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At least 937 records · Page 52

RNAseq-based transcriptome assembly of Clostridium acetobutylicum for functional genome annotation and discovery

Accurate genome annotations are essential in modern biology and biotechnology, yet they are still largely based on genome sequencing and comparative analyses. We show that the Clostridium acetobutylicum genome annotation can be markedly improved by integrating bioinformatic predictions with RNA sequencing (RNAseq) data. Samples were acquired under butanol, butyrate, and unstressed treatments across various growth conditions. Analysis of an initial assembly revealed errors due to background signals and limitations of assembly algorithms. Hurdles for RNAseq transcriptome mapping include optimizing library complexity and sequencing depth, yet most studies report low sequencing depth and ignore the effect of ribosomal RNA abundance. An integrative analysis was developed to combine motif predictions, single-nucleotide resolution sequencing depth, and library complexity to resolve difficulties in assembly curation. This minimized false positive error and determined gene boundaries, in some cases, to the exact base-pair of prior studies. This will be the first strand-specific transcriptome assembly in a Clostridium organism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DIASCoPE: Directly integrated acoustic system combined with pressure experiments—A new method for fast acoustic velocity measurements at high pressure

A novel experimental system to measure elastic wave velocities in samples in situ under extreme conditions of pressure and temperature in a multi-anvil apparatus has been installed at Beamline 6-BM-B of the Advanced Photon Source at Argonne National Laboratory. This system allows for measurement of acoustic velocities via ultrasonic interferometry, and makes use of the synchrotron beam to measure sample densities via X-ray diffraction and sample lengths using X-radiographic imaging. This system is fully integrated into the automated software controls of the beamline and is capable of collecting robust data on elastic wave travel times in less than 1 s, which is an improvement of more than one to two orders of magnitude over existing systems. Moreover, this fast data collection time has been shown to have no effect on the obtained travel time results. This allows for more careful study of time-dependent phenomena with tighter snapshots in time of processes that would otherwise be lost or averaged out in other acoustic measurement systems.

Whitaker, Matthew L.↗

Diel Redox Cycle of Manganese in the Surface Arctic Ocean

Knowledge of the chemical speciation of particulate manganese (pMn) is important for understanding the biogeochemical cycling of Mn and other particle-reactive elements. Here, in this work, we present the synchrotron-based X-ray spectroscopy-derived average oxidation state (AOS) of pMn in the surface Arctic Ocean collected during the United States GEOTRACES Arctic cruise (GN01) in 2015. We show that the pMn AOS is <2.4 when sampled during the day and more than ~3.0 when sampled at night. We hypothesize that an active light-dependent redox cycle between dissolved Mn and particulate Mn(III/IV) exists during the day-night cycle in the surface Arctic Ocean, which occurs on the timescale of hours. The magnitude of observed pMn AOS is likely determined by the net effect of the length of the previous night and integrated light level before the end of pMn sampling.

58 GEOSCIENCES↗

Ocean time-series near Bermuda: Hydrostation S and the US JGOFS Bermuda Atlantic time-series study

Bermuda is the site of two ocean time-series programs. At Hydrostation S, the ongoing biweekly profiles of temperature, salinity and oxygen now span 37 years. This is one of the longest open-ocean time-series data sets and provides a view of decadal scale variability in ocean processes. In 1988, the U.S. JGOFS Bermuda Atlantic Time-series Study began a wide range of measurements at a frequency of 14-18 cruises each year to understand temporal variability in ocean biogeochemistry. On each cruise, the data range from chemical analyses of discrete water samples to data from electronic packages of hydrographic and optics sensors. In addition, a range of biological and geochemical rate measurements are conducted that integrate over time-periods of minutes to days. This sampling strategy yields a reasonable resolution of the major seasonal patterns and of decadal scale variability. The Sargasso Sea also has a variety of episodic production events on scales of days to weeks and these are only poorly resolved. In addition, there is a substantial amount of mesoscale variability in this region and some of the perceived temporal patterns are caused by the intersection of the biweekly sampling with the natural spatial variability. In the Bermuda time-series programs, we have added a series of additional cruises to begin to assess these other sources of variation and their impacts on the interpretation of the main time-series record. However, the adequate resolution of higher frequency temporal patterns will probably require the introduction of new sampling strategies and some emerging technologies such as biogeochemical moorings and autonomous underwater vehicles.

Michaels, Anthony F.↗

PACE OCI Lunar Calibration: Initial Results

Launched in February 2024, the Ocean Color Instrument (OCI) onboard NASA’s Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) mission has started performing its monthly lunar calibrations at ±7degreeslunar phase angle in March 2024. In this paper, we will describe the OCI lunar calibration methodology and show the results of lunar calibration events during the initial months of PACE/OCI operation. A key difference of OCI lunar calibration from heritage sensors is that the lunar disk integrated irradiance is computed from lunar pixel radiance and sampling distance instead of the instrument’s IFOV. PACE provided a near constant sweep rate during lunar calibration allowing accurate determination of OCI pixel sampling extent. OCI performs lunar calibration in baseline science mode with 282 hyperspectral bands from 315 –895 nm and 7 shortwave infrared bands(940 -2260 nm). For each OCI band, we compute the integrated lunar disk irradiance, and compare the result with a lunar irradiance model (ROLO)prediction. The early results presented here clearly show that OCI’s lunar image acquisition is working as intended and will provide accurate data for OCI’s on-orbit radiometric characterization. The hyperspectral lunar irradiances provided by OCI are expected to become a valuable data set for the evaluation of lunar irradiance models.

calibration↗

Effects of carbon and silicon nanotubes and carbon nanofibers on marine microalgae Heterosigma akashiwo

Highlights: • Carbon and silicon nanotubes did not inhibit algal growth up to 10 mg/l. • Carbon nanofibers did not inhibit algal growth at 100 mg/l. • Cell death of marine alga Heterosigma akashiwo was associated with mechanical damage. • Nickel impurities in carbon nanofibers caused irregular shape formation. The effect of carbon and silicon nanotubes (CNTs and SiNTs) and carbon nanofibers (CNFs) to microscopic marine algae Heterosigma akashiwo was studied, using algal growth inhibition for 3 days (acute effect) and 7 days (chronic effect) as toxicity endpoints. The criterion of the toxic effect was the statistically significant reduction of the number of algal cells in the exposed samples compared to the control. Samples did not demonstrate toxic effects at doses 1 mg/l and 10 mg/l. CNTs and SiNTs samples at 100 mg/l exhibited both acute and chronic toxic effects. We assume that the main cause of cell death in these samples was related to the mechanical damage of cell integrity. CNFs at concentrations of 100 mg/l did not inhibit algal growth, but cells with irregular shapes were observed, which were not observed after exposure to CNTs and SiNTs. Nickel impurities present in CNFs samples are presumably the main cause of observed cell deformations.

54 ENVIRONMENTAL SCIENCES↗

Integrated Modeling Approach for the Terrestrial Planet Finder Mission

Because of the complexity of the Terrestrial Planet Finder (TPF) design concepts, the project will rely heavily on the use of engineering and science simulations to predict on-orbit performance. Furthermore, current understanding of these missions indicates that the 3m to 8m class optical systems need to be as stable as picometers in wavefront and sub-milli arcsec in pointing. These extremely small requirements impose on the models a level of predictive accuracy heretofore never achieved, especially in the area of microgravity effects, material property accuracy, thermal solution convergence, and all other second order modeling effects typically ignored. New modeling tools and analysis paradigms are developed which emphasize computational accuracy and fully integrated analytical simulations. The process is demonstrated on sample problems using the TPF Coronagraph design concept. The TPF project is also planning a suite of testbeds through which various aspects of the models and simulations will be verified.

terrestrial planet finder↗

Integrated Design Results for the MSR DAC-0.0 Mars Ascent Vehicle

The NASA Mars Sample Return (MSR) Campaign endeavors to return Martian regolith, rock, and atmospheric samples to Earth for scientific study. One of many significant challenges to overcome in the return of thesesamples lies in transporting them from the Martian surface to space. In order to surmount this challenge, the Campaign has conceptualized the need for a Mars Ascent Vehicle (MAV) to perform this function and deliver Martian samples to orbit. There, the samples will be ejected and captured by a separate spacecraft for return to Earth. Many concepts for a MAV have existed in the past, but it has not been until now that an integrated, detailed design solution has been developed and analyzed. Preliminary assessments of the initial architecture examined multiple methods of propulsion. The team ultimately determined that a Two Stage to Orbit (TSTO) solid propulsion vehicle would provide the most effective performance and be the most technologically ready to support this mission. Following the decision to adopt a TSTO solid propelled vehicle, the first official Design Analysis Cycle, DAC-0.0, was performed in Spring 2020 to formally advance the fidelity of the vehicle to a maturity level acceptable for NASA Key Decision Point A (KDP-A). This paper describes the resultant MAV design concept developed as part of the DAC-0.0 study by the NASA Marshall Space Flight Center (MSFC), in association with the NASA Jet Propulsion Laboratory (JPL). The TSTO vehicle features two solid rocket motors, one powering each stage. Their thrust vectors are controlled with Thrust Vector Control (TVC) systems consisting of independent electromechanical actuators acting on gimballed nozzles. The vehicle is designed to deliver up to 0.47kg of Martian samples to a Mars circular orbit of 343km at 27° inclination. Due to the unique environmental conditions that this vehicle is required to operate in, the subsystem design teams were compelled to develop creative and unorthodox designs to ensure a successful mission. The detailed design and analysis of these subsystems are discussed in this paper and include topics on the MAV Guidance, Navigation, and Control (GNC); structures and mechanisms; integrated vehicle thermal; avionics and flight software; a hydrazine-based Reaction Control System (RCS); aerosciences; and vehicle assembly, integration, and test (AI&T) considerations, among others. Following the conclusion of the MAV DAC-0.0, additional alternative architecture concepts were also studied to further reduce the mass of the overall system.

Mars↗

Small gain robustness issues in the p-integrator repetitive controller

The basic theory of the digital p-integrator controller is utilized to modify the command to a stable analog feedback control system in order to produce zero tracking error of a repetitive command. Mapping of continuous time poles and zeros to the images in the discrete time domain is performed. It is shown that for a pole excess of one, with p odd, the p-integrator learning controller will often produce a stable learning process, even for relatively large sample times. For a pole excess of two, a stable learning process can often be achieved for any p as long as the sample time is kept sufficiently short. Therefore, when the pole excess is zero and one utilizes the proper p-integrator controller with p odd, stable performance is often produced, even for relatively large sample times.

Longman, Richard W.↗

Lunar Instrument Data Integration Into the Virtual Reality Mission Simulation System for Decision Communication and Situational Awareness

In situ resource utilization (ISRU) technologies are a key advancement required to make human habitation on the Moon and Mars viable. The upcoming Volatiles Investigating Polar Exploration Rover (VIPER) mission will provide crucial correlations between volatiles and lunar geology to understand the water content available for ISRU on the moon. The mission will require the coordination of multi-disciplinary teams across the country making real time decisions based on rover instrument data. The virtual reality Mission Simulation System (vMSS) is a virtual reality platform designed at MIT by the Resource Exploration and Science of our Cosmic Environment (RESOURCE) team to provide teams with a collaboration interface for planetary missions like VIPER. Herein we determine the integration pathway for analog based datasets that are examples of VIPER's two main instruments, the near-infrared volatile spectrometer subsystem (NIRVSS) and the neutron spectrometer subsystem (NSS), into vMSS to provide the most valuable visualization tools. Focusing on improving situational awareness, decision making, reducing task load and incorporating comments from scientists working previous analogs and on the current VIPER mission, we recommend critical elements to implement into vMSS and the best approaches for data visualization. We present a review of relevant analogs and state of the art mission software. We have developed a design concept and path to flight of analysed instrument data integrated with data maps that allow for virtual manipulation and annotation between non-co-located team members. We focus on pre-mission mapping of a priori data for improved situational awareness, layering of analysed instrument data, correlative mapping and interactive capabilities for in-mission decision making, as well as archiving and annotation tools for post-mission analysis. Finally, we lay out the roadmap for the future development of immersive sample site visualization capabilities and the use of integrated instrument data in vMSS with automated temporal and geospatial planning.

Cody Alison Paige↗

A multiscale landscape approach for prioritizing river and stream protection and restoration actions

River and stream conservation programs have historically focused on a single spatial scale, for example, a watershed or stream site. Recently, the use of landscape information (e.g., land use and land cover) at multiple spatial scales and over large spatial extents has highlighted the importance of incorporating a landscape perspective into stream protection and restoration activities. Previously, we developed a novel framework that links information about watershed-, catchment-, and reach-scale integrity with stream biological condition using scatterplots and a landscape integrity map. Here we examined an application of this approach for streams in urban and other settings in King County, Washington State, United States, where we related stream macroinvertebrate condition to two indices of landscape integrity, the US Environmental Protection Agency's (USEPA) nationally available Index of Watershed Integrity (IWI) and Index of Catchment Integrity (ICI). We generated a scatterplot of IWI versus ICI for sample sites, where points represented site macroinvertebrate condition from poor to good. The same data were also visualized as a landscape integrity map that displayed catchments of King County according to the level of watershed and catchment integrity (high or low IWI/ICI). Almost three-quarters of poor-condition sites were associated with high-integrity watersheds and catchments (i.e., underperforming sites), which suggested that either one or both national indicators were insufficient for this area, and that sites underperformed because of local-scale factors. In response, we used a catchment-scale indicator related to forest condition (PctForestCat) after examining several GIS-based dispersal indicators from the National Hydrography Dataset and other candidates from the USEPA's StreamCat dataset. We then compared the results of the scatterplots and maps based on the current and original analyses and found that many of the sites previously classified as underperforming now performed as expected, that is, they were poor-condition sites in poor-condition catchments. This analysis demonstrates how results based on a national dataset can be improved by developing an alternative that represents regionally important stressors. The methods used to develop an effective landscape indicator based on StreamCat datasets, and the utility of the multiscale approach, could provide important tools for prioritizing, optimizing, and communicating stream conservation actions.

54 ENVIRONMENTAL SCIENCES↗

Metagenomic clustering links specific metabolic functions to globally relevant ecosystems

ABSTRACT Metagenomic sequencing has advanced our understanding of biogeochemical processes by providing an unprecedented view into the microbial composition of different ecosystems. While the amount of metagenomic data has grown rapidly, simple-to-use methods to analyze and compare across studies have lagged behind. Thus, tools expressing the metabolic traits of a community are needed to broaden the utility of existing data. Gene abundance profiles are a relatively low-dimensional embedding of a metagenome’s functional potential and are, thus, tractable for comparison across many samples. Here, we compare the abundance of KEGG Ortholog Groups (KOs) from 6,539 metagenomes from the Joint Genome Institute’s Integrated Microbial Genomes and Metagenomes (JGI IMG/M) database. We find that samples cluster into terrestrial, aquatic, and anaerobic ecosystems with marker KOs reflecting adaptations to these environments. For instance, functional clusters were differentiated by the metabolism of antibiotics, photosynthesis, methanogenesis, and surprisingly GC content. Using this functional gene approach, we reveal the broad-scale patterns shaping microbial communities and demonstrate the utility of ortholog abundance profiles for representing a rapidly expanding body of metagenomic data. IMPORTANCE Metagenomics, or the sequencing of DNA from complex microbiomes, provides a view into the microbial composition of different environments. Metagenome databases were created to compile sequencing data across studies, but it remains challenging to compare and gain insight from these large data sets. Consequently, there is a need to develop accessible approaches to extract knowledge across metagenomes. The abundance of different orthologs (i.e., genes that perform a similar function across species) provides a simplified representation of a metagenome’s metabolic potential that can easily be compared with others. In this study, we cluster the ortholog abundance profiles of thousands of metagenomes from diverse environments and uncover the traits that distinguish them. This work provides a simple to use framework for functional comparison and advances our understanding of how the environment shapes microbial communities.

54 ENVIRONMENTAL SCIENCES↗

Characterizing Dynamic Structure in Battery Electrodes by Time-Resolved Cryo-TEM

In recent years, cryogenic transmission electron microscopy (cryo-TEM) has enabled high-resolution characterization of sensitive battery materials by minimizing electron beam-induced artifacts and damage. Success of this technique relies on the preparation of thin, rapidly frozen samples, generally by disassembling batteries under inert atmosphere, transferring materials of interest to a TEM grid, and finally plunge freezing into a cryogen. In material degradation studies, this extensive time between electrochemical cycling and cryo-TEM characterization leaves room for structural relaxation, diffusion, and other dynamic processes that make it difficult to precisely correlate the imaged structure with the native structure that evolves during battery cycling or aging. Here, we present a method to integrate battery cycling with fast preparation of electrode samples for cryo-TEM. This enables higher fidelity between the structures characterized and the electrochemical state of interest, which we use to study deformation in silicon nanoparticle anodes for lithium-ion batteries.

CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS↗

Integrated Design Results for the MSR DAC-0.0 Mars Ascent Vehicle

The NASA Mars Sample Return (MSR) Campaign endeavors to return Martian regolith, rock, and atmospheric samples to Earth for scientific study. One of many significant challenges to overcome in the return of these samples lies in transporting them from the Martian surface to space. In order to surmount this challenge, the Campaign has conceptualized the need for a Mars Ascent Vehicle (MAV) to perform this function and deliver Martian samples to orbit. There, the samples will be ejected and captured by a separate spacecraft for return to Earth. Many concepts for a MAV have existed in the past, but it has not been until now that an integrated, detailed design solution has been developed and analyzed. Preliminary assessments of the initial architecture examined multiple methods of propulsion. The team ultimately determined that a Two Stage to Orbit (TSTO) solid propulsion vehicle would provide the most effective performance and be the most technologically ready to support this mission. Following the decision to adopt a TSTO solid propelled vehicle, the first official Design Analysis Cycle, DAC-0.0, was performed in Spring 2020 to formally advance the fidelity of the vehicle to a maturity level acceptable for NASA Key Decision Point A (KDP-A). This paper describes the resultant MAV design concept developed as part of the DAC-0.0 study by the NASA Marshall Space Flight Center (MSFC), in association with the NASA Jet Propulsion Laboratory (JPL). The TSTO vehicle features two solid rocket motors, one powering each stage. Their thrust vectors are controlled with Thrust Vector Control (TVC) systems consisting of independent electromechanical actuators acting on gimballed nozzles. The vehicle is designed to deliver up to 0.47kg of Martian samples to a Mars circular orbit of 343km at 27° inclination. Due to the unique environmental conditions that this vehicle is required to operate in, the subsystem design teams were compelled to develop creative and unorthodox designs to ensure a successful mission. The detailed design and analysis of these subsystems are discussed in this paper and include topics on the MAV Guidance, Navigation, and Control (GNC); structures and mechanisms; integrated vehicle thermal; avionics and flight software; a hydrazine-based Reaction Control System (RCS); aerosciences; and vehicle assembly, integration, and test (AI&T) considerations, among others. Following the conclusion of the MAV DAC-0.0, additional alternative architecture concepts were also studied to further reduce the mass of the overall system. The results of these studies will also be examined in this paper.

Darius Yaghoubi↗

Thermal and Evolved Gas Analysis of Geologic Samples Containing Organic Materials: Implications for the 2007 Mars Phoenix Scout Mission

The Thermal and Evolved Gas Analyzer (TEGA) instrument scheduled to fly onboard the 2007 Mars Phoenix Scout Mission will perform differential scanning calorimetry (DSC) and evolved gas analysis (EGA) of soil samples and ice collected from the surface and subsurface at a northern landing site on Mars. We have been developing a sample characterization data library using a laboratory DSC integrated with a quadrupole mass spectrometer to support the interpretations of TEGA data returned during the mission. The laboratory TEGA test-bed instrument has been modified to operate under conditions similar to TEGA, i.e., reduced pressure (e.g., 100 torr) and reduced carrier gas flow rates. We have previously developed a TEGA data library for a variety of volatile-bearing mineral phases, including Fe-oxyhydroxides, phyllosilicates, carbonates, and sulfates. Here we examine the thermal and evolved gas properties of samples that contain organics. One of the primary objectives of the Phoenix Scout Mission is to search for habitable zones by assessing organic or biologically interesting materials in icy soil. Nitrogen is currently the carrier gas that will be used for TEGA. In this study, we examine two possible modes of detecting organics in geologic samples; i.e., pyrolysis using N2 as the carrier gas and combustion using O2 as the carrier gas.

Lauer, H. V., Jr.↗

Proof Of Concept of Integrated Load Measurement in 3D Printed Structures

Currently, research on structural health monitoring systems is focused on direct integration of the system into a component or structure. The latter results in a so-called smart structure. One example of a smart structure is a component with integrated strain sensing for continuous load monitoring. Additive manufacturing, or 3D printing, now also enables such integration of functions inside components. As a proof-of-concept, the Fused Deposition Modeling (FDM) technique was used to integrate a strain sensing element inside polymer (ABS) tensile test samples. The strain sensing element consisted of a closed capillary filled with a fluid and connected to an externally mounted pressure sensor. The volumetric deformation of the integrated capillary resulted in pressure changes in the fluid. The obtained pressure measurements during tensile testing are reported in this paper and compared to state-of-the-art extensometer measurements. The sensitivity of the 3D printed pressure-based strain sensor is primarily a function of the compressibility of the capillary fluid. Air- and watertightness are of critical importance for the proper functioning of the 3D printed pressure-based strain sensor. Therefore, the best after-treatment procedure was selected on basis of a comparative analysis. The obtained pressure measurements are linear with respect to the extensometer readings, and the uncertainty on the strain measurement of a capillary filled with water (incompressible fluid) is ±3.1 µstrain, which is approximately three times less sensitive than conventional strain gauges (±1 µstrain), but 32 times more sensitive than the same sensor based on air (compressible fluid) (±101 µstrain).

42 ENGINEERING↗

Development of a vadose zone advanced monitoring system: Tools to assess groundwater vulnerability

Performing repeat pore-fluid sampling over long time-scales can provide valuable information on unsaturated zone contaminants and their potential flux to ground water. This information can be used to manage groundwater remedies and identify contaminants that need to be sequestered in the vadose zone to minimize flux to ground water. Pore-water samples are commonly used to obtain contaminant concentrations within the vadose zone, but existing methods are limited as they only provide a single sample at one location and time. The vadose zone advanced monitoring system (VZAMS) has been designed to integrate multiple technologies into a single down-borehole system that allows for sampling of pore fluids (liquid and gas) to provide information about contamination and hydraulic conditions at multiple depths (~0.3-m intervals) within a cased borehole. Testing has been completed at the laboratory scale to verify the sampling elements of VZAMS, including geochemical testing for representative contaminants known to exist at the Hanford Site, located in southeastern Washington State. Physical tests focused on the ability of the sampler to draw fluid under unsaturated conditions. Initial geochemical testing showed that the stainless steel material used with the porous cuff may affect the sampled concentrations of redox-sensitive contaminants under very dry conditions. Additional laboratory testing demonstrated that the VZAMS components are able to collect representative samples for substances of interest under expected field conditions. In this paper, the design and functionality of a novel instrument are demonstrated in support of subsequent testing in the field.

54 ENVIRONMENTAL SCIENCES↗

An expert system shell for inferring vegetation characteristics

The NASA VEGetation Workbench (VEG) is a knowledge based system that infers vegetation characteristics from reflectance data. The report describes the extensions that have been made to the first generation version of VEG. An interface to a file of unkown cover type data has been constructed. An interface that allows the results of VEG to be written to a file has been implemented. A learning system that learns class descriptions from a data base of historical cover type data and then uses the learned class descriptions to classify an unknown sample has been built. This system has an interface that integrates it into the rest of VEG. The VEG subgoal PROPORTION.GROUND.COVER has been completed and a number of additional techniques that infer the proportion ground cover of a sample have been implemented.

Harrison, P. Ann↗