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DOE OSTI2021

Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum

Clostridium thermocellum is a thermophilic bacterium recognized for its natural ability to effectively deconstruct cellulosic biomass. While there is a large body of studies on the genetic engineering of this bacterium and its physiology to-date, there is limited knowledge in the transcriptional regulation in this organism and thermophilic bacteria in general. The study herein is the first report of a large-scale application of DNA-affinity purification sequencing (DAP-seq) to transcription factors (TFs) from a bacterium. We applied DAP-seq to > 90 TFs in C. thermocellum and detected genome-wide binding sites for 11 of them. We then compiled and aligned DNA binding sequences from these TFs to deduce the primary DNA-binding sequence motifs for each TF. These binding motifs are further validated with electrophoretic mobility shift assay (EMSA) and are used to identify individual TFs’ regulatory targets in C. thermocellum . Our results led to the discovery of novel, uncharacterized TFs as well as homologues of previously studied TFs including RexA-, LexA-, and LacI-type TFs. We then used these data to reconstruct gene regulatory networks for the 11 TFs individually, which resulted in a global network encompassing the TFs with some interconnections. As gene regulation governs and constrains how bacteria behave, our findings shed light on the roles of TFs delineated by their regulons, and potentially provides a means to enable rational, advanced genetic engineering of C. thermocellum and other organisms alike toward a desired phenotype.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

The Galaxy–Galaxy Strong Lensing Cross Section and the Internal Distribution of Matter in ΛCDM Substructure

Abstract Strong gravitational lensing offers a powerful probe of the detailed distribution of matter in lenses, while magnifying and bringing faint background sources into view. Observed strong lensing by massive galaxy clusters, which are often in complex dynamical states, has also been used to map their dark matter (DM) substructures on smaller scales. Deep high-resolution imaging has revealed the presence of strong lensing events associated with these substructures, namely galaxy-scale sub-halos. However, an inventory of these observed galaxy–galaxy strong lensing (GGSL) events is noted to be discrepant with state-of-the-art ΛCDM simulations. Cluster sub-halos appear to be over-concentrated compared to their simulated counterparts yielding an order-of-magnitude higher value of GGSL. In this paper, we explore the possibility of resolving this observed discrepancy by redistributing the mass within observed cluster sub-halos in ways that are consistent within the ΛCDM paradigm of structure formation. Lensing mass reconstructions from data provide constraints on the mass enclosed within apertures and are agnostic to the detailed mass profile within them. Therefore, as the detailed density profile within cluster sub-halos currently remains unconstrained by data, we are afforded the freedom to redistribute the enclosed mass. We investigate if rearranging the mass to a more centrally concentrated density profile helps alleviate the GGSL discrepancy. We report that refitting cluster sub-halos to the ubiquitous ΛCDM-motivated Navarro–Frenk–White profile, and further modifying them to include significant baryonic components, does not resolve this tension. A resolution to this persisting GGSL discrepancy may require more careful exploration of alternative DM models.

Astronomy & Astrophysics↗

DOE OSTI2021

Genome-wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum

Clostridium thermocellum is a thermophilic bacterium recognized for its natural ability to effectively deconstruct cellulosic biomass. While there is a large body of studies on the genetic engineering of this bacterium and its physiology to-date, there is limited knowledge in the transcriptional regulation in this organism and thermophilic bacteria in general. The study herein is the first report of a high-throughput application of DNA-affinity purification sequencing (DAP-seq) to transcription factors (TFs) from a thermophile. We applied DAP-seq to >90 TFs in C. thermocellum and detected genome-wide binding sites for 11 of them. We then compiled and aligned DNA binding sequences from these TFs to deduce the primary DNA-binding sequence motifs for each TF. These binding motifs are further validated with electrophoretic mobility shift assay (EMSA) and are used to identify individual TFs’ regulatory targets in C. thermocellum. Our results led to the discovery of novel, uncharacterized TFs as well as homologues of previously studied TFs including RexA-, LexA- and LacI-type TFs. We then used these data to reconstruct gene regulatory networks for the 11 TFs individually, which resulted in a global network encompassing the TFs with some interconnections. As gene regulation governs and constrains how bacteria behave, our findings shed light on the roles of TFs delineated by their regulons, and potentially provides a means to enable rational, advanced genetic engineering of C. thermocellum and other organisms alike towards a desired phenotype.

09 BIOMASS FUELS↗

NASA NTRS1976

Development and evaluation of a Hadamard transform imaging spectrometer and a Hadamard transform thermal imager

A spectrometric imager and a thermal imager, which achieve multiplexing by the use of binary optical encoding masks, were developed. The masks are based on orthogonal, pseudorandom digital codes derived from Hadamard matrices. Spatial and/or spectral data is obtained in the form of a Hadamard transform of the spatial and/or spectral scene; computer algorithms are then used to decode the data and reconstruct images of the original scene. The hardware, algorithms and processing/display facility are described. A number of spatial and spatial/spectral images are presented. The achievement of a signal-to-noise improvement due to the signal multiplexing was also demonstrated. An analysis of the results indicates both the situations for which the multiplex advantage may be gained, and the limitations of the technique. A number of potential applications of the spectrometric imager are discussed.

Harwit, M.↗

NASA NTRS1976

Hadamard transform imager and imaging spectrometer

An imager and a spectrometric imager, which achieve multiplexing by the use of binary optical encoding masks, have been built and tested. The masks are based on orthogonal, pseudorandom digital codes derived from Hadamard matrices. The spatial (and/or spectral) data are therefore obtained in the form of a Hadamard transform of the spatial (and/or spectral) scene. Computer algorithms are used to decode the data and reconstruct images of the original scene. The hardware, algorithms processing and display facility are described. A number of spatial and spatial/spectral images, obtained in the laboratory, are presented.

Swift, R. D.↗

NASA NTRS1978

A recommended entry reconstruction process for the Pioneer Venus multi-probe mission

A method for determining the entry trajectories for the Pioneer Venus multi-probe mission is presented that utilizes earth based Doppler and onboard accelerometry as observables to provide updates for the spacecraft state and atmospheric parameters. The evolution of this method, based on error analyses and actual simulation results, is discussed. A derivative of the Viking radio science orbit determination software is recommended for the reconstruction. Telemetry data pre-processing requirements were defined. A cubic spline derivative routine is recommended to extract accelerations from the accumulated velocity decrements.

Findlay, J. T.↗

NASA NTRS1980

Pulsed holography for combustion diagnostics

Image reconstruction and data extraction techniques were considered with respect to their application to combustion diagnostics. A system was designed and constructed that possesses sufficient stability and resolution to make quantitative data extraction possible. Example data were manually processed using the system to demonstrate its feasibility for the purpose intended. The system was interfaced with the PDP-11-04 computer for maximum design capability. It was concluded that the use of specialized digital hardware controlled by a relatively small computer provides the best combination of accuracy, speed, and versatility for this particular problem area.

Klein, N.↗

NASA NTRS1983

Solar system history as recorded in the Saturnian ring structure

Holberg's analysis of the Voyager Saturn photographs in reflected and transparent light, and occultation data of stars seen through the rings are discussed. A hyperfine structure, with 10,000 ringlets can be explained by the Baxter-Thompson negative diffusion. This gives the ringlets a stability which makes it possible to interpret them as fossils, which originated at cosmogonic times. It is shown that the bulk structure can be explained by the combined cosmogonic shadows of the satellites Mimas, Janus and the Shepherd satellites. This structure originated at the transition from the plasma phase to the planetesimal phase. The shadows are not simple void regions but exhibit a characteristic signature. Parts of the fine structure, explained by Holberg as resonances with satellites, are interpreted as cosmogonic shadow effects. However, there are a number of ringlets which can neither be explained by cosmogonic nor by resonance effects. Analysis of ring data can reconstruct the plasma-planetesimal transition with an accuracy of a few percent.

Alfven, H.↗

NASA NTRS1983

Solar system history as recorded in the Saturnian ring structure

Holberg's analysis of the Voyager Saturn photographs in reflected and transparent light, and occultation data of stars seen through the rings are discussed. A hyperfine structure with 10,000 ringlets can be explained by the Baxter-Thompson negative diffusion. This gives the ringlets a stability which makes it possible to interpret them as fossils which originated at cosmogonic times. It is shown that the bulk structure can be explained by the combined cosmogonic shadows of the satellites Mimas and Janus and the Shepherd satellites. This structure originated at the transition from the plasma phase to the planetesimal phase. The shadows are not simple void regions but exhibit a characteristic signature. Parts of the fine structure, explained by Holberg as resonances with satellites, are interpreted as cosmogonic shadow effects. However, there are a number of ringlets which can neither be explained by cosmogonic nor by resonance effects. Analysis of ring data can reconstruct the plasma-planetesimal transition with an accuracy of a few percent. Previously announced in STAR as N84-12013

Alfven, H.↗

NASA NTRS1988

Infrared spectral studies of asteroids

The research objective is to improve our understanding of the surface mineralogy of asteroids and to link the vast existing body of meteorite geochemical data with specific astronomical objects which may be the targets of future NASA missions. The methodology employed is: (1) use advanced astronomical instrumentation to obtain reflection spectra in the 0.3 to 5.2 micrometer wavelength range of selected astroids; (2) compare the asteroid data with similar data on simulated asteroid regoliths of various compositions to determine the surface mineralogy and meteoritic affinities of asteroid spectral classes and specific asteroids; (3) integrate the mineralogical information with other astronomical data, orbital dynamics studies, and meteorite geochemistry data to reconstruct the condensational, thermal, and collisional history of the present asteroids and their parent planetesimals; and (4) use the information obtained to assist planning of future NASA asteroid missions.

Bell, Jeffrey F.↗

NASA NTRS1988

Small expendable deployer system measurement analysis

The first on-orbit experiment of the Small Expendable Deployer System (SEDS) for tethered satellites will collect telemetry data for tether length, rate of deployment, and tether tension. The post-flight analysis will use this data to reconstruct the deployment history and determine dynamic characteristics such as tether shape and payload position. Linearized observability analysis has determined that these measurements are adequate to define states for a two-mass tether model, and two state estimators were written.

Carrington, Connie K.↗

NASA NTRS1991

Infrared spectral studies of asteroids

The research objective was to improve the understanding of the surface mineralogy of asteroids and to link the vast existing body of meteorite geochemical data with specific astronomical objects which may be the targets of future NASA missions. The methodology used is as follow: (1) to use advanced astronomical instrumentation to obtain reflection spectra in the 0.3 to 5.2 micron wavelength range of selected asteroids; (2) to compare the asteroid data with similar data on simulated asteroid regoliths of various compositions to determine the surface mineralogy and meteoritic affinities of asteroid spectral classes and specific asteroids; (3) to integrate the mineralogical information with other astronomical data, orbital dynamics studies, and meteoritic geochemistry data to reconstruct the condensational, thermal, and collisional history of the present asteroids and their parent planetesimals; and (4) to use the information obtained to assist planning of future NASA asteroid missions such as Galileo and CRAF.

Bell, Jeffrey F.↗

NASA NTRS1999

MOLA: The Future of Mars Global Cartography

The MGS Orbiter is carrying the high-precision Mars Orbiter Laser Altimeter (MOLA) which, when combined with precision reconstructed orbital data and telemetered attitude data, provides a tie between inertial space and Mars-fixed coordinates to an accuracy of 100 m in latitude / longitude and 10 m in radius (1 sigma), orders of magnitude more accurate than previous global geodetic/ cartographic control data. Over the 2 year MGS mission lifetime, it is expected that over 30,000 MOLA Global Cartographic Control Points will be produced to form the basis for new and re-derived map and geodetic products, key to the analysis of existing and evolving MGS data as well as future Mars exploration. Additional information is contained in the original extended abstract.

Duxbury, T. C.↗

NASA NTRS2002

The Fourier-Kelvin Stellar Interferometer Mission Concept

The Fourier-Kelvin Stellar Interferometer (FKSI) is a mission concept for an imaging interferometer for the mid-infrared spectral region (5-30 microns). FKSI is conceived as a scientific and technological precursor to TPF as well as Space Infrared Interferometric Telescope (SPIRIT), Submillimeter Probe Evolution of Cosmic Structure (SPECS), and Single Aperture for Infrared Observatory (SAFIR). It will also be a high angular resolution system complementary to Next Generation Space Telescope (NGST). The scientific emphasis of the mission is on the evolution of protostellar systems, from just after the collapse of the precursor molecular cloud core, through the formation of the disk surrounding the protostar, the formation of planets in the disk, and eventual dispersal of the disk material. FKSI will also search for brown dwarfs and Jupiter mass and smaller planets, and could also play a very powerful role in the investigation of the structure of active galactic nuclei and extra-galactic star formation. We are in the process of studying alternative interferometer architectures and beam combination techniques, and evaluating the relevant science and technology tradeoffs. Some of the technical challenges include the development of the cryocooler systems necessary for the telescopes and focal plane array, light and stiff but well-damped truss systems to support the telescopes, and lightweight and coolable optical telescopes. The goal of the design study is to determine if a mid-infrared interferometry mission can be performed within the cost and schedule requirements of a Discovery class mission. At the present time we envision the FKSI as comprised of five one meter diameter telescopes arranged along a truss structure in a linear non-redundant array, cooled to 35 K. A maximum baseline of 20 meters gives a nominal resolution of 26 mas at 5 microns. Using a Fizeau beam combination technique, a simple focal plane camera could be used to obtain both Fourier and spectral data simultaneously for a given orientation of the array. The spacecraft will be rotated to give sufficient Fourier data to reconstruct complex images of a broad range of astrophysical sources.

Danchi, W. C.↗

NASA NTRS1992

Modelling the Phanerozoic carbon cycle and climate: constraints from the 87Sr/86Sr isotopic ratio of seawater

A numerical model describing the coupled evolution of the biogeochemical cycles of carbon, sulfur, calcium, magnesium, phosphorus, and strontium has been developed to describe the long-term changes of atmospheric carbon dioxide and climate during the Phanerozoic. The emphasis is on the effects of coupling the cycles of carbon and strontium. Various interpretations of the observed Phanerozoic history of the seawater 87Sr/86Sr ratio are investigated with the model. More specifically, the abilities of continental weathering, volcanism, and surface lithology in generating that signal are tested and compared. It is suggested that the observed fluctuations are mostly due to a changing weatherability over time. It is shown that such a conclusion is very important for the modelling of the carbon cycle. Indeed, it implies that the conventional belief that the evolution of atmospheric carbon dioxide and climate on a long time scale is governed by the balance between the volcanic input of CO2 and the rate of silicate weathering is not true. Rather carbon exchanges between the mantle and the exogenic system are likely to have played a key role too. Further, the increase of the global weathering rates with increasing surface temperature and/or atmospheric CO2 pressure usually postulated in long-term carbon cycle and climate modelling is also inconsistent with the new model. Other factors appear to have modulated the weatherability of the continents through time, such as mountain building and the existence of glaciers and ice sheets. Based on these observations, a history of atmospheric carbon dioxide and climate during Phanerozoic time, consistent with the strontium isotopic data, is reconstructed with the model and is shown to be compatible with paleoclimatic indicators, such as the timing of glaciation and the estimates of Cretaceous paleotemperatures.

NASA Discipline Number 52-30↗

NASA NTRS2003

The Fourier-Kelvin Stellar Interferometer (FKSI): A Discovery Class TPF/DARWIN Pathfinder Mission Concept

The Fourier-Kelvin Stellar Interferometer (FKSI) is a mission concept for an imaging and nulling interferometer for the mid-infrared spectral region (5-30 microns). FKSI is conceived as a scientific and technological pathfinder to TPF/DARWIN as well as SPIRIT, SPECS, and SAFIR. It will also be a high angular resolution system complementary to NGST. The scientific emphasis of the mission is on the evolution of protostellar systems, from just after the collapse of the precursor molecular cloud core, through the formation of the disk surrounding the protostar, the formation of planets in the disk, and eventual dispersal of the disk material. FKSI will also search for brown dwarfs and Jupiter mass and smaller planets, and could also play a very powerful role in the investigation of the structure of active galactic nuclei and extra-galactic star formation. We have been studying alternative interferometer architectures and beam combination techniques, and evaluating the relevant science and technology tradeoffs. Some of the technical challenges include the development of the cryocooler systems necessary for the telescopes and focal plane array, light and stiff but well-damped truss systems to support the telescopes, and lightweight and coolable optical telescopes. We present results of detailed design studies of the FKSI starting with a design consisting of five one meter diameter telescopes arranged along a truss structure in a linear non-redundant array, cooled to 35 K. A maximum baseline of 20 meters gives a nominal resolution of 26 mas at 5 microns. Using a Fizeau beam combination technique, a simple focal plane camera could be used to obtain both Fourier and spectral data simultaneously for a given orientation of the array. The spacecraft will be rotated to give sufficient Fourier data to reconstruct complex images of a broad range of astrophysical sources. Alternative and simpler three and two telescope designs emphasizing nulling and spectroscopy also have been investigated and will be discussed.

Danchi, W. C.↗

NASA NTRS2014

The X-15 3-65 Accident: An Aircraft Systems and Flight Control Perspective

Despite the NASA X-15 program's outstanding success in developing and operating the first manned hypersonic research platform, the program suffered a fatal accident on November 15, 1967, when X-15-3, the only aircraft outfitted with advanced pilot displays and an adaptive flight control system, was lost after entering uncontrolled flight at an altitude of 230,000 feet and a velocity near Mach 5. The pilot, Major Michael J. Adams, was incapacitated by the aircraft accelerations and was killed either during the ensuing breakup or upon ground impact. In light of mitigating risk to current and emerging manned aerospace vehicles, a comprehensive systems level analysis of the accident is presented with a focus on the electrical power, flight control, and instrumentation failures that affected not only the vehicle dynamics but substantially impacted the pilot decisions that led to an inevitable loss of control. Insights based on reconstructed flight data as well as analysis and simulation of the X-15's unique adaptive control system, yield new conclusions about the reasons for the control systems anomalous behavior and the system-level interactions and human-machine interface design oversights that led to the accident.

Accident Investigation↗

NASA NTRS2018

Skimming through Saturn's Atmosphere: The Climax of the Cassini Grand Finale Mission

On September 15, 2017, the long-lived Cassini Mission to Saturn came to a triumphant end as the Cassini orbiter plunged deep into Saturn’s atmosphere, all the while transmitting engineering and science data back to Earth before Saturn’s atmosphere destroyed the orbiter. Even before the final plunge, the Cassini spacecraft became the first spacecraft to successfully skim Saturn’s atmosphere and collect atmospheric data during its final five complete orbits around Saturn (Rev-288 through Rev-292). During those five final orbits, the spacecraft was flying in Reaction Control Subsystem (RCS) control in order to maintain greater control authority. Therefore, by analyzing the thruster on-time flight data telemetered back to Earth after each orbit, atmospheric density estimates can be extracted. This paper proposes a method of using Cassini Attitude Control Flight Data to reconstruct Saturn atmospheric density profiles for each of the five final orbits around Saturn.

Andrade, Luis G.↗