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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 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
NASA NTRS2007

Collaborative Resource Allocation

Collaborative Resource Allocation Networking Environment (CRANE) Version 0.5 is a prototype created to prove the newest concept of using a distributed environment to schedule Deep Space Network (DSN) antenna times in a collaborative fashion. This program is for all space-flight and terrestrial science project users and DSN schedulers to perform scheduling activities and conflict resolution, both synchronously and asynchronously. Project schedulers can, for the first time, participate directly in scheduling their tracking times into the official DSN schedule, and negotiate directly with other projects in an integrated scheduling system. A master schedule covers long-range, mid-range, near-real-time, and real-time scheduling time frames all in one, rather than the current method of separate functions that are supported by different processes and tools. CRANE also provides private workspaces (both dynamic and static), data sharing, scenario management, user control, rapid messaging (based on Java Message Service), data/time synchronization, workflow management, notification (including emails), conflict checking, and a linkage to a schedule generation engine. The data structure with corresponding database design combines object trees with multiple associated mortal instances and relational database to provide unprecedented traceability and simplify the existing DSN XML schedule representation. These technologies are used to provide traceability, schedule negotiation, conflict resolution, and load forecasting from real-time operations to long-range loading analysis up to 20 years in the future. CRANE includes a database, a stored procedure layer, an agent-based middle tier, a Web service wrapper, a Windows Integrated Analysis Environment (IAE), a Java application, and a Web page interface.

Wang, Yeou-Fang↗
DOE OSTI2020

The mutualism effector MiSSP7 of Laccaria bicolor alters the interactions between the poplar JAZ6 protein and its associated proteins

Despite the pivotal role of jasmonic acid in the outcome of plant-microorganism interactions, JA-signaling components in roots of perennial trees like western balsam poplar (Populus trichocarpa) are poorly characterized. Here we decipher the poplar-root JA-perception complex centered on PtJAZ6, a co-repressor of JA-signaling targeted by the effector protein MiSSP7 from the ectomycorrhizal basidiomycete Laccaria bicolor during symbiotic development. Through protein–protein interaction studies in yeast we determined the poplar root proteins interacting with PtJAZ6. Moreover, we assessed via yeast triple-hybrid how the mutualistic effector MiSSP7 reshapes the association between PtJAZ6 and its partner proteins. In the absence of the symbiotic effector, PtJAZ6 interacts with the transcription factors PtMYC2s and PtJAM1.1. In addition, PtJAZ6 interacts with it-self and with other Populus JAZ proteins. Finally, MiSSP7 strengthens the binding of PtJAZ6 to PtMYC2.1 and antagonizes PtJAZ6 homo-/heterodimerization. We conclude that a symbiotic effector secreted by a mutualistic fungus may promote the symbiotic interaction through altered dynamics of a JA-signaling-associated protein–protein interaction network, maintaining the repression of PtMYC2.1-regulated genes.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

NASA Tech Briefs, November 2003

Topics covered include: Computer Program Recognizes Patterns in Time-Series Data; Program for User-Friendly Management of Input and Output Data Sets; Noncoherent Tracking of a Source of a Data-Modulated Signal; Software for Acquiring Image Data for PIV; Detecting Edges in Images by Use of Fuzzy Reasoning; A Timer for Synchronous Digital Systems; Prototype Parts of a Digital Beam-Forming Wide-Band Receiver; High-Voltage Droplet Dispenser; Network Extender for MIL-STD-1553 Bus; MMIC HEMT Power Amplifier for 140 to 170 GHz; Piezoelectric Diffraction-Based Optical Switches; Numerical Modeling of Nanoelectronic Devices; Organizing Diverse, Distributed Project Information; Eigensolver for a Sparse, Large Hermitian Matrix; Modified Polar-Format Software for Processing SAR Data; e-Stars Template Builder; Software for Acoustic Rendering; Functionally Graded Nanophase Beryllium/Carbon Composites; Thin Thermal-Insulation Blankets for Very High Temperatures; Prolonging Microgravity on Parabolic Airplane Flights; Device for Locking a Control Knob; Cable-Dispensing Cart; Foam Sensor Structures Would be Self-Deployable and Survive Hard Landings; Real-Gas Effects on Binary Mixing Layers; Earth-Space Link Attenuation Estimation via Ground Radar Kdp; Wedge Heat-Flux Indicators for Flash Thermography; Measuring Diffusion of Liquids by Common-Path Interferometry; Zero-Shear, Low-Disturbance Optical Delay Line; Whispering-Gallery Mode-Locked Lasers; Spatial Light Modulators as Optical Crossbar Switches; Update on EMD and Hilbert-Spectra Analysis of Time Series; Quad-Tree Visual-Calculus Analysis of Satellite Coverage; Dyakonov-Perel Effect on Spin Dephasing in n-Type GaAs; Update on Area Production in Mixing of Supercritical Fluids; and Quasi-Sun-Pointing of Spacecraft Using Radiation Pressure.

Source record↗
DOE OSTI2022

4D electrical resistivity tomography for assessing the influence of vegetation and subsurface moisture on railway cutting condition

Instability of slopes, embankments, and cuttings on the railway network is increasingly prevalent globally. Monitoring vulnerable infrastructure aids in geotechnical asset management, and improvements to transport safety and efficiency. Here, we examine the use of a novel, near-real-time Electrical Resistivity Tomography (ERT) monitoring system for assessing the stability of a railway cutting in Leicestershire, United Kingdom. In 2015, an ERT monitoring system was installed across a relict landslide (grassed) and an area of more stable ground on either side (wooded), to monitor changes in electrical resistivity through time and space, and to assess the influence of different types of vegetation on the stability of transportation infrastructure. Two years of 4-Dimensional ERT monitoring results are presented here, and petrophysical relationships developed in the laboratory are applied to calibrate the resistivity models in order to provide an insight into hydrogeological pathways within a railway cutting. The influence of vegetation type on subsurface moisture pathways and on slope stability is also assessed – here we find that seasonal subsurface changes in moisture content and soil suction are exacerbated by the presence of trees (wooded area). This results in shrink-swell behaviour of the clays comprising the railway cutting, resulting in fissuring and a reduction in shear strength, leading to instability. As such, it is proposed that on slopes comprised of expansive soils, grassed slopes are beneficial for stability. Insights into the use of 4-D ERT for monitoring railway infrastructure gained from this study may be applied to the monitoring of critical geotechnical assets elsewhere.

58 GEOSCIENCES↗
DOE OSTI2026

Feature Engineering and Ensemble Methods for Imbalanced ICS Intrusion Detection: Pipeline Audit and Constrained Evaluation

Industries are becoming increasingly connected and are more vulnerable to cyberattacks due to the widened attack surface. Industrial Control Systems (ICS) are among the most critical sectors that malicious actors can target, as such attacks can cause significant operational disruption and physical damage. It is imperative to detect such attacks as early as possible. This paper evaluates constraint-conditioned optimistic performance estimates for traditional ML models in ICS intrusion detection (i.e., estimates obtained under contiguous, non-shuffled temporal evaluation without test-set alteration, but with pre-split feature engineering that may introduce temporal leakage, due to dataset constraints). Our findings are threefold. First, we quantify how iterative feature engineering affects tree-based ensemble performance and examine how pipeline decisions (split strategy, sampling scope, and cleaning policy) can inflate or reduce reported IDS results under constraint-bound evaluation. Second, we compare intrinsic class-imbalance handling across ensemble models. Third, under our current pipeline constraints (including pre-split feature engineering), CatBoost achieves the best performance on Water Storage Tank (accuracy: 0.9831, class-1 F1: 0.9682), while Light- GBM achieves the best performance on Gas Pipeline (accuracy: 0.9618, class-1 F1: 0.9086).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

A 1D–0D–3D coupled model for simulating blood flow and transport processes in breast tissue

In this work, we present mixed dimensional models for simulating blood flow and transport processes in breast tissue and the vascular tree supplying it. These processes are considered, to start from the aortic inlet to the capillaries and tissue of the breast. Large variations in biophysical properties and flow conditions exist in this system necessitating the use of different flow models for different geometries and flow regimes. In total, we consider four different model types. First, a system of 1D nonlinear hyperbolic partial differential equations (PDEs) is considered to simulate blood flow in larger arteries with highly elastic vessel walls. Second, we assign 1D linearized hyperbolic PDEs to model the smaller arteries with stiffer vessel walls. The third model type consists of ODE systems (0D models). It is used to model the arterioles and peripheral circulation. Finally, homogenized 3D porous media models are considered to simulate flow and transport in capillaries and tissue within the breast volume. Sink terms are used to account for the influence of the venous and lymphatic systems. Combining the four model types, we obtain two different 1D–0D–3D coupled models for simulating blood flow and transport processes: The first model results in a fully coupled 1D–0D–3D model covering the complete path from the aorta to the breast combining a generic arterial network with a patient specific breast network and geometry. The second model is a reduced one based on the separation of the generic and patient specific parts. The information from a calibrated fully coupled model is used as inflow condition for the patient specific sub-model allowing a significant computational cost reduction. Several numerical experiments are conducted to calibrate the generic model parameters and to demonstrate realistic flow simulations compared to existing data on blood flow in the human breast and vascular system. Moreover, we use two different breast vasculature and tissue data sets to illustrate the robustness of our reduced sub-model approach.

multiscale blood flow models↗
NASA NTRS2007

NASA Tech Briefs, March 2007

Topics include: Advanced Systems for Monitoring Underwater Sounds; Wireless Data-Acquisition System for Testing Rocket Engines; Processing Raw HST Data With Up-to-Date Calibration Data; Mobile Collection and Automated Interpretation of EEG Data; System for Secure Integration of Aviation Data; Servomotor and Controller Having Large Dynamic Range; Digital Multicasting of Multiple Audio Streams; Translator for Optimizing Fluid-Handling Components; AIRSAR Web-Based Data Processing; Pattern Matcher for Trees Constructed From Lists; Reducing a Knowledge-Base Search Space When Data Are Missing; Ground-Based Correction of Remote-Sensing Spectral Imagery; State-Chart Autocoder; Pointing History Engine for the Spitzer Space Telescope; Low-Friction, High-Stiffness Joint for Uniaxial Load Cell; Magnet-Based System for Docking of Miniature Spacecraft; Electromechanically Actuated Valve for Controlling Flow Rate; Plumbing Fixture for a Microfluidic Cartridge; Camera Mount for a Head-Up Display; Core-Cutoff Tool; Recirculation of Laser Power in an Atomic Fountain; Simplified Generation of High-Angular-Momentum Light Beams; Imaging Spectrometer on a Chip; Interferometric Quantum-Nondemolition Single-Photon Detectors; Ring-Down Spectroscopy for Characterizing a CW Raman Laser; Complex Type-II Interband Cascade MQW Photodetectors; Single-Point Access to Data Distributed on Many Processors; Estimating Dust and Water Ice Content of the Martian Atmosphere From THEMIS Data; Computing a Stability Spectrum by Use of the HHT; Theoretical Studies of Routes to Synthesis of Tetrahedral N4; Estimation Filter for Alignment of the Spitzer Space Telescope; Antenna for Measuring Electric Fields Within the Inner Heliosphere; Improved High-Voltage Gas Isolator for Ion Thruster; and Hybrid Mobile Communication Networks for Planetary Exploration.

Source record↗
NASA NTRS2012

Wide Range SET Pulse Measurement

A method for measuring a wide range of SET pulses is demonstrated. Use of dynamic logic, faster than ordinary CMOS, allows capture of short pulses. A weighted binning of SET lengths allows measurement of a wide range of pulse lengths with compact circuitry. A pulse-length-conservative pulse combiner tree routes SETs from combinational logic to the measurement circuit, allowing SET measurements in circuits that cannot easily be arranged in long chains. The method is applied to add-multiplex combinational logic, and to an array of NFET routing switches, at .35 micron. Pulses are captured in a chain of Domino Logic AND gates. Propagation through the chain is frozen on the trailing edge by dropping low the second "enable" input to the AND gates. Capacitive loading is increased in the latter stages to create an approximately logarithmic weighted binning, so that a broad range of pulse lengths can be captured with a 10 stage capture chain. Simulations show pulses can be captured which are 1/5th the length of those typically captured with leading edge triggered latch methods, and less than the length of those captured with a trailing edge latch method. After capture, the pulse pattern is transferred to an SEU protected shift register for readout. 64 instances of each of two types of logic are used as targets. One is a full adder with a 4 to 1 mux on its inputs. The other is a 4 x 4 NFET routing matrix. The outputs are passed through buffered XNOR comparators to identify pulses, which are merged in a buffered not-nand (OR) tree designed to avoid pulse absorption as much as possible. The output from each of the two test circuits are input into separate pulse measurement circuits. Test inputs were provided so that the circuit could be bench tested and calibrated. A third SET measurement circuit with no inputs was used to judge the contribution from direct hits on the measurement circuit. Heavy ions were used with an LET range from 12 to 176. At LET of 21 and below, the very small number of SETs were not significantly higher in the test over the control circuits. At higher LET the test circuit SETs are one or two orders of magnitude greater than for the control circuit. The NFET circuit produces more and slightly longer SETs as expected. But the differences do not appear to be significant enough to modify strategies now used to avoid capture of SETs in chips such as FPGAs. Complete data and graphs will be in the full paper / presentation. In the summary figure below left, NOCL is the reference circuit without any input, and number of stages triggered is plotted. Simulation at right shows the smallest pulse captured (stage 2) at about 300 ps. Our conclusion is that the method is promising, but that improvements in the merge network are desirable before applying in a deep submicron process

Shuler, Robert L.↗
DOE OSTI2024

Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses

Thermophily is a trait scattered across the fungal tree of life, with its highest prevalence within three fungal families (Chaetomiaceae, Thermoascaceae, and Trichocomaceae), as well as some members of the phylum Mucoromycota. We examined 37 thermophilic and thermotolerant species and 42 mesophilic species for this study and identified thermophily as the ancestral state of all three prominent families of thermophilic fungi. Thermophilic fungal genomes were found to encode various thermostable enzymes, including carbohydrate-active enzymes such as endoxylanases, which are useful for many industrial applications. At the same time, the overall gene counts, especially in gene families responsible for microbial defense such as secondary metabolism, are reduced in thermophiles compared to mesophiles. We also found a reduction in the core genome size of thermophiles in both the Chaetomiaceae family and the Eurotiomycetes class. The Gene Ontology terms lost in thermophilic fungi include primary metabolism, transporters, UV response, and O-methyltransferases. Comparative genomics analysis also revealed higher GC content in the third base of codons (GC3) and a lower effective number of codons in fungal thermophiles than in both thermotolerant and mesophilic fungi. Furthermore, using the Support Vector Machine classifier, we identified several Pfam domains capable of discriminating between genomes of thermophiles and mesophiles with 94% accuracy. Using AlphaFold2 to predict protein structures of endoxylanases (GH10), we built a similarity network based on the structures. We found that the number of disulfide bonds appears important for protein structure, and the network clusters based on protein structures correlate with the optimal activity temperature. Thus, comparative genomics offers new insights into the biology, adaptation, and evolutionary history of thermophilic fungi while providing a parts list for bioengineering applications.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2005

Evidence of Urban-Induced Precipitation Variability in Arid Climate Regimes

Water is essential to life in the Earth system. The water cycle components that sustain life are becoming more scarce and polluted. The most recent (1999-2004) drought experienced in the southwestern United States is the seventh worst in the approximately 500-year proxy tree-ring record. As a result, many regions contemplated drought emergencies in which severe water restrictions are implemented. Though larger weather and climate processes likely control drought processes, there is increasing evidence that anthropogenic or human-related activities can significantly alter precipitation processes. Urbanization is an example of anthropogenic forcing. Recent studies continue to provide evidence that urban environments can modify or induce precipitation under a specific set of conditions. Arid and semi-arid regions of the southwestern United States and other parts of the world are rapidly developing and placing greater demands on the environmental system. In the past fifty years, Phoenix has expanded from a predominantly agricultural center to an urbanized region with extent 700 percent larger than its size in the middle of the twentieth century. Riyadh's population grew from about a half million people in 1972 to almost two million by 2000. Saudi Arabia experienced urbanization later than many other countries; in the early 1970s its urban-rural ratio was still about 1:3. By 1990 the ratio had reversed to about 3:l. In the mid-1970s Riyadh's population was increasing by about 10 percent a year. Irrigation also significantly increased between 1972 and 1990 southeast of Riyadh. The study employs a 108-year precipitation historical data record, global climate observing network observations and satellite data to identify possible anomalies in rainfall in and around two major arid urban areas, Phoenix, Arizona and Riyadh, Saudi Arabia. It provides statistically sound evidence that rainfall distribution and magnitude is statistically different in post-urban than in pre-urban (1900-1950) Phoenix. The study hypothesis that a complex interaction between the city landscape, irrigated lands, and nearby mountains have created preferred regions for rainfall development. The study also provides early evidence that rapidly urbanizing parts of the arid Middle East may also be experiencing different precipitation regimes in response to urbanization and irrigation.

Shepherd, J. Marshall↗
NASA NTRS2014

Ultra-Wideband, Dual-Polarized, Beam-Steering P-Band Array Antenna

A dual-polarized, wide-bandwidth (200 MHz for one polarization, 100 MHz for the orthogonal polarization) antenna array at P-band was designed to be driven by NASA's EcoSAR digital beam former. EcoSAR requires two wide P-band antenna arrays mounted on the wings of an aircraft, each capable of steering its main beam up to 35deg off-boresight, allowing the twin radar beams to be steered at angles to the flight path. The science requirements are mainly for dual-polarization capability and a wide bandwidth of operation of up to 200 MHz if possible, but at least 100 MHz with high polarization port isolation and low cross-polarization. The novel design geometry can be scaled with minor modifications up to about four times higher or down to about half the current design frequencies for any application requiring a dual-polarized, wide-bandwidth steerable antenna array. EcoSAR is an airborne interferometric P-band synthetic aperture radar (SAR) research application for studying two- and three-dimensional fine-scale measurements of terrestrial ecosystem structure and biomass, which will ultimately aid in the broader study of the carbon cycle and climate change. The two 2×8 element Pband antenna arrays required by the system will be separated by a baseline of about 25 m, allowing for interferometry measurements. The wide 100-to- 200-MHz bandwidth dual-polarized beams employed will allow the determination of the amount of biomass and even tree height on the ground. To reduce the size of the patches along the boresight dimension in order to fit them into the available space, two techniques were employed. One technique is to add slots along the edges of each patch where the main electric currents are expected to flow, and the other technique is to bend the central part of the patch away from the ground plane. The latter also facilitates higher mechanical rigidity. The high port isolation of more than 40 dB was achieved by employing a highly symmetrical feed mechanism for each pair of elements: three apertures coupling to the patch elements were placed along the two symmetry lines of the antenna element pair. Two apertures were used in tandem to excite two of the stacked patch elements for one polarization; the other was used to excite one element from one side and the other element from the other side, opposite in phase, taking care of the remaining polarization. The apertures narrow down to a small gap where they are excited by a crossing microstrip line to prevent any asymmetrical excitation of the two sides of the aperture gap, minimizing port-to-port coupling. Using patches that are non-planar leads to higher mechanical rigidity and smaller patch sizes to fit into the available space. Aperture coupling minimizes direct metal-to-metal connections. Using an aperture coupling feed mechanism results in a feed network for two antenna elements with a total of three feed points, plus one simple in-phase combiner to reduce it to two ports. It greatly reduces the complexity of the alternative, but more conventional, way of feeding a pair of two dual-polarized elements with high port isolation.

duToit, Cornelis↗
DOE OSTI2025

Leveraging structure-informed machine learning for fast steric zipper propensity prediction across whole proteomes

Predicting the amyloid fold and the propensity of peptide segments to adopt amyloid-like structures remain a challenge. However, recent progress has facilitated structure-based prediction of steric zipper propensity and the use of machine learning to accelerate the calculation of predictive models across many scientific areas. Leveraging these advances, we have developed a new approach for rapid proteome-wide assessment of zipper profiles that is informed by four million steric zipper predictions collected over ten years. This collection is used to build a machine learning model capable of rapidly predicting steric zipper propensity, and allowing for the assessment of zippers at both the protein and proteome level. Our predictions show enrichment for zipper forming segments in proteins involved in cell wall reorganization in yeast, highlighting a potential category of interest for experimental characterization. Overall, our predictive model allows for the exploration of amyloid formation across the tree of life and provides a tool for assessment of both novel and designed sequences for zipper density.

Biochemistry & Molecular Biology↗
DOE OSTI2024

COMPASS-FME Synoptic Sites Level 1 Sensor Data v1-2

This is the version 1-2 Level 1 (L1) data release for COMPASS-FME environmental sensors located at our synoptic field sites. COMPASS-FME is studying sites in two distinct regions, the Chesapeake Bay and the Western Lake Erie Basin. We established the network at seven "synoptic" (observational) sites along the Chesapeake Bay and Lake Erie coastlines, collectively generating over three million observations per month, to track and comprehend environmental changes where land and water intersect. Additionally, the two regions provide an interesting contrast of saltwater and freshwater coasts that allow us to differentiate the impacts of inundation and coastal water chemistries in two nationally important coastal systems.L1 data are close to raw, but are units-transformed and have out-of-instrument-bounds and out-of-service flags added. Duplicates and missing data are removed but otherwise these data are not filtered, and have not been subject to any additional algorithmic or human QA/QC. Any scientific analyses of L1 data should be performed with care. **This dataset will be updated quarterly with new data for the duration of the project**This dataset includes:- An overall dataset README file that describes the current version, gives citation and contact information, etc.- Site- and year-specific folders, each holding up to 12 CSV (comma separated value) data files for each site and plot in that year.- Metadata files within each site-year folder provide full information on data units, expected ranges, contact information, as well as a general description of the site.- Environmental sensor types that appear in the data files include weather (ClimaVUE50, CS, RM Young, and LI instruments in the graphs below); soil conditions (TEROS12); soil redox state (Redox); groundwater variables (AquaTROLL200 and AquaTROLL600); open water sondes (Exo); tree sap velocity (Sapflow); and system voltage and state (Datalogger). Data are normally logged every 15 minutes. Please see v1-2 Synoptic L1 Sensor Package Quick Start.pdf for detailed information on data package structure, temporal coverage, and versioning.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

COMPASS-FME Synoptic Sites Level 1 Sensor Data v2-1

This is the version 2-1 Level 1 (L1) data release for COMPASS-FME environmental sensors located at our synoptic field sites. COMPASS-FME is studying sites in two distinct regions, the Chesapeake Bay and the Western Lake Erie Basin. We established the network at seven "synoptic" (observational) sites along the Chesapeake Bay and Lake Erie coastlines, collectively generating over three million observations per month, to track and comprehend environmental changes where land and water intersect. Additionally, the two regions provide an interesting contrast of saltwater and freshwater coasts that allow us to differentiate the impacts of inundation and coastal water chemistries in two nationally important coastal systems. L1 data are close to raw, but are units-transformed and have out-of-instrument-bounds, out-of-service, and outlier flags added. Duplicates and missing data are removed but otherwise these data are not filtered, and have not been subject to any additional algorithmic or human QA/QC. Any scientific analyses of L1 data should be performed with care. **This dataset will be updated quarterly with new data for the duration of the project** This dataset includes: - An overall dataset README file that describes the current version, gives citation and contact information, etc. - Site- and year-specific folders, each holding up to 12 CSV (comma separated value) data files for each site and plot in that year. - Metadata files within each site-year folder provide full information on data units, expected ranges, contact information, as well as a general description of the site. - Environmental sensor types that appear in the data files include weather (ClimaVUE50, CS, RM Young, and LI instruments in the graphs below); soil conditions (TEROS12); soil redox state (Redox); groundwater variables (AquaTROLL200 and AquaTROLL600); open water sondes (Exo); tree sap velocity (Sapflow); and system voltage and state (Datalogger). Data are normally logged every 15 minutes. Please see v2-0 Synoptic L1 Sensor Package Quick Start.pdf for detailed information on data package structure, temporal coverage, and versioning. This dataset was updated 2026-03-12: (i) data now go through 2025-12-31 (previous end was 2025-06-30) and (ii) dataset and file names updated to “…v2-1” (previously was “v2-0”).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Rapid Cis–Trans Coevolution Driven by a Novel Gene Retroposed from a Eukaryotic Conserved CCR4–NOT Component in Drosophila

Young, or newly evolved, genes arise ubiquitously across the tree of life, and they can rapidly acquire novel functions that influence a diverse array of biological processes. Previous work identified a young regulatory duplicate gene in Drosophila, Zeus that unexpectedly diverged rapidly from its parent, Caf40, an extremely conserved component in the CCR4–NOT machinery in post-transcriptional and post-translational regulation of eukaryotic cells, and took on roles in the male reproductive system. This neofunctionalization was accompanied by differential binding of the Zeus protein to loci throughout the Drosophila melanogaster genome. However, the way in which new DNA-binding proteins acquire and coevolve with their targets in the genome is not understood. Here, by comparing Zeus ChIP-Seq data from D. melanogaster and D. simulans to the ancestral Caf40 binding events from D. yakuba, a species that diverged before the duplication event, we found a dynamic pattern in which Zeus binding rapidly coevolved with a previously unknown DNA motif, which we term Caf40 and Zeus-Associated Motif (CAZAM), under the influence of positive selection. Interestingly, while both copies of Zeus acquired targets at male-biased and testis-specific genes, D. melanogaster and D. simulans proteins have specialized binding on different chromosomes, a pattern echoed in the evolution of the associated motif. Using CRISPR-Cas9-mediated gene knockout of Zeus and RNA-Seq, we found that Zeus regulated the expression of 661 differentially expressed genes (DEGs). Our results suggest that the evolution of young regulatory genes can be coupled to substantial rewiring of the transcriptional networks into which they integrate, even over short evolutionary timescales. Our results thus uncover dynamic genome-wide evolutionary processes associated with new genes.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2005

Effects of artificial defoliation of pines on the structure and physiology of the soil fungal community of a mixed pine-spruce forest

Loss of photosynthetic area can affect soil microbial communities by altering the availability of fixed carbon. We used denaturing gradient gel electrophoresis (DGGE) and Biolog filamentous-fungus plates to determine the effects of artificial defoliation of pines in a mixed pine-spruce forest on the composition of the fungal community in a forest soil. As measured by DGGE, two fungal species were affected significantly by the defoliation of pines (P < 0.001); the frequency of members of the ectomycorrhizal fungus genus Cenococcum decreased significantly, while the frequency of organisms of an unidentified soil fungus increased. The decrease in the amount of Cenococcum organisms may have occurred because of the formation of extensive hyphal networks by species of this genus, which require more of the carbon fixed by their host, or because this fungus is dependent upon quantitative differences in spruce root exudates. The defoliation of pines did not affect the overall composition of the soil fungal community or fungal-species richness (number of species per core). Biolog filamentous-fungus plate assays indicated a significant increase (P < 0.001) in the number of carbon substrates utilized by the soil fungi and the rate at which these substrates were used, which could indicate an increase in fungal-species richness. Thus, either small changes in the soil fungal community give rise to significant increases in physiological capabilities or PCR bias limits the reliability of the DGGE results. These data indicate that combined genetic and physiological assessments of the soil fungal community are needed to accurately assess the effect of disturbance on indigenous microbial systems.

Pinus/growth & development/physiology↗
DOE OSTI2020

Using CESM-RESFire to understand climate–fire–ecosystem interactions and the implications for decadal climate variability

Large wildfires exert strong disturbance on regional and global climate systems and ecosystems by perturbing radiative forcing as well as the carbon and water balance between the atmosphere and land surface, while short- and long-term variations in fire weather, terrestrial ecosystems, and human activity modulate fire intensity and reshape fire regimes. The complex climate–fire–ecosystem interactions were not fully integrated in previous climate model studies, and the resulting effects on the projections of future climate change are not well understood. Here we use the fully interactive REgion-Specific ecosystem feedback Fire model (RESFire) that was developed in the Community Earth System Model (CESM) to investigate these interactions and their impacts on climate systems and fire activity. We designed two sets of decadal simulations using CESM-RESFire for present-day (2001–2010) and future (2051–2060) scenarios, respectively, and conducted a series of sensitivity experiments to assess the effects of individual feedback pathways among climate, fire, and ecosystems. Our implementation of RESFire, which includes online land–atmosphere coupling of fire emissions and fire-induced land cover change (LCC), reproduces the observed aerosol optical depth (AOD) from space-based Moderate Resolution Imaging Spectroradiometer (MODIS) satellite products and ground-based AErosol RObotic NETwork (AERONET) data; it agrees well with carbon budget benchmarks from previous studies. We estimate the global averaged net radiative effect of both fire aerosols and fire-induced LCC at –0.59±0.52 W m –2 , which is dominated by fire aerosol–cloud interactions (–0.82±0.19 W m –2 ), in the present-day scenario under climatological conditions of the 2000s. The fire-related net cooling effect increases by ~170 % to –1.60±0.27 W m –2 in the 2050s under the conditions of the Representative Concentration Pathway 4.5 (RCP4.5) scenario. Such considerably enhanced radiative effect is attributed to the largely increased global burned area (+19 %) and fire carbon emissions (+100 %) from the 2000s to the 2050s driven by climate change. The net ecosystem exchange (NEE) of carbon between the land and atmosphere components in the simulations increases by 33 % accordingly, implying that biomass burning is an increasing carbon source at short-term timescales in the future. High-latitude regions with prevalent peatlands would be more vulnerable to increased fire threats due to climate change, and the increase in fire aerosols could counter the projected decrease in anthropogenic aerosols due to air pollution control policies in many regions. We also evaluate two distinct feedback mechanisms that are associated with fire aerosols and fire-induced LCC, respectively. On a global scale, the first mechanism imposes positive feedbacks to fire activity through enhanced droughts with suppressed precipitation by fire aerosol–cloud interactions, while the second one manifests as negative feedbacks due to reduced fuel loads by fire consumption and post-fire tree mortality and recovery processes. These two feedback pathways with opposite effects compete at regional to global scales and increase the complexity of climate–fire–ecosystem interactions and their climatic impacts.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2011

Tracking Climate Effects on Plant-Pollinator Interaction Phenology with Satellites and Honey Bee Hives

Background/Question/Methods: The complexity of plant-pollinator interactions, the large number of species involved, and the lack of species response functions present challenges to understanding how these critical interactions may be impacted by climate and land cover change on large scales. Given the importance of this interaction for terrestrial ecosystems, it is desirable to develop new approaches. We monitor the daily weight change of honey bee (Apis mellifera) colonies to record the phenology of the Honey Bee Nectar Flow (HBNF) in a volunteer network (honeybeenet.gsfc.nasa.gov). The records document the successful interaction of a generalist pollinator with a variety of plant resources. We extract useful HBNF phenology metrics for three seasons. Sites currently exist in 35 states/provinces in North America, with a concentration in the Mid-Atlantic region. HBNF metrics are compared to standard phenology metrics derived from remotely sensed vegetation indices from NASA's MODIS sensor and published results from NOAA's A VHRR. At any given time the percentage of plants producing nectar is usually a sma11 fraction of the total satellite sensor signal. We are interested in determining how well the 'bulk' satellite vegetation parameters relate to the phenology of the HBNF, and how it varies spatially on landscape to continental scales. Results/Conclusions: We found the median and peak seasonal HBNF dates to be robust, with variation between replicate scale hives of only a few days. We developed quality assessment protocols to identify abnormal colony artifacts. Temporally, the peak and median of the HBNF in the Mid-Atlantic show a significant advance of 0.58 d/y beginning about 1970, very similar to that observed by the A VHRR since 1982 (0.57 d/y). Spatially, the HBNF metrics are highly correlated with elevation and winter minimum temperature distribution, and exhibit significant but regionally coherent inter-annual variation. The relationship between median of the spring HBNF with the "Green-up" metric from the 500 meter MODIS NDVI phenology product, for sites throughout the Eastern US 2000-2009, is well described by a single linear fit (r(exp 2) = 0.72). We conclude.that for the tree-dominated areas of the Eastern US at least the spring HBNF can be tracked very well by MODIS phenology. Analysis of other regions and seasons is presently underway but with more limited data. Spatial patterns in the eastern US and management implications will be presented and discussed.

Esaias, Wayne E.↗