Results for “sample identifier” — Page 44

NASA NTRS1998

The Athena Mars Rover Science Payload

The Mars Surveyor missions that will be launched in April of 2001 will include a highly capable rover that is a successor to the Mars Pathfinder mission's Sojourner rover. The design goals for this rover are a total traverse distance of at least 10 km and a total lifetime of at least one Earth year. The rover's job will be to explore a site in Mars' ancient terrain, searching for materials likely to preserve a record of ancient martian water, climate, and possibly biology. The rover will collect rock and soil samples, and will store them for return to Earth by a subsequent Mars Surveyor mission in 2005. The Athena Mars rover science payload is the suite of scientific instruments and sample collection tools that will be used to perform this job. The specific science objectives that NASA has identified for the '01 rover payload are to: (1) Provide color stereo imaging of martian surface environments, and remotely-sensed point discrimination of mineralogical composition. (2) Determine the elemental and mineralogical composition of martian surface materials. (3) Determine the fine-scale textural properties of these materials. (4) Collect and store samples. The Athena payload has been designed to meet these objectives. The focus of the design is on field operations: making sure the rover can locate, characterize, and collect scientifically important samples in a dusty, dirty, real-world environment. The topography, morphology, and mineralogy of the scene around the rover will be revealed by Pancam/Mini-TES, an integrated imager and IR spectrometer. Pancam views the surface around the rover in stereo and color. It uses two high-resolution cameras that are identical in most respects to the rover's navigation cameras. The detectors are low-power, low-mass active pixel sensors with on-chip 12-bit analog-to-digital conversion. Filters provide 8-12 color spectral bandpasses over the spectral region from 0.4 to 1.1 micron Narrow-angle optics provide an angular resolution of 0.28 mrad/pixel, nearly a factor of four higher than that of the Mars Pathfinder and Mars Surveyor '98 cameras. Image compression will be performed using a wavelet compression algorithm. The Mini-Thermal Emission Spectrometer (Mini-TES) is a point spectrometer operating in -the thermal IR. It produces high spectral resolution (5 /cm) image cubes with a wavelength range of 5-40 gm, a nominal signal/noise ratio of 500:1, and a maximum angular resolution of 7 mrad (7 cm at a distance of 10 in). The wavelength region over which it operates samples the diagnostic fundamental absorption features of rockforming minerals, and also provides some capability to see through dust coatings that could tend to obscure spectral features. The mineralogical information that Mini-TES provides will be used to select from a distance the rocks and soils that will be investigated in more detail and ultimately sampled. Mini-TES is derived from the MO/MGS TES instrument, but is significantly smaller and simpler. The instrument uses an 8-cm Cassegrain telescope, a Michelson interferometer, and uncooled pyroelectric detectors. Along with its mineralogical capabilities, Mini-TES can provide information on the thermophysical properties of rocks and soils. Viewing upward, it can also provide temperature profiles through the martian atmospheric boundary layer. Elemental and Mineralogical Composition: Once promising samples have been identified from a distance using Pancam/Mini-TES, they will be studied in detail using up to three compositional sensors that can be placed directly against them by an Instrument Arm. The two compositional sensors, presently on the payload are an Alpha-Proton-X-Ray Spectrometer (APXS), and a Mossbauer Spectrometer. The APXS is derived closely from the instrument that flew on Mars Pathfinder. Radioactive alpha sources and three detection modes (alpha, proton, and x-ray) provide elemental abundances of rocks and soils to complement and constrain mineralogical data. The Athena APXS will have a revised mechanical design that will cut down significantly on backscattering of alpha particles from martian atmospheric carbon. It will also include a target of known elemental composition that will be used for calibration purposes. The Athena Mossbauer Spectrometer is a diagnostic instrument for the mineralogy and oxidation state of Fe-bearing phases, which are particularly important on Mars. The instrument measures the resonant absorption of gamma rays produced by a Co-57 source to determine splitting of nuclear energy levels in Fe atoms that is related to the electronic environment surrounding them. It has been under development for space flight for many years at the Technical University of Darmstadt. The Mossbauer Spectrometer (and the other arm instruments) will be able to view a small permanent magnet array that will attract magnetic particles in the martian soil. The payload may also include a Raman Spectrometer. If included, the Raman Spectrometer will provide precise identification of major and minor mineral phases. It requires no sample preparation, and is also sensitive to organics. Fine-Scale Texture: The Instrument Arm a also carries a Microscopic Imager that will obtain high-resolution monochromatic images of the same materials for which compositional data will be obtained. Its spatial resolution is 20 micron/pixel over a 1 cm depth of field, and 40 micron/pixel over a 1-cm depth of field. Like Pancam, it uses the same active pixel sensor detectors and electronics as the rover's navigation cameras. The Instrument Arm is a three degree-of-freedom arm that uses designs and components from the Mars Pathfinder and Mars Surveyor '98 projects. Its primary function is instrument positioning. Along with the instruments noted above, it also carries a brush that can be used to remove dust and other loose coatings from rocks. Sample Collection and Storage: Martian rock and soil samples will be collected using a low-power rotary coring drill called the Mini-Corer. An important characteristic of this device is that it can obtain intact samples of rock from up to 5 cm within strong boulders and bedrock, Nominal core dimensions are 8xl7 mm. The Mini-Corer drills a core to the commanded depth in a rock, shears it off, retains it, and extracts it. It can also acquire samples of loose soil, using soil sample cups that are pressed downward into loose material. The Mini-Corer can drill at angles from vertical to 45' off vertical. It has six interchangeable bits for long life. Mechanical damage to the sample during drilling is minimal, and heating is negligible. After acquisition, the sample may be viewed by the arm instruments, and/or placed in one of 104 compartments in the Sample Container. A subset of the acquired samples may be replaced with other samples obtained later if desired. The Sample Container has no moving parts, and is mounted external to the rover for easy removal by the Mars Surveyor 2005 flight system. Operation of the rover will make extensive use of automated onboard navigation and hazard avoidance capabilities. Otherwise, use of onboard autonomy is minimal. Data downlink capability is about 40 Mbit/sol, and the use of the Mars Surveyor '01 orbiter for data relay imposes a limit of at most two command cycles per sol. Because of the significant amount of time available between command cycles, all payload elements will be operated sequentially, rather than in parallel.; this approach also significantly simplifies operations and minimizes peak power usage. The landing site for the '01 rover has not been selected yet. Site selection will make as full use as possible of Mars Global Surveyor data, and will involve substantial input from the broad Mars science community. Summary: The following table describes the mass, power, providers, and key scientific objectives of all the major elements of the Athena payload. Additional Athena payload information may be found at: http://astrosun.tn.cornell.edu/athena/index.html. Additional information contained in the original.

Squyes, S. W.↗

NASA NTRS1980

Sampling of rectangular regions

There are no author-identified significant results in this report.

Terrell, G.↗

NASA NTRS2003

Geology of the Icy Galilean Satellites: Understanding Crustal Processes and Geologic Histories Through the JIMO Mission

Knowledge of the geology, style and time history of crustal processes on the icy Galilean satellites is necessary to understanding how these bodies formed and evolved. Data from the Galileo mission have provided a basis for detailed geologic and geo- physical analysis. Due to constrained downlink, Galileo Solid State Imaging (SSI) data consisted of global coverage at a -1 km/pixel ground sampling and representative, widely spaced regional maps at -200 m/pixel. These two data sets provide a general means to extrapolate units identified at higher resolution to lower resolution data. A sampling of key sites at much higher resolution (10s of m/pixel) allows evaluation of processes on local scales. We are currently producing the first global geological map of Europa using Galileo global and regional-scale data. This work is demonstrating the necessity and utility of planet-wide contiguous image coverage at global, regional, and local scales.

Figueredo, P. H.↗

NASA NTRSDate not supplied

ISS External Microorganisms: Collecting Planetary Protection Samples During Extravehicular Activity

Introduction: We have designed1, built, and tested a sampling kit (Fig. 1) to aseptically collect microbiological samples from exterior surfaces on the ISS (International Space Station). The kit was flown to ISS as part of the NG-19 commercial cargo mission in August of 2023. Astronauts will use the kit to collect samples from six exterior surfaces on ISS. These samples will be frozen at -80°C after collection and returned to the ground for next generation DNA sequencing. The results of this experiment will help inform planetary protection requirements for crewed missions. We hypothesize that there are detectable microbial communities outside ISS and that these communities originate from inside ISS. Current life support systems do not include any components for reducing microbial leakage. Gases are vented from inside ISS without filtration and there are currently no protocols in place to minimize bioburden on space suit exteriors prior to use. It is important to quantify the bioburden on current vehicles so that achievable limits can be set for crewed missions to astrobiologically relevant locations like Mars. Figure 1: The sampling kit contains eight swab canisters in total (six on the top and two on the bottom). A resuable end effector (1) is used to remove and reinstall the swabs. The kit also contains a handrail (2), tether loop (3), and, bayonet probes(4) to allow easy manipulation during EVA. Methods: We have designed a kit to carry 8 commercially available foam swabs into and out of vacuum without compromising the swabs’ sterility. The specially designed swab canisters contain a 0.2 µm Teflon filter that allows the canister to accommodate pressure changes without introducing unwanted contaminants. The kit meets existing EVA (Extravehicular Activity) safety requirements and has been used by human test subjects in the neutral buoyance lab and at vacuum in test chambers at the Johnson Space Center. In the early part of 2024, astronauts will use this sampling kit to swab six surfaces on the exterior of ISS. We will collect samples from: the airlock vestibule, the interior surface of the airlock thermal cover, an exterior handrail, a vent connected to the CO2 removal system, and a vent connected to the payload vacuum system inside ISS. Approximately 300 cm2 will be swabbed at each location. A seventh swab will be exposed to the vacuum of space without touching any surfaces as a blank. The eighth swab will remain sealed as a process control. After the EVA the swab kit will be frozen at -80°C and returned to earth at the earliest possible opportunity. The samples will remain frozen until they are thawed for next generation DNA sequencing on earth. We will use amplicon sequencing to identify any bacteria, archaea or fungi present in the samples. If there is enough DNA present, we will use shotgun metagenomic sequencing to further characterize the microbial ecology outside ISS. Preliminary Results: Results from ground-based testing demonstrate that the swab kit is capable of cycling in and out of vacuum without contaminating the swabs. Test subjects, wearing flight-like EVA gloves could remove swabs from the canister and sample discrete locations without inadvertently touching any other surfaces. Several types of bacteria and fungi were collected during these ground tests and survived up to 6 hours at vacuum. This includes non-spore forming bacterial like Staphyloccus capitis that are not traditionally considered extremophiles. Shotgun metagenomic sequencing of the ground-test samples revealed bacteria associated with human skin and airways on the exterior of space suits used during these tests 2 In addition to these results we will present preliminary results from our space-flight samples. We will also present lessons learned from attempting to collect microbiological samples during an EVA and describe how our results will affect planetary protection requirements for future crewed missions.

Aaron B. Regberg↗

NASA NTRSDate not supplied

ISS External Microorganisms: Collecting Planetary Protection Samples During Extravehicular Activity

Introduction: We have designed1, built, and tested a sampling kit (Fig. 1) to aseptically collect microbiological samples from exterior surfaces on the ISS (International Space Station). The kit was flown to ISS as part of the NG-19 commercial cargo mission in August of 2023. Astronauts will use the kit to collect samples from six exterior surfaces on ISS. These samples will be frozen at -80°C after collection and returned to the ground for next generation DNA sequencing. The results of this experiment will help inform planetary protection requirements for crewed missions. We hypothesize that there are detectable microbial communities outside ISS and that these communities originate from inside ISS. Current life support systems do not include any components for reducing microbial leakage. Gases are vented from inside ISS without filtration and there are currently no protocols in place to minimize bioburden on space suit exteriors prior to use. It is important to quantify the bioburden on current vehicles so that achievable limits can be set for crewed missions to astrobiologically relevant locations like Mars. Figure 1: The sampling kit contains eight swab canisters in total (six on the top and two on the bottom). A resuable end effector (1) is used to remove and reinstall the swabs. The kit also contains a handrail (2), tether loop (3), and, bayonet probes(4) to allow easy manipulation during EVA. Methods: We have designed a kit to carry 8 commercially available foam swabs into and out of vacuum without compromising the swabs’ sterility. The specially designed swab canisters contain a 0.2 µm Teflon filter that allows the canister to accommodate pressure changes without introducing unwanted contaminants. The kit meets existing EVA (Extravehicular Activity) safety requirements and has been used by human test subjects in the neutral buoyance lab and at vacuum in test chambers at the Johnson Space Center. In the early part of 2024, astronauts will use this sampling kit to swab six surfaces on the exterior of ISS. We will collect samples from: the airlock vestibule, the interior surface of the airlock thermal cover, an exterior handrail, a vent connected to the CO2 removal system, and a vent connected to the payload vacuum system inside ISS. Approximately 300 cm2 will be swabbed at each location. A seventh swab will be exposed to the vacuum of space without touching any surfaces as a blank. The eighth swab will remain sealed as a process control. After the EVA the swab kit will be frozen at -80°C and returned to earth at the earliest possible opportunity. The samples will remain frozen until they are thawed for next generation DNA sequencing on earth. We will use amplicon sequencing to identify any bacteria, archaea or fungi present in the samples. If there is enough DNA present, we will use shotgun metagenomic sequencing to further characterize the microbial ecology outside ISS. Preliminary Results: Results from ground-based testing demonstrate that the swab kit is capable of cycling in and out of vacuum without contaminating the swabs. Test subjects, wearing flight-like EVA gloves could remove swabs from the canister and sample discrete locations without inadvertently touching any other surfaces. Several types of bacteria and fungi were collected during these ground tests and survived up to 6 hours at vacuum. This includes non-spore forming bacterial like Staphyloccus capitis that are not traditionally considered extremophiles. Shotgun metagenomic sequencing of the ground-test samples revealed bacteria associated with human skin and airways on the exterior of space suits used during these tests 2 In addition to these results we will present preliminary results from our space-flight samples. We will also present lessons learned from attempting to collect microbiological samples during an EVA and describe how our results will affect planetary protection requirements for future crewed missions.

Aaron B. Regberg↗

DOE OSTI2021

Novel data analysis method for obtaining better performance from a complex 3D-printed collimator

Additively manufactured scattered beam collimators are increasingly being employed to boost the sample to cell peak signal ratio in high pressure neutron diffraction studies because of manufacturing versatility and performance improvements. We study how the measured diffraction pattern is affected by the presence of a collimator downstream of the sample, and develop a novel protocol that provides more effective background rejection. This protocol takes into account critical performance-determinants that were identified in this study, namely: (i) effectively identifying the collimator pattern on the detector; (ii) understanding the dependence of this pattern on sample and cell composition; and (iii) accurately identifying and differentiating the different regions of the pattern on the detector based on the dependency of the cell or sample and finally (iv) resolving the intensities at regions of the detector where neutrons scattered from the sample are preferentially represented, in order to boost the sample to cell peak signal ratio. Application of this novel analysis protocol is shown to increase the collimator performance over the traditional method.

3D printing↗

NASA NTRS2010

Bringing a Chemical Laboratory Named Sam to Mars on the 2011 Curiosity Rover

An important goal of upcoming missions to Mars is to understand if life could have developed there. The task of the Sample Analysis at Mars (SAM) suite of instruments [1] and the other Curiosity investigations [2] is to move us steadily toward that goal with an assessment of the habitability of our neighboring planet through a series of chemical and geological measurements. SAM is designed to search for organic compounds and inorganic volatiles and measure isotope ratios. Other instruments on Curiosity will provide elemental analysis and identify minerals. SAM will analyze both atmospheric samples and gases evolved from powdered rocks that may have formed billions of years ago with Curiosity providing access to interesting sites scouted by orbiting cameras and spectrometers.

Mahaffy, P. R.↗

DOE OSTI2022

Illitization in the Mt. Simon Sandstone, Illinois Basin, USA: Implications for carbon dioxide storage

Clay mineral cementation is one of the most important controls on sandstone reservoir properties. Here, in this paper, the diagenetic history of the Mt. Simon reservoir complex is studied to reveal the origin, timing, and controls of illitization. Samples of sandstone and shale from Mt. Simon reservoir complex were acquired from the Illinois Basin–Decatur Project (IBDP), a CO 2 storage demonstration project in the central Illinois Basin. Petrographic, SEM, TEM, XRD analyses and K/Ar age dating were completed to identify the major detrital and diagenetic components of the samples and reveal illite to be the major clay component in all samples. Illitic clay coatings in the lower Mt. Simon reservoir are identified as a major control on reservoir properties by inhibiting major precipitation of authigenic quartz during illitization, resulting in highly permeable sandstone, essential for CO 2 storage. The coating box-work morphology and mineralogy are indicative of a detrital smectite origin with subsequent illite growth associated with feldspar dissolution and kaolinite alteration. The mineralogy of bulk material and separate grain size fractions (2–0.6 μm; 0.6–0.2 μm; < 0.2 μm) with illite polytypes 2M 1 , 1M, and 1M d were quantified and age dated via 40 K- 40 Ar methods. The shales or reservoir seals contain the highest proportions of detrital illite with illite in the lower Mt. Simon Sandstone reservoir identified as solely diagenetic. Two major events of illitization are identified throughout the Mt. Simon with more porous reservoir rock exhibiting the older event from approximately 360 to 315 Ma and tighter sandstone units with reservoir properties too low to be considered reservoir exhibiting illite dates from 250 to 220 Ma. This partitioning of illitization is attributed to varied mineralogy controlled by depositional changes and evolution of the greater basin.

58 GEOSCIENCES↗

NASA NTRS1990

A redshift survey of IRAS galaxies. I - Sample selection

A complete all-sky sample of objects, flux-limited at 60 microns, has been extracted from the data base of the IRAS. The sample consists of 5014 objects, of which 2649 are galaxies and 13 are not yet identified. In order to study large-scale structure with this sample, it must be free of systematic biases. Corrections are applied for a major systematic effect in the flux densities listed in the IRAS Point Source Catalog: sources resolved by the IRAS beam have flux densities systematically underestimated. In addition, accurate flux densities are obtained for sources flagged as variable, or of moderate flux quality at 60 microns. The IRAS detectors suffered radiation-induced responsivity enhancement (hysteresis) due to crossings of the satellite scans across the Galactic plane; this effect is measured and is shown to be negligible.

Strauss, Michael A.↗

NASA NTRS1994

The ensemble variability properties of faint QSOs

A refined sample of 64 variable objects with stellar image structure has been identified in SA 57 to B approximately = 22.5, over a time baseline of 15 yr, sampled at 11 distinct epochs. The photometric data typically have a root-mean-square (rms) error at B = 22 of only 0.05 mag. Thirty-five quasars in this field have already been spectroscopically confirmed, 34 of which are among the sample of variables. Of the other variables, six are known spectroscopically to be stars, 10 additional objects are stars based on reliable detection of proper motion, and one is spectroscopically a narrow emission line galaxy. Of the 13 remaining variables, it is argued that they are a mixture of distant halo subdwarfs and quasars with starlike colors. We compute the ensemble average structure function and autocorrelation function from the light curves in the respective quasar rest frames, which are used to investigate the general dependences on apparent magnitude, absolute magnitude, and redshift.

Trevese, Dario↗

DOE OSTI2024

Optical Photometric Indicators of Galaxy Cluster Relaxation

Abstract The most dynamically relaxed clusters of galaxies play a special role in cosmological studies as well as astrophysical studies of the intracluster medium (ICM) and active galactic nucleus feedback. While high-spatial-resolution imaging of the morphology of the ICM has long been the gold standard for establishing a cluster’s dynamical state, such data are not available from current or planned surveys, and thus require separate, pointed follow-up observations. With optical and/or near-IR photometric imaging, and red-sequence cluster finding results from those data, expected to be ubiquitously available for clusters discovered in upcoming optical and millimeter-wavelength surveys, it is worth asking how effectively photometric data alone can identify relaxed cluster candidates, before investing in, e.g., high-resolution X-ray observations. Here we assess the ability of several simple photometric measurements, based on the redMaPPer cluster finder run on Sloan Digital Sky Survey data, to reproduce X-ray classifications of dynamical state for an X-ray selected sample of massive clusters. We find that two simple metrics contrasting the bright central galaxy (BCG) to other cluster members can identify a complete sample of relaxed clusters with a purity of ∼40% in our data set. Including minimal ICM information in the form of a center position increases the purity to ∼60%. However, all three metrics depend critically on correctly identifying the BCG, which is presently a challenge for optical red-sequence cluster finders.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

What more can be done with XPS? Highly informative but underused approaches to XPS data collection and analysis

Because of the importance of surfaces and interfaces in many scientific and technological areas, the use of x-ray photoelectron spectroscopy (XPS) has been growing exponentially. Although XPS is being used to obtain useful information about the surface composition of samples, much more information about materials and their properties can be extracted from XPS data than commonly obtained. This paper describes some of the areas where alternative analysis methods or experimental design can obtain information about the near-surface region of a sample, often information not available in other ways. Experienced XPS analysts are familiar with many of these methods, but they may not be known to new or casual XPS users, and sometimes, they have not been used because of an inappropriately assumed complexity. The information available includes optical, electronic, and electrical properties; nanostructure; expanded chemical information; and enhanced analysis of biological materials and solid/liquid interfaces. Many of these analyses can be conducted on standard laboratory XPS systems, with either no or relatively minor system alterations. Topics discussed include (1) considerations beyond the “traditional” uniform surface layer composition calculation, (2) using the Auger parameter to determine a sample property, (3) use of the D parameter to identify sp 2 and sp 3 carbon information, (4) information from the XPS valence band, (5) using cryocooling to expand range of samples that can be analyzed and minimize damage, and (6) using electrical potential effects on XPS signals to extract chemically resolved electrical measurements including band alignment and electrical property information.

Baer, Donald R. [Pacific Northwest National Labora↗

NASA NTRS2011

The SEEDS of Planet Formation: Observations of Transitional Disks

As part of its 5-year study, the Strategic Exploration of Exoplanets and Disk Systems (SEEDS) has already observed a number of YSOs with circumstellar disks, including 13 0.5- 8 Myr old A-M stars with indications that they host wide gaps or central cavities in their circumstellar disks in millimeter or far-IR observations, or from deficits in warm dust thermal emission. For 8 of the disks, the 0.15" inner working angle of HiCIAO+A0188 samples material in the millimeter or mid-IR identified cavity. In one case we reprt detection of a previously unrecognized wide gap. For the remaining 4 stars, the SEEDS data sample the outer disk: in 3 cases, we present the first NIR imagery of the disks. The data for the youngest sample members (less than 1-2 Myr) closely resemble coeval primordial disks. After approximately 3 Myr, the transitional disks show a wealth of structure including spiral features, rings, divots, and in some cases, largely cleared gaps in the disks which are not seen in coeval primordial disks. Some of these structural features are predicted consequences of lovianmass planets having formed in the disk, while others are novel features. We discuss the implications for massive planet formation timescales and mechanisms.

Grady, Carol↗

NASA NTRS2011

The SEEDS of Planet Formation: Observations of Transitional Disks

As part of its 5-year study, the Strategic Exploration of Exoplanets and Disk Systems (SEEDS) has already observed a number of YSOs with circumstellar disks, including 13 0.5-8 Myr old A-M stars with indications that they host wide gaps or central cavities in their circumstellar disks in millimeter or far-IR observations, or from deficits in warm dust thermal emission. For 8 of the disks, the 0.15" inner working angle of HiCIAO+A0188 samples material in the millimeter or mid-IR identified cavity. In one case we report detection of a previously unrecognized wide gap. For the remaining 4 stars, the SEEDS data sample the outer disk: in 3 cases, we present the first NIR imagery of the disks. The data for the youngest sample members 1-2 Myr) closely resemble coeval primordial disks. After approximately 3 Myr, the transitional disks show a wealth of structure including spiral features, rings, divots, and in some cases, largely cleared gaps in the disks which are not seen in coeval primordial disks. Some of these structural features are predicted consequences of Jovian-mass planets having formed in the disk, while others are novel features. We discuss the implications for massive planet formation timescales and mechanisms.

Grady, Carol A.↗

DOE OSTI2021

Co-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discovery

The unicellular green alga Chlamydomonas reinhardtii is a choice reference system for the study of photosynthesis and chloroplast metabolism, cilium assembly and function, lipid and starch metabolism, and metal homeostasis. Despite decades of research, the functions of thousands of genes remain largely unknown, and new approaches are needed to categorically assign genes to cellular pathways. Growing collections of transcriptome and proteome data now allow a systematic approach based on integrative co-expression analysis. We used a dataset comprising 518 deep transcriptome samples derived from 58 independent experiments to identify potential co-expression relationships between genes. We visualized co-expression potential with the R package corrplot, to easily assess co-expression and anti-correlation between genes. We extracted several hundred high-confidence genes at the intersection of multiple curated lists involved in cilia, cell division, and photosynthesis, illustrating the power of our method. Surprisingly, Chlamydomonas experiments retained a significant rhythmic component across the transcriptome, suggesting an underappreciated variable during sample collection, even in samples collected in constant light. Our results therefore document substantial residual synchronization in batch cultures, contrary to assumptions of asynchrony. We provide step-by-step protocols for the analysis of co-expression across transcriptome data sets from Chlamydomonas and other species to help foster gene function discovery.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Metagenomic strategies identify diverse integron–integrase and antibiotic resistance genes in the Antarctic environment

The objective of this study is to identify and analyze integrons and antibiotic resistance genes (ARGs) in samples collected from diverse sites in terrestrial Antarctica. Integrons were studied using two independent methods. One involved the construction and analysis of intI gene amplicon libraries. In addition, we sequenced 17 metagenomes of microbial mats and soil by high-throughput sequencing and analyzed these data using the IntegronFinder program. As expected, the metagenomic analysis allowed for the identification of novel predicted intI integrases and gene cassettes (GCs), which mostly encode unknown functions. However, some intI genes are similar to sequences previously identified by amplicon library analysis in soil samples collected from non-Antarctic sites. ARGs were analyzed in the metagenomes using ABRIcate with CARD database and verified if these genes could be classified as GCs by IntegronFinder. We identified 53 ARGs in 15 metagenomes, but only four were classified as GCs, one in MTG12 metagenome (Continental Antarctica), encoding an aminoglycoside-modifying enzyme (AAC(6´)acetyltransferase) and the other three in CS1 metagenome (Maritime Antarctica). One of these genes encodes a class D β-lactamase (blaOXA-205) and the other two are located in the same contig. One is part of a gene encoding the first 76 amino acids of aminoglycoside adenyltransferase (aadA6), and the other is a qacG2 gene.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Improved precision in As speciation analysis with HERFD-XANES at the As K -edge: the case of As speciation in mine waste

High-energy-resolution fluorescence-detected (HERFD) X-ray absorption near-edge spectroscopy (XANES) is a spectroscopic method that allows for increased spectral feature resolution, and greater selectivity to decrease complex matrix effects compared with conventional XANES. XANES is an ideal tool for speciation of elements in solid-phase environmental samples. Accurate speciation of As in mine waste materials is important for understanding the mobility and toxicity of As in near-surface environments. In this study, linear combination fitting (LCF) was performed on synthetic spectra generated from mixtures of eight measured reference compounds for both HERFD-XANES and transmission-detected XANES to evaluate the improvement in quantitative speciation with HERFD-XANES spectra. The reference compounds arsenolite (As 2 O 3 ), orpiment (As 2 S 3 ), getchellite (AsSbS 3 ), arsenopyrite (FeAsS), kaňkite (FeAsO 4 ·3.5H 2 O), scorodite (FeAsO 4 ·2H 2 O), sodium arsenate (Na 3 AsO 4 ), and realgar (As 4 S 4 ) were selected for their importance in mine waste systems. Statistical methods of principal component analysis and target transformation were employed to determine whether HERFD improves identification of the components in a dataset of mixtures of reference compounds. LCF was performed on HERFD- and total fluorescence yield (TFY)-XANES spectra collected from mine waste samples. Arsenopyrite, arsenolite, orpiment, and sodium arsenate were more accurately identified in the synthetic HERFD-XANES spectra compared with the transmission-XANES spectra. In mine waste samples containing arsenopyrite and either scorodite or kaňkite, LCF with HERFD-XANES measurements resulted in fits with smaller R -factors than concurrently collected TFY measurements. The improved accuracy of HERFD-XANES analysis may provide enhanced delineation of As phases controlling biogeochemical reactions in mine wastes, contaminated soils, and remediation systems.

58 GEOSCIENCES↗

DOE OSTI2022

What’s in My Toolkit? A Review of Technologies for Assessing Changes in Habitats Caused by Marine Energy Development

Marine energy devices are installed in highly dynamic environments and have the potential to affect the benthic and pelagic habitats around them. Regulatory bodies often require baseline characterization and/or post-installation monitoring to determine whether changes in these habitats are being observed. However, a great diversity of technologies is available for surveying and sampling marine habitats, and selecting the most suitable instrument to identify and measure changes in habitats at marine energy sites can become a daunting task. We conducted a thorough review of journal articles, survey reports, and grey literature to extract information about the technologies used, the data collection and processing methods, and the performance and effectiveness of these instruments. We examined documents related to marine energy development, offshore wind farms, oil and gas offshore sites, and other marine industries around the world over the last 20 years. A total of 120 different technologies were identified across six main habitat categories: seafloor, sediment, infauna, epifauna, pelagic, and biofouling. The technologies were organized into 12 broad technology classes: acoustic, corer, dredge, grab, hook and line, net and trawl, plate, remote sensing, scrape samples, trap, visual, and others. Visual was the most common and the most diverse technology class, with applications across all six habitat categories. Technologies and sampling methods that are designed for working efficiently in energetic environments have greater success at marine energy sites. In addition, sampling designs and statistical analyses should be carefully thought through to identify differences in faunal assemblages and spatiotemporal changes in habitats.

16 TIDAL AND WAVE POWER↗