equipment. Cylindric glass tubes are fitted over the external portion of the electrodes to provide physical support and silicone rubber or a similar material serves to retain the glass cylinders in place and form a gas tight seal between the cylinders and the electrodes. Shrinkable tubing is shrunk over the glass tubes to afford further mechanical support and sealing. A final relatively large diameter shrinkable tube is shrunk over both electrodes and their associated glass cylinders. The support and sealing means for the electrodes is confined to a limited portion of the medial region of the disc so that the remainder of such region can be punctured by a hollow needle to introduce a test sample within the flask.

Gilbreath, W. P.↗

NASA NTRS1981

Ion source design for industrial applications

The design of broad-beam industrial ion sources is described. The approach used emphasizes refractory metal cathodes and permanent-magnet multipole discharge chambers. Design procedures and sample calculations are given for the discharge chamber, ion optics, cathodes, and magnetic circuit. Hardware designs are included for the isolator, cathode supports, anode supports, pole-piece assembly, and ion-optics supports. There are other ways of designing most ion source components, but the designs presented are representative of current technology and adaptable to a wide range of configurations.

Kaufman, H. R.↗

NASA NTRS2012

Mass Spectrometric Studies of Oxides

Current studies at NASA Glenn on oxide thermodynamics are discussed. Previous studies on the vaporization of B2O3 in reducing atmospheres led to inconsistent studies when B was used as a reductant. It is shown that liquid B2O3 does not wet B and a clear phase separation was noted in the Knudsen cell. This problem was solved by using FeB and Fe2B to supply a different and constant activity of B. The thermodynamic data thus derived are compared to quantum chemical composite calculations. A major problem in high temperature mass spectrometry is the determination of accurate ionization cross sections, particularly for molecules. The method of Deutsch and Mark shows promise and some sample calculations are discussed. Finally current studies on the thermodynamics of rare earth silicates are discussed. Here the problems are obtaining a measurable signal from SiO2 vaporization and non-equilibrium vaporization. The use of a Ta reducing agent provides a stronger signal, which is related to silica activity. The Whitman-Motzfeld relation adapted to KEMS measurements is applied to obtain equilibrium pressures.

Jacobson, Nathan S.↗

DOE OSTI2016

Novel covariance-based neutrality test of time-series data reveals asymmetries in ecological and economic systems

Systems as diverse as the interacting species in a community, alleles at a genetic locus, and companies in a market are characterized by competition (over resources, space, capital, etc) and adaptation. Neutral theory, built around the hypothesis that individual performance is independent of group membership, has found utility across the disciplines of ecology, population genetics, and economics, both because of the success of the neutral hypothesis in predicting system properties and because deviations from these predictions provide information about the underlying dynamics. However, most tests of neutrality are weak, based on static system properties such as species-abundance distributions or the number of singletons in a sample. Time-series data provide a window onto a system’s dynamics, and should furnish tests of the neutral hypothesis that are more powerful to detect deviations from neutrality and more informative about to the type of competitive asymmetry that drives the deviation. Here, we present a neutrality test for time-series data. We apply this test to several microbial time-series and financial time-series and find that most of these systems are not neutral. Our test isolates the covariance structure of neutral competition, thus facilitating further exploration of the nature of asymmetry in the covariance structure of competitive systems. Much like neutrality tests from population genetics that use relative abundance distributions have enabled researchers to scan entire genomes for genes under selection, we anticipate our time-series test will be useful for quick significance tests of neutrality across a range of ecological, economic, and sociological systems for which time-series data are available. Here, future work can use our test to categorize and compare the dynamic fingerprints of particular competitive asymmetries (frequency dependence, volatility smiles, etc) to improve forecasting and management of complex adaptive systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Discovering the Molecular Determinants of Phaeobacter inhibens Susceptibility to Phaeobacter Phage MD18

Bacteriophages are useful nonantibiotic therapeutics for bacterial infections as well as threats to industries utilizing bacterial agents. This study identified Phaeobacter virus MD18 , a phage antagonist of Phaeobacter inhibens , a bacterium with promising use as a probiotic for aquatic farming industries. Genomic analysis suggested that Phaeobacter phage MD18 has evolved to enhance its replication in P. inhibens by adopting favorable tRNA genes as well as through genomic sequence adaptation to resemble host codon usage. Lastly, a high-throughput analysis of P. inhibens transposon insertion mutants identified genes that modulate host susceptibility to phage MD18 and implicated the type IV pilus as the likely receptor recognized for adsorption. This study marks the first characterization of the relationship between P. inhibens and an environmentally sampled phage, which informs our understanding of natural threats to the bacterium and may promote the development of novel phage technologies for genetic manipulation of this host.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Extreme-Scale Bayesian Inference for Uncertainty Quantification of Complex Simulations

Uncertainty quantification (UQ)—that is, quantifying uncertainties in complex mathematical models and their large-scale computational implementations—is widely viewed as one of the outstanding challenges facing the field of CS&E over the coming decade. The EUREKA project set to address the most difficult class of UQ problems: those for which both the underlying PDE model as well as the uncertain parameters are of extreme scale. In the project we worked on these extreme-scale challenges in the following four areas: 1. Scalable parallel algorithms for sampling and characterizing the posterior distribution that exploit the structure of the underlying PDEs and parameter-to-observable map. These include structure-exploiting versions of the randomized maximum likelihood method, which aims to overcome the intractability of employing conventional MCMC methods for solving extreme-scale Bayesian inversion problems by appealing to and adapting ideas from large-scale PDE-constrained optimization, which have been very successful at exploring high-dimensional spaces. 2. Scalable parallel algorithms for construction of prior and likelihood functions based on learning methods and non-parametric density estimation. Constructing problem-specific priors remains a critical challenge in Bayesian inference, and more so in high dimensions. Another challenge is construction of likelihood functions that capture unmodeled couplings between observations and parameters. We will create parallel algorithms for non-parametric density estimation using high dimensional N-body methods and combine them with supervised learning techniques for the construction of priors and likelihood functions. 3. Bayesian inadequacy models, which augment physics models with stochastic models that represent their imperfections. The success of the Bayesian inference framework depends on the ability to represent the uncertainty due to imperfections of the mathematical model of the phenomena of interest. This is a central challenge in UQ, especially for large-scale models. We propose to develop the mathematical tools to address these challenges in the context of extreme-scale problems. 4. Parallel scalable algorithms for Bayesian optimal experimental design (OED). Bayesian inversion yields quantified uncertainties in the model parameters, which can be propagated forward through the model to yield uncertainty in outputs of interest. This opens the way for designing new experiments to reduce the uncertainties in the model parameters and model predictions. Such experimental design problems have been intractable for large-scale problems using conventional methods; we will create OED algorithms that exploit the structure of the PDE model and the parameter-to-output map to overcome these challenges. Parallel algorithms for these four problems were created, analyzed, prototyped, implemented, tuned, and scaled up for leading-edge supercomputers, including UT-Austin’s own 10 petaflops Stampede system, ANL’s Mira system, and ORNL’s Titan system. While our focus is on fundamental mathematical/computational methods and algorithms, we will assess our methods on model problems derived from several DOE mission applications, including multiscale mechanics and ice sheet dynamics.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

Data from: Insights into the maize pan-genome and pan-transcriptome

Genomes at the species level are dynamic, with genes present in every individual (core) and genes in a subset of individuals (dispensable) that collectively constitute the pan-genome. Using transcriptome sequencing of seedling RNA from 503 maize (Zea mays) inbred lines to characterize the maize pan-genome, we identified 8681 representative transcript assemblies (RTAs) with 16.4% expressed in all lines and 82.7% expressed in subsets of the lines. Interestingly, with linkage disequilibrium mapping, 76.7% of the RTAs with at least one single nucleotide polymorphism (SNP) could be mapped to a single genetic position, distributed primarily throughout the nonpericentromeric portion of the genome. Stepwise iterative clustering of RTAs suggests, within the context of the genotypes used in this study, that the maize genome is restricted and further sampling of seedling RNA within this germplasm base will result in minimal discovery. Genome-wide association studies based on SNPs and transcript abundance in the pan-genome revealed loci associated with the timing of the juvenile-to-adult vegetative and vegetative-to-reproductive developmental transitions, two traits important for fitness and adaptation. This study revealed the dynamic nature of the maize pan-genome and demonstrated that a substantial portion of variation may lie outside the single reference genome for a species.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1998

Biomarkers in Carbonate Thermal Springs: Implications for Mars

Evidence of possible relict biogenic activity has been reported in carbonate inclusions within martian meteorite ALH 84001. The initial evidence included ovoid and elongated forms 50 - 500 nanometers in length, morphologically similar to but significantly smaller than many terrestrial microbes. More recently, thin structures resembling the remains of organic biofilms have been reported in the same meteorite. Carbonates have also been discussed in the context of Mars sample return missions. Thermal spring deposits have often been cited as prime locations for exobiological exploration. By analogy to Earth, specialized microbes may have existed in the heated, mineralized waters, and precipitates of carbonate and/or silica from these waters may have trapped and preserved evidence of life. Since the geological interactions that produce thermal springs can be recognized in orbital imagery, directed searches for microfossils in such deposits are deemed possible. We are engaged in a study of the signatures produced by contemporary biogenic activity (biomarkers) in carbonate thermal springs. We are examining the microbes that live in such environments and the preservation of microbial forms, biofilms, and petrographic fabrics indicative of life in thermal spring mineral deposits. This work is part of a much more extensive study to refine the appropriate tools, techniques, and approaches to seek evidence of life in a range of planetary samples. A deeper understanding of biological signatures will prepare us for the detailed search for life on Mars and eventually on other planets. Overall. the study of biomarkers in rocks and soils will provide insight into the evolution of life because such signatures are a record of how life interacts with its environment, how it adapts to changing conditions, and how life can influence geology and climate.

Allen, C. C.↗

NASA NTRS2012

Forming Human-Robot Teams Across Time and Space

NASA pushes telerobotics to distances that span the Solar System. At this scale, time of flight for communication is limited by the speed of light, inducing long time delays, narrow bandwidth and the real risk of data disruption. NASA also supports missions where humans are in direct contact with robots during extravehicular activity (EVA), giving a range of zero to hundreds of millions of miles for NASA s definition of "tele". . Another temporal variable is mission phasing. NASA missions are now being considered that combine early robotic phases with later human arrival, then transition back to robot only operations. Robots can preposition, scout, sample or construct in advance of human teammates, transition to assistant roles when the crew are present, and then become care-takers when the crew returns to Earth. This paper will describe advances in robot safety and command interaction approaches developed to form effective human-robot teams, overcoming challenges of time delay and adapting as the team transitions from robot only to robots and crew. The work is predicated on the idea that when robots are alone in space, they are still part of a human-robot team acting as surrogates for people back on Earth or in other distant locations. Software, interaction modes and control methods will be described that can operate robots in all these conditions. A novel control mode for operating robots across time delay was developed using a graphical simulation on the human side of the communication, allowing a remote supervisor to drive and command a robot in simulation with no time delay, then monitor progress of the actual robot as data returns from the round trip to and from the robot. Since the robot must be responsible for safety out to at least the round trip time period, the authors developed a multi layer safety system able to detect and protect the robot and people in its workspace. This safety system is also running when humans are in direct contact with the robot, so it involves both internal fault detection as well as force sensing for unintended external contacts. The designs for the supervisory command mode and the redundant safety system will be described. Specific implementations were developed and test results will be reported. Experiments were conducted using terrestrial analogs for deep space missions, where time delays were artificially added to emulate the longer distances found in space.

Hambuchen, Kimberly↗

DOE OSTI2015

Selecting registration schemes in case of interstitial lung disease follow-up in CT

Purpose: Primary goal of this study is to select optimal registration schemes in the framework of interstitial lung disease (ILD) follow-up analysis in CT. Methods: A set of 128 multiresolution schemes composed of multiresolution nonrigid and combinations of rigid and nonrigid registration schemes are evaluated, utilizing ten artificially warped ILD follow-up volumes, originating from ten clinical volumetric CT scans of ILD affected patients, to select candidate optimal schemes. Specifically, all combinations of four transformation models (three rigid: rigid, similarity, affine and one nonrigid: third order B-spline), four cost functions (sum-of-square distances, normalized correlation coefficient, mutual information, and normalized mutual information), four gradient descent optimizers (standard, regular step, adaptive stochastic, and finite difference), and two types of pyramids (recursive and Gaussian-smoothing) were considered. The selection process involves two stages. The first stage involves identification of schemes with deformation field singularities, according to the determinant of the Jacobian matrix. In the second stage, evaluation methodology is based on distance between corresponding landmark points in both normal lung parenchyma (NLP) and ILD affected regions. Statistical analysis was performed in order to select near optimal registration schemes per evaluation metric. Performance of the candidate registration schemes was verified on a case sample of ten clinical follow-up CT scans to obtain the selected registration schemes. Results: By considering near optimal schemes common to all ranking lists, 16 out of 128 registration schemes were initially selected. These schemes obtained submillimeter registration accuracies in terms of average distance errors 0.18 ± 0.01 mm for NLP and 0.20 ± 0.01 mm for ILD, in case of artificially generated follow-up data. Registration accuracy in terms of average distance error in clinical follow-up data was in the range of 1.985–2.156 mm and 1.966–2.234 mm, for NLP and ILD affected regions, respectively, excluding schemes with statistically significant lower performance (Wilcoxon signed-ranks test, p < 0.05), resulting in 13 finally selected registration schemes. Conclusions: Selected registration schemes in case of ILD CT follow-up analysis indicate the significance of adaptive stochastic gradient descent optimizer, as well as the importance of combined rigid and nonrigid schemes providing high accuracy and time efficiency. The selected optimal deformable registration schemes are equivalent in terms of their accuracy and thus compatible in terms of their clinical outcome.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Analysis of twelve genomes of the bacterium Kerstersia gyiorum from brown-throated sloths ( Bradypus variegatus ), the first from a non-human host

Kerstersia gyiorum is a Gram-negative bacterium found in various animals, including humans, where it has been associated with various infections. Knowledge of the basic biology of K. gyiorum is essential to understand the evolutionary strategies of niche adaptation and how this organism contributes to infectious diseases; however, genomic data about K. gyiorum is very limited, especially from non-human hosts. In this work, we sequenced 12 K. gyiorum genomes isolated from healthy free-living brown-throated sloths (Bradypus variegatus) in the Parque Estadual das Fontes do Ipiranga (São Paulo, Brazil), and compared them with genomes from isolates of human origin, in order to gain insights into genomic diversity, phylogeny, and host specialization of this species. Phylogenetic analysis revealed that these K. gyiorum strains are structured according to host. Despite the fact that sloth isolates were sampled from a single geographic location, the intra-sloth K. gyiorum diversity was divided into three clusters, with differences of more than 1,000 single nucleotide polymorphisms between them, suggesting the circulation of various K. gyiorum lineages in sloths. Genes involved in mobilome and defense mechanisms against mobile genetic elements were the main source of gene content variation between isolates from different hosts. Sloth-specific K. gyiorum genome features include an IncN2 plasmid, a phage sequence, and a CRISPR-Cas system. The broad diversity of defense elements in K. gyiorum (14 systems) may prevent further mobile element flow and explain the low amount of mobile genetic elements in K. gyiorum genomes. Gene content variation may be important for the adaptation of K. gyiorum to different host niches. This study furthers our understanding of diversity, host adaptation, and evolution of K. gyiorum, by presenting and analyzing the first genomes of non-human isolates.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Adaptive variation and plasticity in non‐structural carbohydrate storage in a temperate tree species

Abstract Trees' total amount of non‐structural carbohydrate (NSC) stores and the proportion of these stores residing as insoluble starch are vital traits for individuals living in variable environments. However, our understanding of how stores vary in response to environmental stress is poorly understood as the genetic component of storage is rarely accounted for in studies. Here, we quantified variation in NSC traits in branch samples taken from over 600 clonally transplanted black cottonwood ( Populus trichocarpa) trees grown in two common gardens. We found heritable variation in both total NSC stores and the proportion of stores in starch (H 2 TNC = 0.19, H 2 PropStarch = 0.31), indicating a substantial genetic component of variation. In addition, we found high amounts of plasticity in both traits in response to cold temperatures and significant genotype‐by‐environment (GxE) interactions in the total amount of NSC stored (54% of P is GxE). This finding of high GxE indicates extensive variation across trees in their response to environment, which may explain why previous studies of carbohydrate stores' responses to stress have failed to converge on a consistent pattern. Overall, we found high amounts of environmental and genetic variation in NSC storage concentrations, which may bolster species against future climate change.

Blumstein, Meghan↗