Search NASA⌕ Search

SEARCH · Search NASA

Results for “base editing”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 307 records · Page 17

Viral delivery of recombinases activates heritable genetic switches in plants

Viral vectors provide an increasingly versatile platform for transformation-free reagent delivery to plants. RNA viral vectors can be used to induce gene silencing, overexpress proteins, or introduce gene editing reagents; however, they are often constrained by carrying capacity or restricted tropism in germline cells. Site-specific recombinases that catalyze precise genetic rearrangements are powerful tools for genome engineering that vary in size and, potentially, efficacy in plants. In this work, we show that viral vectors based on tobacco rattle virus (TRV) deliver and stably express four recombinases ranging in size from ~0.6kb to ~1.5kb and achieve simultaneous marker removal and reporter activation through targeted excision in transgenic Nicotiana benthamiana lines. TRV vectors with Cre, FLP, CinH, and Integrase13 efficiently mediated recombination in infected somatic tissue and led to heritable modifications at high frequency. Here, an excision-activated Ruby reporter enabled simple and high-resolution tracing of infected cell lineages without the need for molecular genotyping. Together, our experiments broaden the scope of viral recombinase delivery and offer insights into infection dynamics that may be useful in developing future viral vectors.

59 BASIC BIOLOGICAL SCIENCES↗

Catalog of infrared observations. Part 1: Data

The Catalog of Infrared Observations (CIO) is a compilation of infrared astronomical observational data obtained from an extensive literature search of astronomical journals and major astronomical catalogs and surveys. The literature searches are complete for 1965 through 1986 in this Second Edition. The Catalog is published in two parts, with the observational data (roughly 200,000 observations of 20,000 individual sources) listed in Part I, and supporting appendices in Part II. The expanded Second Edition contains a new feature: complete IRAS 4-band data for all CIO sources detected, listed with the main Catalog observations, as well as in complete detail in the Appendix. The appendices include an atlas of infrared source positions, two bibliographies of infrared literature upon which the search was based, and, keyed to the main Catalog listings (organized alphabetically by author and then chronologically), an atlas of infrared spectral ranges, and IRAS data from the CIO sources. The complete CIO database is available to qualified users in printed microfiche and magnetic tape formats.

Gezari, Daniel Y.↗

Geographic Information Systems and Web Page Development

The Facilities Engineering and Architectural Branch is responsible for the design and maintenance of buildings, laboratories, and civil structures. In order to improve efficiency and quality, the FEAB has dedicated itself to establishing a data infrastructure based on Geographic Information Systems, GIs. The value of GIS was explained in an article dating back to 1980 entitled "Need for a Multipurpose Cadastre which stated, "There is a critical need for a better land-information system in the United States to improve land-conveyance procedures, furnish a basis for equitable taxation, and provide much-needed information for resource management and environmental planning." Scientists and engineers both point to GIS as the solution. What is GIS? According to most text books, Geographic Information Systems is a class of software that stores, manages, and analyzes mapable features on, above, or below the surface of the earth. GIS software is basically database management software to the management of spatial data and information. Simply put, Geographic Information Systems manage, analyze, chart, graph, and map spatial information. At the outset, I was given goals and expectations from my branch and from my mentor with regards to the further implementation of GIs. Those goals are as follows: (1) Continue the development of GIS for the underground structures. (2) Extract and export annotated data from AutoCAD drawing files and construct a database (to serve as a prototype for future work). (3) Examine existing underground record drawings to determine existing and non-existing underground tanks. Once this data was collected and analyzed, I set out on the task of creating a user-friendly database that could be assessed by all members of the branch. It was important that the database be built using programs that most employees already possess, ruling out most AutoCAD-based viewers. Therefore, I set out to create an Access database that translated onto the web using Internet Explorer as the foundation. After some programming, it was possible to view AutoCAD files and other GIS-related applications on Internet Explorer, while providing the user with a variety of editing commands and setting options. I was also given the task of launching a divisional website using Macromedia Flash and other web- development programs.

Reynolds, Justin↗

Machine learning predicts new anti-CRISPR proteins

The increasing use of CRISPR–Cas9 in medicine, agriculture, and synthetic biology has accelerated the drive to discover new CRISPR–Cas inhibitors as potential mechanisms of control for gene editing applications. Many anti-CRISPRs have been found that inhibit the CRISPR–Cas adaptive immune system. However, comparing all currently known anti-CRISPRs does not reveal a shared set of properties for facile bioinformatic identification of new anti-CRISPR families. Here, we describe AcRanker, a machine learning based method to aid direct identification of new potential anti-CRISPRs using only protein sequence information. Using a training set of known anti-CRISPRs, we built a model based on XGBoost ranking. We then applied AcRanker to predict candidate anti-CRISPRs from predicted prophage regions within self-targeting bacterial genomes and discovered two previously unknown anti-CRISPRs: AcrllA20 (ML1) and AcrIIA21 (ML8). We show that AcrIIA20 strongly inhibits Streptococcus iniae Cas9 (SinCas9) and weakly inhibits Streptococcus pyogenes Cas9 (SpyCas9). We also show that AcrIIA21 inhibits SpyCas9, Streptococcus aureus Cas9 (SauCas9) and SinCas9 with low potency. The addition of AcRanker to the anti-CRISPR discovery toolkit allows researchers to directly rank potential anti-CRISPR candidate genes for increased speed in testing and validation of new anti-CRISPRs. A web server implementation for AcRanker is available online at http://acranker.pythonanywhere.com/.

59 BASIC BIOLOGICAL SCIENCES↗

Directed evolution expands CRISPR–Cas12a genome-editing capacity

CRISPR-Cas12a enzymes are versatile RNA-guided genome-editing tools with applications encompassing viral diagnosis, agriculture, and human therapeutics. However, their dependence on a 5'-TTTV-3' protospacer adjacent motif (PAM) next to DNA target sequences restricts Cas12a's gene targeting capability to only ∼1% of a typical genome. To mitigate this constraint, we used a bacterial-based directed evolution assay combined with rational engineering to identify variants of Lachnospiraceae bacterium Cas12a with expanded PAM recognition. The resulting Cas12a variants use a range of noncanonical PAMs while retaining recognition of the canonical 5'-TTTV-3' PAM. In particular, biochemical and cell-based assays show that the variant Flex-Cas12a utilizes 5'-NYHV-3' PAMs that expand DNA recognition sites to ∼25% of the human genome. With enhanced targeting versatility, Flex-Cas12a unlocks access to previously inaccessible genomic loci, providing new opportunities for both therapeutic and agricultural genome engineering.

Ma, Enbo↗

Crew procedures development techniques

The study developed requirements, designed, developed, checked out and demonstrated the Procedures Generation Program (PGP). The PGP is a digital computer program which provides a computerized means of developing flight crew procedures based on crew action in the shuttle procedures simulator. In addition, it provides a real time display of procedures, difference procedures, performance data and performance evaluation data. Reconstruction of displays is possible post-run. Data may be copied, stored on magnetic tape and transferred to the document processor for editing and documentation distribution.

Arbet, J. D.↗

EAGLEView: A surface and grid generation program and its data management

An old and proven grid generation code, the EAGLE grid generation package, is given an added dimension of a graphical interface and a real time data base manager. The Numerical Aerodynamic Simulation (NAS) Panel Library is used for the graphical user interface. Through the panels, EAGLEView constructs the EAGLE script command and sends it to EAGLE to be processed. After the object is created, the script is saved in a mini-buffer which can be edited and/or saved and reinterpreted. The graphical objects are set-up in a linked-list and can be selected or queried by pointing and clicking the mouse. The added graphical enhancement to the EAGLE system emphasizes the unique capability to construct field points around complex geometry and visualize the construction every step of the way.

Remotigue, M. G.↗

Current-State Constrained Filter Bank for Wald Testing of Spacecraft Conjunctions

We propose a filter bank consisting of an ordinary current-state extended Kalman filter, and two similar but constrained filters: one is constrained by a null hypothesis that the miss distance between two conjuncting spacecraft is inside their combined hard body radius at the predicted time of closest approach, and one is constrained by an alternative complementary hypothesis. The unconstrained filter is the basis of an initial screening for close approaches of interest. Once the initial screening detects a possibly risky conjunction, the unconstrained filter also governs measurement editing for all three filters, and predicts the time of closest approach. The constrained filters operate only when conjunctions of interest occur. The computed likelihoods of the innovations of the two constrained filters form a ratio for a Wald sequential probability ratio test. The Wald test guides risk mitigation maneuver decisions based on explicit false alarm and missed detection criteria. Since only current-state Kalman filtering is required to compute the innovations for the likelihood ratio, the present approach does not require the mapping of probability density forward to the time of closest approach. Instead, the hard-body constraint manifold is mapped to the filter update time by applying a sigma-point transformation to a projection function. Although many projectors are available, we choose one based on Lambert-style differential correction of the current-state velocity. We have tested our method using a scenario based on the Magnetospheric Multi-Scale mission, scheduled for launch in late 2014. This mission involves formation flight in highly elliptical orbits of four spinning spacecraft equipped with antennas extending 120 meters tip-to-tip. Eccentricities range from 0.82 to 0.91, and close approaches generally occur in the vicinity of perigee, where rapid changes in geometry may occur. Testing the method using two 12,000-case Monte Carlo simulations, we found the method achieved a missed detection rate of 0.1%, and a false alarm rate of 2%.

Carpenter, J. Russell↗

Missile aerodynamics

The fundamental aerodynamics of slender bodies is examined in the reprint edition of an introductory textbook originally published in 1960. Chapters are devoted to the formulas commonly used in missile aerodynamics; slender-body theory at supersonic and subsonic speeds; vortices in viscid and inviscid flow; wing-body interference; downwash, sidewash, and the wake; wing-tail interference; aerodynamic controls; pressure foredrag, base drag, and skin friction; and stability derivatives. Diagrams, graphs, tables of terms and formulas are provided.

Nielsen, Jack N.↗

GeoAI advances in specific landform mapping

Landform mapping (also referred to as geomorphology or geomorphometry) can be divided into two domains: general and specific (Evans 2012). Whereas general landform mapping categorizes all elements of the study area into landform classes, such as ridges, valleys, peaks, and depressions, the mapping of specific landforms requires the delineation (even if fuzzy) of individual landforms. The former is mainly driven by physical properties such as elevation, slope, and curvature. The latter, however, must consider the cognitive (human) reasoning that discriminates individual landforms in addition to these physical properties (Arundel and Sinha 2018). Both mapping forms are important. General geomorphometry is needed to understand geological and ecological processes and as boundary layer input to climate and environmental models. Specific geomorphometry supports such activities as disaster management and recovery, emergency response, transportation, and navigation. In the United States, individual landforms of interest are named in the U.S. Geological Survey (USGS) Geographic Names Information System, a point dataset captured specifically to digitize geographic names from the USGS Historical Topographic Map Collection (HTMC). Named landform extent is represented only by the name placement in the HTMC. Recent work has investigated CNN-based deep learning methods to capture these extents in machine-readable form. These studies first relied on physical properties (Arundel et al. 2020) and then included the HTMC as a band in RGB images in limited testing (Arundel et al. 2023). Results from the HTMC dataset surpassed those using just physical properties and using the HTMC alone performed best due to the hillshading and elevation (contour) data incorporated into the topographic maps. However, results fell short of an operational capacity to map all named landforms in the United States. Thus, our current work expands upon past research by focusing on the HTMC and physical information as inputs and the named landform label extents. Specifically, we propose to leverage pre-trained foundation models for segmentation and optical character recognition (OCR) models to jointly map landforms in the United States. Our approach aims to bridge the disparities among the independent information sources to facilitate informed decision-making. The modeling pipeline performs (1) segmentation using the physical information and (2) information extraction using OCR, in parallel. Then a computer vision approach merges the two branches into a labeled segmentation. References: Arundel, Samantha T., Wenwen Li, and Sizhe Wang. 2020. “GeoNat v1.0: A Dataset for Natural Feature Mapping with Artificial Intelligence and Supervised Learning.” Transactions in GIS 24 (3): 556–72. https://doi.org/10.1111/tgis.12633. Arundel, Samantha T, and Gaurav Sinha. 2018. “Validating GEOBIA Based Terrain Segmentation and Classification for Automated Delineation of Cognitively Salient Landforms BT - Proceedings of Workshops and Posters at the 13th International Conference on Spatial Information Theory (COSIT 2017).” In Proceedings of Workshops and Posters at the 13th International Conference on Spatial Information Theory (COSIT 2017), Lecture Notes in Geoinformation and Cartography, edited by Paolo Fogliaroni, Andrea Ballatore, and Eliseo Clementini, 9–14. Cham: Springer International Publishing. Arundel, Samantha T., Gaurav Sinha, Wenwen Li, David P. Martin, Kevin G. McKeehan, and Philip T. Thiem. 2023. “Historical Maps Inform Landform Cognition in Machine Learning.” Abstracts of the ICA 6 (August): 1–2. https://doi.org/10.5194/ica-abs-6-10-2023. Evans, Ian S. 2012. “Geomorphometry and Landform Mapping: What Is a Landform?” Geomorphology 137 (1): 94–106. https://doi.org/10.1016/j.geomorph.2010.09.029.

machine learning↗

SAGA: A project to automate the management of software production systems

The current work in progress for the SAGA project are described. The highlights of this research are: a parser independent SAGA editor, design for the screen editing facilities of the editor, delivery to NASA of release 1 of Olorin, the SAGA parser generator, personal workstation environment research, release 1 of the SAGA symbol table manager, delta generation in SAGA, requirements for a proof management system, documentation for and testing of the cyber pascal make prototype, a prototype cyber-based slicing facility, a June 1984 demonstration plan, SAGA utility programs, summary of UNIX software engineering support, and theorem prover review.

Campbell, R. H.↗

X-Plane Knowledge Capture Workshop Summary Report

The history of experimental aircraft research and development at the National Aeronautics and Space Administration (NASA) provides a large body of work for current and future team members to learn from and apply. NASA values the knowledge it gains from all the research it performs and desires to have that knowledge grow with each new project, incrementally adding to the collective knowledge base. To support this knowledge growth and sharing, in May 2019, NASA convened over 60 engineers; researchers; and other personnel (internal and external to NASA) for the X-plane1 Knowledge Capture Workshop to discuss their over 50-years’ worth of experiences in developing, operating, and managing experimental aircraft. Over the course of a two-day workshop, the group not only focused, primarily, on current X-plane development but also discussed a wide range of topics about experimental aircraft and flight research. In addition to the discussions, senior NASA aeronautics leaders shared their personal lessons learned with the workshop audience. Broadly, these discussions centered around the topics of organizational and cultural practices, the project lifecycle, flight, and risk and safety. Many of the observations offered by participants are applicable to other NASA team-based projects, demonstrating the value in sharing lessons learned and best practices across projects regardless of their research focus. To share the most valuable lessons learned as broadly as possible, a summary of these discussions has been compiled into the following report. These discussions are mostly included in their entirety, with some light editing for clarity and privacy. NASA is sharing this knowledge internally and making it available to the public in hopes that others can learn from the experimental aircraft challenges and successes at NASA. Note: this document represents the perspectives, experiences, and opinions of others but does not necessarily represent the official view of NASA.

Steven R Hirshorn↗

Comparison of Marine Boundary Layer Cloud Properties from CERES-MODIS Edition 4 and DOE ARM AMF Measurements at the Azores

Marine boundary layer (MBL) cloud properties derived from the NASA Clouds and the Earth's Radiant Energy System (CERES) project using Terra and Aqua Moderate Resolution Imaging Spectroradiometer (MODIS) data are compared with observations taken at the Department of Energy Atmospheric Radiation Measurement (ARM) Mobile Facility at the Azores (AMF-Azores) site from June 2009 through December 2010. Cloud properties derived from ARM ground-based observations were averaged over a 1 h interval centered at the satellite overpass time, while the CERES-MODIS (CM) results were averaged within a 30 km×30 km grid box centered over the Azores site. A total of 63 daytime and 92 nighttime single-layered overcast MBL cloud cases were selected from 19 months of ARM radar-lidar and satellite observations. The CM cloud top/base heights (Htop/Hbase) were determined from cloud top/base temperatures (Ttop/Tbase) using a regional boundary layer lapse rate method. For daytime comparisons, the CM-derived Htop (Hbase), on average, is 0.063 km (0.068 km) higher (lower) than its ARM radar-lidar-observed counterpart, and the CM-derived Ttop and Tbase are 0.9 K less and 2.5 K greater than the surface values with high correlations (R(sup 2) = 0.82 and 0.84, respectively). In general, the cloud top comparisons agree better than the cloud base comparisons, because the CM cloud base temperatures and heights are secondary products determined from cloud top temperatures and heights. No significant day-night difference was found in the analyses. The comparisons of MBL cloud microphysical properties reveal that when averaged over a 30 km× 30 km area, the CM-retrieved cloud droplet effective radius (re) at 3.7 micrometers is 1.3 micrometers larger than that from the ARM retrievals (12.8 micrometers), while the CM-retrieved cloud liquid water path (LWP) is 13.5 gm( exp -2) less than its ARM counterpart (114.2 gm( exp-2) due to its small optical depth (9.6 versus 13.7). The differences are reduced by 50% when the CM averages are computed only using the MODIS pixel nearest the AMF site. Using the effective radius retrieved using 2.1 micrometers channel to calculate LWP can reduce the difference between the CM and ARM microwave radiometer retrievals from 13.7 to 2.1 gm2. The 10% differences between the ARM and CERES-MODIS LWP and r(sub e) retrievals are within the uncertainties of the ARM LWP (approximately 20gm( exp -2)) and r(sub e) (approximately 10%) retrievals; however, the 30% difference in optical depth is significant. Possible reasons contributing to this discrepancy are increased sensitivities in optical depth from both surface retrievals when τ is approximately 10 and topography. The τ differences vary with wind direction and are consistent with the island orography.Much better agreement in τ is obtained when using only those data taken when the wind is from the northeast, where topographical effects on the sampled clouds are minimal.

Xi, Baike↗

Spectrum Orbit Utilization Program Documentation: SOUP5 Version 3.8 User's Manual, Volume 2, Appendices a Through G

The appendixes of the user manual are presented. Input forms which may be used to prepare data for the SOUP5V3.4 of the R2BCSAT-83 data base are given. The IBM job control language which can be used to run the SOUP5 system from a magnetic tape is described. Copies of a run using the delivered tape and IBM OS/MVS Job Control Language card deck are illustrated. Numerical limits on scenario data requests are listed. Error handling, error messages and editing procedures are also listed. Instructions as to how to enter a protection ratio template are given. And relation between PARC prameter, channelization, channel families, and interference categories are also listed.

Davidson, J.↗

Secular Variation Across the Oceans: a Retrospective Study from 35 Years of Shipboard Total Field Measurements in the NE Atlantic

This is a pilot study to determine whether secular variation information can be retrieved from underway shipboard total field measurements with sufficient accuracy to complement geomagnetic data from land-based observatories. Applying the various new techniques described in this report, we extracted values of the total field at 42,677 crossovers or ship track intersection points contained in data sets collected between 18 degrees N and 50 degress N in the NE Atlantic, and extending temporally from 1955 to 1990. We used an edited subset of these total field values to derive the secular variation at 30,140 different locations in the study area, and compared the results with DGRF secular variation over the study area, calculated at 5 year intervals. The derived and DGRF values agree well, showing that indeed marine data can be a source for secular variations. However the analysis demonstrated that due to inherent noise in the marine data, only minor improvements on the DGRF values for the secular variation can be achieved.

Williams, C. A.↗

HYTHIRM Radiance Modeling and Image Analyses in Support of STS-119, STS-125 and STS-128 Space Shuttle Hypersonic Re-entries

We provide the first geometrically accurate (i.e., 3-D) temperature maps of the entire windward surface of the Space Shuttle during hypersonic reentry. To accomplish this task we began with estimated surface temperatures derived from CFD models at integral high Mach numbers and used them, the Shuttle's surface properties and reasonable estimates of the sensor-to-target geometry to predict the emitted spectral radiance from the surface (in units of W sr-1 m-2 nm-1). These data were converted to sensor counts using properties of the sensor (e.g. aperture, spectral band, and various efficiencies), the expected background, and the atmosphere transmission to inform the optimal settings for the near-infrared and midwave IR cameras on the Cast Glance aircraft. Once these data were collected, calibrated, edited, registered and co-added we formed both 2-D maps of the scene in the above units and 3-D maps of the bottom surface in temperature that could be compared with not only the initial inputs but also thermocouple data from the Shuttle itself. The 3-D temperature mapping process was based on the initial radiance modeling process. Here temperatures were guessed for each node in a well-resolved 3-D framework, a radiance model was produced and compared to the processed imagery, and corrections to the temperature were estimated until the iterative process converged. This process did very well in characterizing the temperature structure of the large asymmetric boundary layer transition the covered much of the starboard bottom surface of STS-119 Discovery. Both internally estimated accuracies and differences with CFD models and thermocouple measurements are at most a few percent. The technique did less well characterizing the temperature structure of the turbulent wedge behind the trip due to limitations in understanding the true sensor resolution. (Note: Those less inclined to read the entire paper are encouraged to read an Executive Summary provided at the end.)

Gibson, David M.↗

Building Performance Standards and Energy Code Alignment - Technical Brief

Building energy codes focus on building design, construction and renovation and have significantly increased building efficiency since the first national energy code was published in 1975. Most jurisdictions have energy codes based on ANSI/ASHRAE/IES Standard 90.1 (hereto referred to as Standard 90.1) and the International Energy Conservation Code (IECC). Compliance options available in these model energy codes include a prescriptive path, whole building performance paths – including IECC Total Building Performance (TBP), Standard 90.1 Energy Cost Budget (ECB) method and Performance Rating Method (PRM) – and system performance paths for envelope and heating, ventilation, and air-conditioning systems. Building performance standard (BPS) policies are an emerging policy tool used by jurisdictions to reduce the operational energy use or greenhouse gas (GHG) emissions of the existing commercial building stock. BPS policies vary widely between jurisdictions and are tailored to each location’s climate and energy goals. Intuitively, projects that met a recent edition of the energy code should comply with the BPS targets. However, some new buildings may struggle with meeting the BPS for the following reasons: 1. Energy codes focus on the design of the building and its projected ability to perform efficiently, while BPS compliance is dependent on the actual ongoing performance of the building, considering variables like occupancy, operation, and maintenance. 2. There are significant differences in the methodologies used to determine BPS compliance versus code compliance, including how each handles compliance metrics, handling of building amenities, and renewable energy generation. 3. The prescriptive compliance path in the energy code is based on performance of individual building components, as opposed to the performance compliance path which accounts for holistic building design strategies and interdependent building systems. This can result in a significant variability in post-occupancy performance for buildings built using the prescriptive path. Designs on the lower end of the permitted efficiency range may struggle with meeting the BPS.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Inventory of Composable Elements (ICE) v6.0.0

The Inventory of Composable Elements (ICE) is an open source registry software platform for managing information about biological parts. It is capable of recording information about plasmids, microbial host strains and seeds, as well as DNA parts. Includes features such as DNA sequence visualization, editing and annotation, auto-aligning sequencing trace files against reference templates, SBOL XML/RDF support, and web-of-registries functionality. The web of registries functionality provides strong support for distributed interconnected use and enables sharing and transfer of biological parts across various independent ICE instances. ICE adopts modern software development principles, leveraging component-base frameworks, offering a REST API for convenient third-party integration and emphasizing scalability, security, and service integrations for dynamic content availability. The source code is hosted at https://github.com/JBEI/ice. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects.

Plahar, Hector↗