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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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All sourcesNASA NTRSDOE OSTI
NASA NTRS2010

High-Speed Ring Bus

The high-speed ring bus at the Jet Propulsion Laboratory (JPL) allows for future growth trends in spacecraft seen with future scientific missions. This innovation constitutes an enhancement of the 1393 bus as documented in the Institute of Electrical and Electronics Engineers (IEEE) 1393-1999 standard for a spaceborne fiber-optic data bus. It allows for high-bandwidth and time synchronization of all nodes on the ring. The JPL ring bus allows for interconnection of active units with autonomous operation and increased fault handling at high bandwidths. It minimizes the flight software interface with an intelligent physical layer design that has few states to manage as well as simplified testability. The design will soon be documented in the AS-1393 standard (Serial Hi-Rel Ring Network for Aerospace Applications). The framework is designed for "Class A" spacecraft operation and provides redundant data paths. It is based on "fault containment regions" and "redundant functional regions (RFR)" and has a method for allocating cables that completely supports the redundancy in spacecraft design, allowing for a complete RFR to fail. This design reduces the mass of the bus by incorporating both the Control Unit and the Data Unit in the same hardware. The standard uses ATM (asynchronous transfer mode) packets, standardized by ITU-T, ANSI, ETSI, and the ATM Forum. The IEEE-1393 standard uses the UNI form of the packet and provides no protection for the data portion of the cell. The JPL design adds optional formatting to this data portion. This design extends fault protection beyond that of the interconnect. This includes adding protection to the data portion that is contained within the Bus Interface Units (BIUs) and by adding to the signal interface between the Data Host and the JPL 1393 Ring Bus. Data transfer on the ring bus does not involve a master or initiator. Following bus protocol, any BIU may transmit data on the ring whenever it has data received from its host. There is no centralized arbitration or bus granting. The JPL design provides for autonomous synchronization of the nodes on the ring bus. An address-synchronous latency adjust buffer (LAB) has been designed that cannot get out of synchronization and needs no external input. Also, a priority-driven cable selection behavior has been programmed into each unit on the ring bus. This makes the bus able to connect itself up, according to a maximum redundancy priority system, without the need for computer intervention at startup. Switching around a failed or switched-off unit is also autonomous. The JPL bus provides a map of all the active units for the host computer to read and use for fault management. With regard to timing, this enhanced bus recognizes coordinated timing on a spacecraft as critical and addresses this with a single source of absolute and relative time, which is broadcast to all units on the bus with synchronization maintained to the tens of nanoseconds. Each BIU consists of up to five programmable triggers, which may be programmed for synchronization of events within the spacecraft of instrument. All JPL-formatted data transmitted on the ring bus are automatically time-stamped.

Wysocky, Terry↗
NASA NTRS2019

Flood Mapping of Recent Major Hurricane Events with Synthetic Aperture Radar, Commercial Imaging, and Aerial Observations

Floodwater mapping is an important remote sensing process that is used for disaster response, recovery, and damage assessment practices. Developing a system to read in Synthetic Aperture Radar (SAR) data and perform land cover classification will allow for the production of near real-time inundation mapping, enabling government and emergency response entities to get a preliminary idea of the situation. SAR is a unique remote sensing tool. Data in this project was obtained by NASA Jet Propulsion Laboratory’s Uninhabited Aerial Vehicle SAR (UAVSAR), an L-band radar mounted to a Gulfstream III jet. Data collected by UAVSAR is similar to what will be available from the NASA-Indian Space Research Organization (NISAR) mission starting in early 2022. Using Python and ArcGIS applications, a model was developed using training samples taken from NOAA post-event aerial photography and UAVSAR data gathered in the aftermath of Hurricane Florence in September 2018.

Melancon, Alexander M.↗
DOE OSTI2017

Comparative analysis of metagenomes of Italian top soil improvers

Biosolids originating from Municipal Waste Water Treatment Plants are proposed as top soil improvers (TSI) for their beneficial input of organic carbon on agriculture lands. Their use to amend soil is controversial, as it may lead to the presence of emerging hazards of anthropogenic or animal origin in the environment devoted to food production. In this study, we used a shotgun metagenomics sequencing as a tool to perform a characterization of the hazards related with the TSIs. The samples showed the presence of many virulence genes associated to different diarrheagenic E. coli pathotypes as well as of different antimicrobial resistance-associated genes. The genes conferring resistance to Fluoroquinolones was the most relevant class of antimicrobial resistance genes observed in all the samples tested. To a lesser extent traits associated with the resistance to Methicillin in Staphylococci and genes conferring resistance to Streptothricin, Fosfomycin and Vancomycin were also identified. The most represented metal resistance genes were cobalt-zinc-cadmium related, accounting for 15–50% of the sequence reads in the different metagenomes out of the total number of those mapping on the class of resistance to compounds determinants. Moreover the taxonomic analysis performed by comparing compost-based samples and biosolids derived from municipal sewage-sludges treatments divided the samples into separate populations, based on the microbiota composition. The results confirm that the metagenomics is efficient to detect genomic traits associated with pathogens and antimicrobial resistance in complex matrices and this approach can be efficiently used for the traceability of TSI samples using the microorganisms’ profiles as indicators of their origin. - Highlights: • Sludge- and green- based biosolids analysed by metagenomics. • Biosolids may introduce microbial hazards in the food chain. • Metagenomics enables tracking biosolids’ sources.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Gut microbiota carbon and sulfur metabolisms support Salmonella infections

Abstract Salmonella enterica serovar Typhimurium is a pervasive enteric pathogen and ongoing global threat to public health. Ecological studies in the Salmonella impacted gut remain underrepresented in the literature, discounting microbiome mediated interactions that may inform Salmonella physiology during colonization and infection. To understand the microbial ecology of Salmonella remodeling of the gut microbiome, we performed multi-omics on fecal microbial communities from untreated and Salmonella-infected mice. Reconstructed genomes recruited metatranscriptomic and metabolomic data providing a strain-resolved view of the expressed metabolisms of the microbiome during Salmonella infection. These data informed possible Salmonella interactions with members of the gut microbiome that were previously uncharacterized. Salmonella-induced inflammation significantly reduced the diversity of genomes that recruited transcripts in the gut microbiome, yet increased transcript mapping was observed for seven members, among which Luxibacter and Ligilactobacillus transcript read recruitment was most prevalent. Metatranscriptomic insights from Salmonella and other persistent taxa in the inflamed microbiome further expounded the necessity for oxidative tolerance mechanisms to endure the host inflammatory responses to infection. In the inflamed gut lactate was a key metabolite, with microbiota production and consumption reported amongst members with detected transcript recruitment. We also showed that organic sulfur sources could be converted by gut microbiota to yield inorganic sulfur pools that become oxidized in the inflamed gut, resulting in thiosulfate and tetrathionate that support Salmonella respiration. This research advances physiological microbiome insights beyond prior amplicon-based approaches, with the transcriptionally active organismal and metabolic pathways outlined here offering intriguing intervention targets in the Salmonella-infected intestine.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Likelihood-based interactive local docking into cryo-EM maps in ChimeraX

The interpretation of cryo-EM maps often includes the docking of known or predicted structures of the components, which is particularly useful when the map resolution is worse than 4 Å. Although it can be effective to search the entire map to find the best placement of a component, the process can be slow when the maps are large. However, frequently there is a well-founded hypothesis about where particular components are located. In such cases, a local search using a map subvolume will be much faster because the search volume is smaller, and more sensitive because optimizing the search volume for the rotation-search step enhances the signal to noise. A Fourier-space likelihood-based local search approach, based on the previously published em_placement software, has been implemented in the new emplace_local program. Tests confirm that the local search approach enhances the speed and sensitivity of the computations. An interactive graphical interface in the ChimeraX molecular-graphics program provides a convenient way to set up and evaluate docking calculations, particularly in defining the part of the map into which the components should be placed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Data from: "Lab and Field Warming Similarly Advance Germination Date and Limit Germination Rate for High and Low Elevation Provenances of Two Widespread Subalpine Conifers"

This archive contains data used to draw conclusions in “Lab and Field Warming Similarly Advance Germination Date and Limit Germination Rate for High and Low Elevation Provenances of Two Widespread Subalpine Conifers”, by Kueppers et al. 2017. Cone collection and field experiments were conducted on Niwot Ridge, Colorado, with the latter completed within the Alpine Treeline Warming Experiment (ATWE). Laboratory germination experiments were conducted at the University of California Merced. Geospatial files are also provided for additional geographical context.There are four data file formats in this package: comma-separated values (.csv), Microsoft Excel (.xlsx), keyhole markup language (.kml), and ESRI shapefile (.shp). The latter two are geospatial file formats. .csv files can be opened using any simple text editor program such as TextEdit (Mac) and Notepad (Windows), and .xlsx files can be opened using Microsoft Excel or Google Sheets. The .kml file contains coordinate data, and is compatible with Google Earth and Google Maps. ESRI shapefiles (.shp) are compatible with any geospatial software able to read the file type, such as QGIS and ESRI’s ArcGIS Suite. This data user’s guide is available in as a .pdf, and can be opened using software such as Adobe Acrobat Reader.-----------------------------------------------------------------------------------------------------------------------------------Accurately predicting upslope shifts in subalpine tree ranges with warming requires understanding how future forest populations will be affected by climate change, as these are the seed sources for new tree line and alpine populations. Early life history stages are particularly sensitive to climate and are also influenced by genetic variation among populations. We tested the climate sensitivity of germination and initial development for two widely distributed subalpine conifers, using controlled-environment growth chambers with one temperature regime from subalpine forest in the Colorado Rocky Mountains and one 5 °C warmer, and two soil moisture levels. We tracked germination rate and timing, rate of seedling development, and seedling morphology for two seed provenances separated by ~300 m elevation. Warming advanced germination timing and initial seedling development by a total of ~2 weeks, advances comparable to mean differences between provenances. Advances were similar for both provenances and species; however, warming reduced the overall germination rate, as did low soil moisture, only for Picea engelmannii. A three-year field warming and watering experiment planted with the same species and provenances yielded responses qualitatively consistent with the lab trials. Together these experiments indicate that in a warmer, drier climate, P. engelmannii germination, and thus regeneration, could decline, which could lead to declining subalpine forest populations, while Pinus flexilis forest populations could remain robust as a seed source for upslope range shifts.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Optimizing Cell-based Antimicrobials through Pooled Genomic Libraries

DNA synthesis and assembly technologies ushered in through synthetic biology have great promise for biomanufacturing, bioremediation, and the development of living therapeutics. Unfortunately, predicting sequence to function relationships, including for biosynthetic pathways expressed in a new host organism, is difficult and often requires many iterative cycles of design, construction, and testing. We are working to develop data-driven approaches to identify the genetic determinants of growth defects and productivity for the expression of a cell-based antimicrobial. We assayed the growth, pigment production, and antimicrobial activity of a collection of over 10,000 genetic mutants of the violacein biosynthetic pathway and sequenced the genetic variation of these mutants. Through this project, we have developed an innovative codebase to automate the determination of pigmentation and antimicrobial clearing diameter for tens of thousands of genetic mutants cultivated on agar dishes. Further, we have written DNA sequence analysis code to demultiplex & provide consensus sequences from high-throughput PacBio long-read circular consensus sequencing (CCS) datasets. From this foundation, we plan to map DNA sequence to function to predict an optimal genetic design to maximize antimicrobial activity while minimizing deleterious growth effects. The workflows and algorithms developed through this project can be broadly applied to other engineered functions in microbes, uncovering sequence to function relationships for complex phenotypes where function impacts fitness.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1997

Functional specializations in human cerebral cortex analyzed using the Visible Man surface-based atlas

We used surface-based representations to analyze functional specializations in the human cerebral cortex. A computerized reconstruction of the cortical surface of the Visible Man digital atlas was generated and transformed to the Talairach coordinate system. This surface was also flattened and used to establish a surface-based coordinate system that respects the topology of the cortical sheet. The linkage between two-dimensional and three-dimensional representations allows the locations of published neuroimaging activation foci to be stereotaxically projected onto the Visible Man cortical flat map. An analysis of two activation studies related to the hearing and reading of music and of words illustrates how this approach permits the systematic estimation of the degree of functional segregation and of potential functional overlap for different aspects of sensory processing.

Non-NASA Center↗
NASA NTRS2017

Close Range Photogrammetry in Space - Measuring the On-Orbit Clearance between Hardware on the International Space Station

When photogrammetrists read an article entitled "Photogrammetry in Space" they immediately think of terrestrial mapping using satellite imagery. However in the last 19 years the roll of close range photogrammetry in support of the manned space flight program has grown exponentially. Management and engineers have repeatedly entrusted the safety of the vehicles and their crews to the results of photogrammetric analysis. In February 2010, the Node 3 module was attached to the port side Common Berthing Mechanism (CBM) of the International Space Station (ISS). Since this was not the location at which the module was originally designed to be located on the ISS, coolant lines containing liquid ammonia, were installed externally from the US Lab to Node 3 during a spacewalk. During mission preparation I had developed a plan and a set of procedures to have the astronauts acquire stereo imagery of these coolant lines at the conclusion of the spacewalk to enable us to map their as-installed location relative to the rest of the space station. Unfortunately, the actual installation of the coolant lines took longer than expected and in an effort to wrap up the spacewalk on time, the mission director made a real-time call to drop the photography. My efforts to reschedule the photography on a later spacewalk never materialized, so rather than having an as-installed model for the location of coolant lines, the master ISS CAD database continued to display an as-designed model of the coolant lines. Fast forward to the summer of 2015, the ISS program planned to berth a Japanese cargo module to the nadir Common Berthing Mechanism (CBM), immediately adjacent to the Node 3 module. A CAD based clearance analysis revealed a negative four inch clearance between the ammonia lines and a thruster nozzle on the port side of the cargo vehicle. Recognizing that the model of the ammonia line used in the clearance analysis was "as-designed" rather than "as-installed", I was asked to determine the real clearance between the ammonia lines and expected position of the thruster bell using existing on-orbit imagery. Imagery of the area of interest, taken several years earlier from the Space Shuttle during a fly-around of the ISS, was found and used to set a stereo pair. Space Vision System Targets and Handrail bolts measured in the ISS analytical coordinate system (ISSACS) prior to launch, were used to obtain an absolute orientation so all photogrammetric measurement's would be in the ISSACS coordinate system. Coordinates for the design location of the edges of the thruster bell, when the cargo vehicle was fully berthed to the ISS, were displayed in 3-D relative to the as-installed ammonia lines. This immediately revealed a positive clearance, which was later quantified to be a minimum of 10" +/0.5". The analysis was completed over a single weekend by a single analyst. Using updated imagery, acquired from the station's robotic arm, a complete as-installed model of the coolant lines was generated from stereo photography and replaced the design model in the master ISS CAD database.

Liddle, Donn↗
NASA NTRS1991

CD-ROM publication of the Mars digital cartographic data base

The recently completed Mars mosaicked digital image model (MDIM) and the soon-to-be-completed Mars digital terrain model (DTM) are being transcribed to optical disks to simplify distribution to planetary investigators. These models, completed in FY 1991, provide a cartographic base to which all existing Mars data can be registered. The digital image map of Mars is a cartographic extension of a set of compact disk read-only memory (CD-ROM) volumes containing individual Viking Orbiter images now being released. The data in these volumes are pristine in the sense that they were processed only to the extent required to view them as images. They contain the artifacts and the radiometric, geometric, and photometric characteristics of the raw data transmitted by the spacecraft. This new set of volumes, on the other hand, contains cartographic compilations made by processing the raw images to reduce radiometric and geometric distortions and to form geodetically controlled MDIM's. It also contains digitized versions of an airbrushed map of Mars as well as a listing of all feature names approved by the International Astronomical Union. In addition, special geodetic and photogrammetric processing has been performed to derive rasters of topographic data, or DTM's. The latter have a format similar to that of MDIM, except that elevation values are used in the array instead of image brightness values. The set consists of seven volumes: (1) Vastitas Borealis Region of Mars; (2) Xanthe Terra of Mars; (3) Amazonis Planitia Region of Mars; (4) Elysium Planitia Region of Mars; (5) Arabia Terra of Mars; (6) Planum Australe Region of Mars; and (7) a digital topographic map of Mars.

Batson, R. M.↗
NASA NTRS2005

Jet-Intracluster Medium Interactions of the Head Tail Radio Galaxy 3C 129

The 50 ksec XMM observations of the galaxy cluster 3C 129 were taken as scheduled, and the data are of good quality. We analyzed the data in the following way. After standard cleaning, we flat-fielded the XMM surface brightness maps. Combining the data from the EPIC MOS and PN Camera CCDs, we performed a cross-correlation analysis of the X-ray surface brightness distribution with the 1.4 GHz VLA radio map. We found evidence for cavities in the X-ray emitting Intra-Cluster Medium (ICM) associated with the radio tail of the head-tail radio galaxy 3C 129. This discovery is very interesting as it excludes the presence of a large fraction of thermal plasma in the radio tail. Together with the observation of an apparent pressure mismatch between the radio plasma and the ICM, and an upper limit on the magnetic field inside the radio tail (from the radio spectral indices map) the observation implies that the tail pressure is dominated either by low-energy electrons/positrons, or, by relativistic protons. Furthermore, we studied the energy spectrum of an X-ray "hot-spot" associated with the head of the radio galaxy 3C 129. It seems likely that the X-ray hot-spot originates from shocked gas in front of the radio galaxy. , The analysis turned out to be much more difficult than anticipated. The main reason is the lack of a comprehensive, publicly available background model that is key for the analysis of extended sources. Small groups like our do not have the man-power to come up with a background model themselves. We used the model from Read & Ponman (A&A 409, 395, 2003). However, the background subtracted X-ray surface brightness maps show a bright ring in the outer 20% of the camera. We tried to get rid of this ring and contacted the XMM helpdesk and Read & Ponman, the authors of the background paper. However, up to this day, we did not entirely succeed to remove the brightness enhancement at the outer parts of the camera. Unfortunately, our results are somewhat sensitive to the uncertainty, as the radio galaxy 3C 129 is very large and occupies a rather large fraction of the XMM field of view. We are now working on a paper describing the results. The paper will include a detailed discussion of the uncertainties associated with the non- perfect background subtraction.

Krawczynski, Henric S. W.↗
NASA NTRS1976

Applied photo interpretation for airbrush cartography

Lunar and planetary exploration has required the development of new techniques of cartographic portrayal. Conventional photo-interpretive methods employing size, shape, shadow, tone, pattern, and texture are applied to computer-processed satellite television images. Comparative judgements are affected by illumination, resolution, variations in surface coloration, and transmission or processing artifacts. The portrayal of tonal densities in a relief illustration is performed using a unique airbrush technique derived from hill-shading of contour maps. The control of tone and line quality is essential because the mid-gray to dark tone densities must be finalized prior to the addition of highlights to the drawing. This is done with an electric eraser until the drawing is completed. The drawing density is controlled with a reflectance-reading densitometer to meet certain density guidelines. The versatility of planetary photo-interpretive methods for airbrushed map portrayals is demonstrated by the application of these techniques to the synthesis of nonrelief data.

Inge, J. L.↗
DOE OSTI2019

Image quality and diagnostic accuracy of complex-averaged high b value images in diffusion-weighted MRI of prostate cancer

Purpose: To evaluate the impact of complex-averaging on image quality (IQ) and diagnostic accuracy of acquired and calculated high b value (aHBV, cHBV) images in diffusion-weighted prostate MRI. Materials and methods: This retrospective study included 84 patients who underwent multiparametric prostate MRI at 3 Tesla without endorectal coil. DWIs were acquired at three different b values which included two lower b values (b = 50,900 s/mm{sup 2}) and one higher b value (aHBV at 2000 s/mm{sup 2}). The acquired data were postprocessed to generate two different types of trace-weighted images—using conventional magnitude-averaging and complex-averaging. Using lower b values (b = 50,900 s/mm{sup 2}) from both conventional and complex-averaged image sets, cHBV images (b = 2000 s/mm{sup 2}) and ADC maps were derived. All image sets were reviewed by two radiologists in different reading sessions to assess image quality and PIRADS. The diagnostic accuracy of different image sets for the detection of prostate lesions was performed by correlating PIRADS and Gleason scores. Results: Complex-averaging did not impact ADC values of the prostate lesions compared to magnitude-averaging (P = 0.08). Complex-averaging improved image quality of acquired high b value and calculated high b value images (P < 0.0001). Complex-averaging also improved the level of confidence (LOC) of the acquired high b value for both readers (P < 0.0001, P < 0.05), but only for reader A in calculated high b value (P < 0.0001). The image quality of calculated high b value images was not significantly different than acquired high b value images. The dataset combining complex-averaging and calculated high b value provided the highest diagnostic accuracy (but not statistically significant) for detection of the significant prostate lesion compared to the magnitude-averaged acquired high b value (79.55% vs. 72.73%; P = 0.317). The mean acquisition time for b = 2000 s/mm{sup 2} sequence (aHBV) was 6 min 30 s (± 1 min 16 s) out of a total of 28 min 31 s (± 4 min 26 s) for the entire mp-MRI protocol (approximately 25% of total scan time). Conclusion: Complex-averaging provides better image quality and level of confidence without significant impact on ADC values and diagnostic accuracy for detection of the significant prostate lesions . The calculated high b value images are also comparable to (and can substitute) the acquired high b value images which can help in reducing the imaging time.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2018

Fine-Root Ecology Database (FRED): A Global Collection of Root Trait Data with Coincident Site, Vegetation, Edaphic, and Climatic Data, Version 2.

The second version of the Fine-Root Ecology Database is available for download! Download the full FRED 2.0 data set, user guidance document, map, and list of data sources here. Prior to downloading the data, please read and follow the Data Use Guidelines, and it's worth checking out some tips for using FRED before you begin your analyses. Also, see here for an updating list of corrections to FRED 2.0.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1981

The workshop

The plan is presented for a two day workshop held to provide educational and training experience in the reading, interpretation, and application of LANDSAT and correlated larger scale imagery, digital printout maps, and other collateral material for a large number of participants with widely diverse levels of expertise, backgrounds, and occupations in government, industry, and education. The need for using surface truth field studies with correlated aerial imagery in solving real world problems was demonstrated.

Wake, W. H.↗
DOE OSTI2019

High Density Genetic Maps of Seashore Paspalum Using Genotyping-By-Sequencing and Their Relationship to The Sorghum Bicolor Genome

As a step towards trait mapping in the halophyte seashore paspalum (Paspalum vaginatum Sw.), we developed an F 1 mapping population from a cross between two genetically diverse and heterozygous accessions, 509022 and HI33. Progeny were genotyped using a genotyping-by-sequencing (GBS) approach and sequence reads were analyzed for single nucleotide polymorphisms (SNPs) using the UGbS-Flex pipeline. More markers were identified that segregated in the maternal parent (HA maps) compared to the paternal parent (AH maps), suggesting that 509022 had overall higher levels of heterozygosity than HI33. We also generated maps that consisted of markers that were heterozygous in both parents (HH maps). The AH, HA and HH maps each comprised more than 1000 markers. Markers formed 10 linkage groups, corresponding to the ten seashore paspalum chromosomes. Comparative analyses showed that each seashore paspalum chromosome was syntenic to and highly colinear with a single sorghum chromosome. Four inversions were identified, two of which were sorghum-specific while the other two were likely specific to seashore paspalum. These high-density maps are the first available genetic maps for seashore paspalum. The maps will provide a valuable tool for plant breeders and others in the Paspalum community to identify traits of interest, including salt tolerance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

High-Density Single Nucleotide Polymorphism Linkage Maps of Lowland Switchgrass using Genotyping-by-Sequencing

Switchgrass (Panicum virgatum L.) is a warm-season perennial grass with promising potential as a bioenergy crop in the United States. However, the lack of genomic resources has slowed the development of plant lines with optimal characteristics for sustainable feedstock production. We generated high-density single nucleotide polymorphism (SNP) linkage maps using a reduced-representation sequencing approach by genotyping 231 F 1 progeny of a cross between two parents of lowland ecotype from the cultivars Kanlow and Alamo. Over 350 million reads were generated and aligned, which enabled identification and ordering of 4611 high-quality SNPs. The total lengths of the resulting framework maps were 1770 cM for the Kanlow parent and 2059 cM for the Alamo parent. These maps show collinearity with maps generated with polymerase chain reaction (PCR)-based simple-sequence repeat (SSR) markers, and new SNP markers were identified in previously unpopulated regions of the genome. Transmission segregation distortion affected all linkage groups (LGs) to differing degrees, and ordering of distorted markers highlighted several regions of unequal inheritance. Framework maps were adversely affected by the addition of distorted markers with varying severity, but distorted maps were of higher marker density and provided additional information for analysis. Alignment of these linkage maps with a draft version of the switchgrass genome assembly demonstrated high levels of collinearity and provides greater confidence in the validity of both resources. This methodology has proven to be a rapid and cost-effective way to generate high-quality linkage maps of an outcrossing species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Likelihood-based docking of models into cryo-EM maps

Optimized docking of models into cryo-EM maps requires exploiting an understanding of the signal expected in the data to minimize the calculation time while maintaining sufficient signal. The likelihood-based rotation function used in crystallography can be employed to establish plausible orientations in a docking search. A phased likelihood translation function yields scores for the placement and rigid-body refinement of oriented models. Optimized strategies for choices of the resolution of data from the cryo-EM maps to use in the calculations and the size of search volumes are based on expected log-likelihood-gain scores computed in advance of the search calculation. Tests demonstrate that the new procedure is fast, robust and effective at placing models into even challenging cryo-EM maps.

59 BASIC BIOLOGICAL SCIENCES↗