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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

TracKlinic: Diagnosis of Challenge Factors in Visual Tracking

Generic visual object tracking is difficult due to many challenge factors (e.g., occlusion, blur, etc.). Each of these factors may cause serious problems for a tracker, and when they work together can make things even more complicated. Despite a great amount of efforts devoted to understanding the behavior of trackers, reliable and quantifiable ways for studying the per factor tracking behavior remain barely available. Addressing this issue, in this paper we contribute to the community a tracking diagnosis toolkit, TracKlinic, for diagnosis of challenge factors of tracking algorithms. TracKlinic consists of two novel components focusing on the data and analysis aspects, respectively. For the data component, we carefully prepare a set of 2,390 annotated videos, each involving one and only one major challenge factor. When analyzing an algorithm for a specific challenge factor, such one-factor-per-sequence rule greatly inhibits the disturbance from other factors and consequently leads to more faithful analysis. For the analysis component, given the tracking results on all sequences, it investigates the behavior of the tracker under each individual factor and generates the report automatically. With TracKlinic, a thorough study is conducted on ten state-of-the-art trackers on nine challenge factors (including two compound ones). The results suggest that, heavy shape variation and occlusion are the two most challenging factors faced by most trackers. Besides, out-of-view, though does not happen frequently, is often fatal. By sharing TracKlinic1, we expect to make it much easier for diagnosing tracking algorithms, and to thus facilitate developing better ones.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Response of Subsurface Nitrogen-Cycling Microbial Communities to Environmental Fluctuations (Final Technical Report)

Riparian floodplains are dynamic ecosystems linking terrestrial and riverine systems. These floodplains experience hydrological shifts such as changes in water table height, flooding, and drought and can be ‘hotspots’ of biogeochemical cycling due to shifting sediment moisture (and saturation) and subsurface exchanges of water, nutrients, and other compounds across different sediment layers. Subsurface microbial communities are the primary drivers of biogeochemical processes in floodplains, and thus their structure and function can directly influence both surface and groundwater quality. The microbial nitrogen (N) cycle is particularly important in floodplains as it affects nutrient availability and removal. Two functional guilds of chemoautotrophic (i.e. CO2-fixing) microorganisms are responsible for the first oxidative step of the N cycle, nitrification: ammonia-oxidizing archaea (AOA) and bacteria (AOB) catalyze the oxidation of ammonia to nitrite, while nitrite-oxidizing bacteria (NOB) oxidize nitrite to nitrate. Despite the critical role nitrification plays in N-cycling in both terrestrial and aquatic ecosystems, our understanding of the diversity, ecophysiology, and activity of nitrifying organisms in subsurface floodplain soils/sediments is extremely limited. To help address this critical knowledge gap, the overarching goal of this project was to determine how shifts in key environmental parameters and gradients impact microbial N-cycling communities/processes, with particular emphasis on nitrification, within hydrologically-variable floodplain sediments in the Wind River Basin near Riverton, Wyoming. The three specific objectives of this project were to: (1) to associate in situ environmental drivers of N cycling with distinct functional guilds; (2) determine the guild response to variation in key ecosystem drivers; and (3) develop a dynamic ecosystem model of the microbial N cycle with the Riverton subsurface using community genomic and biogeochemical data collected in the first two objectives. Over the course of this project, we employed both 16S rRNA gene amplicon sequencing and genome-resolved metagenomics to examine the phylogenetic diversity and metabolic potential of subsurface nitrifier communities within 68 samples collected across multiple sites, depths, and time points within the Riverton floodplain, allowing for both spatial and temporal investigations at different scales. This project benefitted tremendously from recent advances in high-throughput sequencing technologies coupled with dramatic improvements in the computational tools and algorithms available for analyzing such large, complex genomic datasets. By pairing these cutting-edge genomic approaches with depth-resolved sampling and detailed geochemical analyses of the Riverton floodplain, we have gained novel insights into the structure and function of subsurface nitrifier communities in relation to both hydrology and biogeochemistry. This project resulted in the most detailed and comprehensive characterization of N-cycling floodplain microbial communities to date and will hopefully inspire and pave the way for future studies using similar approaches in other floodplains. Indeed, such information is critical for understanding subsurface biogeochemical cycling and how elemental stores are altered from perturbations initiated by the water cycle within floodplains. Finally, because of the terrestrial-aquatic nature of the Riverton floodplain, results from this project are also of relevance to disciplines such as soil science, estuarine science, limnology & oceanography, biogeochemistry, geobiology, environmental engineering, as well as genomics and data science.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Multiple highly expressed phospho enol pyruvate carboxylase genes have divergent enzyme kinetic properties in two C4 grasses

Abstract Background and Aims Phosphoenolpyruvate (PEP) carboxylase (PEPC) catalyses the irreversible carboxylation of PEP with bicarbonate to produce oxaloacetate. This reaction powers the carbon-concentrating mechanism (CCM) in plants that perform C4 photosynthesis. This CCM is generally driven by a single PEPC gene product that is highly expressed in the cytosol of mesophyll cells. We found two C4 grasses, Panicum miliaceum and Echinochloa colona, that each have two highly expressed PEPC genes. We characterized the kinetic properties of the two most abundant PEPCs in E. colona and P. miliaceum to better understand how the enzyme’s amino acid structure influences its function. Methods Coding sequences of the two most abundant PEPC proteins in E. colona and P. miliaceum were synthesized by GenScript and were inserted into bacteria expression plasmids. Point mutations resulting in substitutions at conserved amino acid residues (e.g. N-terminal serine and residue 890) were created via site-directed PCR mutagenesis. The kinetic properties of semi-purified plant PEPCs from Escherichia coli were analysed using membrane-inlet mass spectrometry and a spectrophotometric enzyme-coupled reaction. Key Results The two most abundant P. miliaceum PEPCs (PmPPC1 and PmPPC2) have similar sequence identities (>95 %), and as a result had similar kinetic properties. The two most abundant E. colona PEPCs (EcPPC1 and EcPPC2) had identities of ~78 % and had significantly different kinetic properties. The PmPPCs and EcPPCs had different responses to allosteric inhibitors and activators, and substitutions at the conserved N-terminal serine and residue 890 resulted in significantly altered responses to allosteric regulators. Conclusions The two, significantly expressed C4Ppc genes in P. miliaceum were probably the result of genomes combining from two closely related C4Panicum species. We found natural variation in PEPC’s sensitivity to allosteric inhibition that seems to bypass the conserved 890 residue, suggesting alternative evolutionary pathways for increased malate tolerance and other kinetic properties.

DiMario, Robert J. (ORCID:0000000250566868)↗
NASA NTRS2003

Common 5S rRNA variants are likely to be accepted in many sequence contexts

Over evolutionary time RNA sequences which are successfully fixed in a population are selected from among those that satisfy the structural and chemical requirements imposed by the function of the RNA. These sequences together comprise the structure space of the RNA. In principle, a comprehensive understanding of RNA structure and function would make it possible to enumerate which specific RNA sequences belong to a particular structure space and which do not. We are using bacterial 5S rRNA as a model system to attempt to identify principles that can be used to predict which sequences do or do not belong to the 5S rRNA structure space. One promising idea is the very intuitive notion that frequently seen sequence changes in an aligned data set of naturally occurring 5S rRNAs would be widely accepted in many other 5S rRNA sequence contexts. To test this hypothesis, we first developed well-defined operational definitions for a Vibrio region of the 5S rRNA structure space and what is meant by a highly variable position. Fourteen sequence variants (10 point changes and 4 base-pair changes) were identified in this way, which, by the hypothesis, would be expected to incorporate successfully in any of the known sequences in the Vibrio region. All 14 of these changes were constructed and separately introduced into the Vibrio proteolyticus 5S rRNA sequence where they are not normally found. Each variant was evaluated for its ability to function as a valid 5S rRNA in an E. coli cellular context. It was found that 93% (13/14) of the variants tested are likely valid 5S rRNAs in this context. In addition, seven variants were constructed that, although present in the Vibrio region, did not meet the stringent criteria for a highly variable position. In this case, 86% (6/7) are likely valid. As a control we also examined seven variants that are seldom or never seen in the Vibrio region of 5S rRNA sequence space. In this case only two of seven were found to be potentially valid. The results demonstrate that changes that occur multiple times in a local region of RNA sequence space in fact usually will be accepted in any sequence context in that same local region.

NASA Discipline Exobiology↗
DOE OSTI2020

Regional Differences in the Structure of Juglans nigra Phytobiome Reflect Geographical Differences in Thousand Cankers Disease Severity

Thousand cankers disease threatens Juglans nigra (Eastern Black Walnut) in urban and natural landscapes. Incidence and severity of thousand cankers disease is higher in the host’s introduced range in the western United States. We hypothesized that these differences are driven partly by geographical variation in the host phytobiome due to its roles in host stress tolerance, nutrient acquisition, and defense. To evaluate the role of the phytobiome in mediating thousand cankers disease, we characterized the J. nigra phytobiome of diseased and healthy trees in portions of its native (Indiana and Tennessee) and introduced (Washington) ranges. Grafted clones present in each state and open-pollinated populations were sampled. DNA was extracted from soil and branch (caulosphere) tissues and internal transcribed spacer and 16s regions were sequenced for characterization of fungal and bacterial communities. We found that microbial communities in the caulosphere and soil differ between native and introduced ranges of J. nigra and harbor different mutualistic and pathogenic microorganisms. Additionally, caulosphere microbial communities were more species rich and diverse in the native range of J. nigra, suggesting greater levels of functional redundancy and multifunctionality in the native-range phytobiome compared with the introduced range. We also found higher network complexity in the caulosphere of trees in the introduced range and evidence for two alternative stable community states associated with diseased and healthy trees. Our results provide support for the hypothesis that geographical variation in thousand cankers disease incidence and severity is partially driven by differences in the phytobiome of J. nigra in its introduced and native ranges.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Complex ancestries of lager-brewing hybrids were shaped by standing variation in the wild yeast Saccharomyces eubayanus

Lager-style beers constitute the vast majority of the beer market, and yet, the genetic origin of the yeast strains that brew them has been shrouded in mystery and controversy. Unlike alestyle beers, which are generally brewed with Saccharomyces cerevisiae , lagers are brewed at colder temperatures with allopolyploid hybrids of Saccharomyces eubayanus x S. cerevisiae . Since the discovery of S. eubayanus in 2011, additional strains have been isolated from South America, North America, Australasia, and Asia, but only interspecies hybrids have been isolated in Europe. Here, using genome sequence data, we examine the relationships of these wild S. eubayanus strains to each other and to domesticated lager strains. Our results support the existence of a relatively low-diversity (π = 0.00197) lineage of S. eubayanus whose distribution stretches across the Holarctic ecozone and includes wild isolates from Tibet, new wild isolates from North America, and the S. eubayanus parents of lager yeasts. This Holarctic lineage is closely related to a population with higher diversity (π = 0.00275) that has been found primarily in South America but includes some widely distributed isolates. A second diverse South American population (π = 0.00354) and two early-diverging Asian subspecies are more distantly related. We further show that no single wild strain from the Holarctic lineage is the sole closest relative of lager yeasts. Instead, different parts of the genome portray different phylogenetic signals and ancestry, likely due to outcrossing and incomplete lineage sorting. Indeed, standing genetic variation within this wild Holarctic lineage of S. eubayanus is responsible for genetic variation still segregating among modern lager-brewing hybrids. Furthermore, we conclude that the relationships among wild strains of S. eubayanus and their domesticated hybrids reflect complex biogeographical and genetic processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture

Production of most eukaryotic mRNAs requires splicing of introns from pre-mRNA. The splicing reaction requires definition of splice sites, which are initially recognized in either intron-spanning (‘intron definition’) or exon-spanning (‘exon definition’) pairs. To understand how exon and intron length and splice site recognition mode impact splicing, we measured splicing rates genome-wide in Drosophila , using metabolic labeling/RNA sequencing and new mathematical models to estimate rates. We found that the modal intron length range of 60–70 nt represents a local maximum of splicing rates, but that much longer exon-defined introns are spliced even faster and more accurately. Here, we observed unexpectedly low variation in splicing rates across introns in the same gene, suggesting the presence of gene-level influences, and we identified multiple gene level variables associated with splicing rate. Together our data suggest that developmental and stress response genes may have preferentially evolved exon definition in order to enhance the rate or accuracy of splicing.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1983

HD 207739 - A strange composite star

This star, classified F8 IIe + B:, has a very unusual ultraviolet spectrum, with abnormally strong and numerous absorption features in the far-UV and exceptionally strong Mg II emission. There is some resemblance to shell and pre-main-sequence B stars, but it more closely matches the strange spectra of the eclipsing systems VV Cep and SX Cas, and it probably has considerable circumstellar material at fairly high temperature. HD 207739 is probably an interacting binary and needs to be monitored for light and velocity variations.

Parsons, S. B.↗
NASA NTRS1991

Time domain convergence properties of Lyapunov stable penalty methods

Linear hyperbolic partial differential equations are analyzed using standard techniques to show that a sequence of solutions generated by the Liapunov stable penalty equations approaches the solution of the differential-algebraic equations governing the dynamics of multibody problems arising in linear vibrations. The analysis does not require that the system be conservative and does not impose any specific integration scheme. Variational statements are derived which bound the error in approximation by the norm of the constraint violation obtained in the approximate solutions.

Kurdila, A. J.↗
NASA NTRS1998

Ma'adim Vallis Estuarine Delta in Elysium Basin and Its Relevance as a Landing Site for Exobiology Exploration on Mars

The debouche of Ma'adim Vallis in the Elysium Basin generated a transitional transported sediment structure, which planimetric shape is controlled by the enclosing topography of a deep reentrant gulf of the Basin into the highland. We defined it as an estuarine delta. The location and the importance of this estuarine delta is supported by the theoretical model of graded profile constructed for Ma'adim Vallis, and by two approaches: (i) the reconstruction of Ma'adim Vallis downstream course from Gusev to Elysium Basin, and (ii) the survey of the sediment deposit in the alleged estuary. The longitudinal graded profile of Ma'adim Vallis finds its base-level in the Elysium Basin, at a about 1000 m elevation, which is in agreement with the observed Basin shoreline. This model is supported by observational evidence of flow between the northern rim of Gusev crater, and the Elysium Basin shoreline. This downstream course of Ma'adim Vallis can be divided into three hydrogeologic regions. into three hydrogeologic regions. (a) The first region is a flooded plain (Zephiria Mensae), consisting in chaotic terrain formed by highland rocks, and disintegrated lava of the western flank of Apollinaris. Morphologic indicators of the flood process are: (1) the sediment deposit over the Gusev crater northern rim that reflects the overspilling of the crater-lake water through a 40-km wide gap provided by an ancient impact crater, (2) the tear-drop shaped feature on the northeastern flank of Apollinaris Patera, and (3) the chaotic terrain that suggest the emergence of ground water generated by the seepage of the crater lake through high-permeable broken rampart material. This underground water circulation sustained by the hydrostatic pressure of the crater-lake has likely generated a hydrothermal system in the volcanic environment of Apollinaris Patera. The stratigraphy of the flooded area is identified as Hesperian age, with occurrences of Noachian hilly individual features, and as Amazonian flooded plain and chaotic material, (b) The second region is located on the western flank of Apollinaris Patera. It is surrounded by relics of deep valleys that suggest a former downstream course of Ma'adim Vallis. The geologic setting of this region (Lucus Planum) is interpreted to be an Amazonian formation composed by the middle and lower members of the Medusae Formation., c) The third region corresponds to the convergence of the west and east branches of Ma'adirn Vallis into a deep re-entrant wide gulf that penetrates about 100 km into the highland. This topographic depression is delineated by the 1000 in elevation contour. This gulf has formed an estuarine configuration centered at 3S/190W within the Elysium Basin. This configuration has favored the formation of a estuarine sedimentary delta, because of topographically controlled lateral migration. This estuarine structure is strongly dominated by the incoming supply of Ma'adim Vallis fluvial sediment extracted from Zephiria Mensae and Lucus Planum. The obtuse-angle geometry of the estuary increases the sedimentation rate, which is higher than in the course of the channel. The sediment deposition process is governed by the estuarine water circulation. The inflowing loaded fluvial water enters the estuary as a bottom current, and mixes with the relatively less-loaded water of the receiving basin. When they mixed. the inflowing fluvial material, and the landward basin circulating water generate an accumulation of highly-diversified estuarine deposit stratification. This accumulation of material is mostly centered in the transitional zone of the delta. The sediment trapping efficiency of the estuary is function of the energy balance between the inflowing fluvial water, and the ingoing basin current. The submergence of the delta by the rising of the water-level increases the estuary water-depth, and consequently the sediment entrapment is favored. The locus of sediment accumulation moves landward in the zone of inflowing fluvial water. This results in the rising of the channel base-level, thus in the increase of the length of the longitudinal graded-profile. The sediment deposit facies of the zone A shows a generally smooth surface. The longitudinal deposit is bordered by alluvial terraces that reflect the variations of the channel level. The waning of the Elysium Basin caused the erosion of the Basin estuarine zone by small channels, this episode being characterized by dissected tear-drop shaped mesa-like morphologies in the delta. Our estuarine delta model predicts a lithostratigraphic depositional sequence associated with the water submergence and the transgression of Elysium Basin. The thickness of the estuarine sediment corresponds to the Elysium Basin levels changes relatively to the bed floor of the estuary, The depositional sequence of Ma'adim Vallis are described: (1) a pro-current filled region (A), where fluvial are longitudinally accumulated by the inflowing water, (2) inverse current from Elysium Basin (B), where fluvial and lacustrine sediments are accumulated, and (3) zone of current equilibrium (C), where the sediments are distributed as a shoreline at the boundary of the estuarine delta. The estuary sedimentology dynamics collects and keeps the record of the geologic unit material crossed by Ma'adim Vallis, and those of the lakebed deposit of Elysium Basin. The predicted mixed stratigraphic sequence from fluvial and lacustrine sediment makes this site an exceptional environment to concentrate potential multi-origin biologic records. We envision four possible strategies to explore this sedimentologic record: (1) longitudinal surface and subsurface traverses in region A to investigate outcrop levees, (2) exploration of the mesa walls in region B, (3) deep drilling hole lodging of the sequential deposits in the zones A and B, and (4) surface and subsurface exploration of the shoreline delta. The expected results for each of these strategies are: (1) in the deepest layers of region A are predicted frequent and abundant coarse material, sandy lenses lamination grading downward from sand to cobbles. Volcanic debris from the Noachian crustal Plateau unit material, hydrothermal altered rocks, carbonates, Hesperian and possibly Amazonian volcanic material, from Apollinaris Patera, altered rocks and carbonates from Zephiria Mensae are expected. As a favorable environment for inception of life, possible biological records are expected in transported rock, (2) At the surface, and subsurface (<=100 m), large deposits sandy to silted material from Elysium paleolake basin mixed with fine-grained sediments from Ma'adim Vallis are expected mostly in the upstream part of region B, (3) on the shoreline of the estuarine delta, abundant fine material from Elysium paleolake basin (evaporites, carbonates), mostly Amazonian in age are expected. The Ma'adini estuary is a favorable landing site for all the above mentioned science aspects, and .for its location. The site lies near the equator, which is favorable for the rover solar power supply, and at 1000m elevation, which is a favorable configuration for the descent system braking. Another advantage is the extent of the area of high scientific interest (33,000 sq km), which provides a good ellipse, and potential long study traverses.

Grin, E. A.↗
NASA NTRS2004

Time-Variable Gravity from Satellite Laser-Ranging: The Low-Degree Components and Their Connections with Geophysical/Climatic Changes

Satellite laser-ranging (SLR) has been observing the tiny variations in Earth s global gravity for over 2 decades. The oblateness of the Earth's gravity field, J2, has been observed to undergo a secular decrease of J2 due mainly to the post-glacial rebound of the mantle. Sometime around 1998 this trend reversed quite suddenly. This reversal persisted until 2001, at which point the atmosphere-corrected time series appears to have reversed yet again towards normal. This anomaly signifies a large interannual change in global mass distribution. A number of possible causes have been considered, with oceanic mass redistribution as the leading candidate although other effects, such as glacial melting and core effects may be contributing. In fact, a strong correlation has been found between the J2 variability and the Pacific decadal oscillation. It is relatively more difficult to solve for corresponding signals in the shorter wavelength harmonics from the existing SLR-derived time variable gravity results, although it appears that geophysical fluid mass transport is being observed. For example, the recovered J3 time series shows remarkable agreement with NCEP-derived estimates of atmospheric gravity variations. Likewise, some of the non-zonal harmonic components have significant interannual signal that appears to be related to mass transport related to climatic effects such as El Nino Southern Oscillation. We will present recent updates on the J2 evolution, as well as a monthly time sequence of low-degree component map of the time-variable gravity complete through degree 4, and examine possible geophysical/climatic causes.

Chao, Benjamin F.↗
DOE OSTI2026

Data for Promoter Deletion in the Soybean Compact Mutant Leads to Overexpression of a Gene with Homology to the C20-Gibberellin 2-Oxidase Family

Height is a critical component of plant architecture, significantly affecting crop yield. The genetic basis of this trait in soybean remains unclear. In this study, we report the characterization of the Compact mutant of soybean, which has short internodes. The candidate gene was mapped to chromosome 17, and the interval containing the causative mutation was further delineated using biparental mapping. Whole-genome sequencing of the mutant revealed an 8.7 kb deletion in the promoter of the Glyma.17g145200 gene, which encodes a member of the class III gibberellin (GA) 2-oxidases. The mutation has a dominant effect, likely via increased expression of the GA 2-oxidase transcript observed in green tissue, as a result of the deletion in the promoter of Glyma.17g145200. We further demonstrate that levels of GA precursors are altered in the Compact mutant, supporting a role in GA metabolism, and that the mutant phenotype can be rescued with exogenous GA3. We also determined that overexpression of Glyma.17g145200 in Arabidopsis results in dwarfed plants. Thus, gain of promoter activity in the Compact mutant leads to a short internode phenotype in soybean through altered metabolism of gibberellin precursors. These results provide an example of how structural variation can control an important crop trait and a role for Glyma.17g145200 in soybean architecture, with potential implications for increasing crop yield.

Biomass Analytics↗
NASA NTRS1992

A variational approach to three-dimensional elasticity solutions of laminated composite plates

The displacements in a laminated composite are represented as products of two sets of unknown functions, one of which is only a function of the thickness coordinate and the other is a function of the in-plane coordinates (i.e., separation of variables approach), and the minimization of the total potential energy is reduced to a sequence of iterative linear problems. Analytical solutions are developed for cross-ply and angle-ply laminated composite rectangular plates. The solution for simply-supported cross-ply plates under sinusoidal transverse load reduces to that of Pagano. Numerical results for stresses and is placements for antisymmetric angle-ply laminates are presented. The three-dimensional elasticity solutions developed are important because they can be used to study the behavior of composite laminates, in addition to serving as reference for approximate solutions by numerical methods and two-dimensional theories.

Savoia, M.↗
DOE OSTI2023

Natural transformation as a tool in Acinetobacter baylyi : Evolution by amplification of gene copy number

For many years, the natural competency of Acinetobacter baylyi ADP1 facilitated studies of bacterial metabolism, biochemistry, and physiology. With the advent of synthetic biology, new opportunities arise to exploit the remarkable transformability and chromosomal plasticity of this model organism. In this chapter, we describe a recently developed method, “Evolution by Amplification and Synthetic Biology” (EASy). EASy allows the targeted amplification of chromosomal segments that give rise to new phenotypes. Increased gene dosage regulates protein expression in a rudimentary fashion by establishing a chromosomal array in which copy number adjusts via recombination between repeated DNA sequences. Selective conditions enrich for cells within the population that confer a growth advantage. Under continuous selective pressure, beneficial mutations may accumulate in any genomic region. Such mutations favor decreases in the average copy number of the target region. Thus, the genetic flexibility afforded by transient copy number variation helps accelerate the selection of engineered strains with desired traits during laboratory evolution. As a result, thanks to the extremely simple genetic manipulation of Acinetobacter baylyi ADP1, the EASy method can be readily implemented by researchers without the need for advanced instrumentation or complex cloning techniques.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis

Advances in high-throughput sequencing have facilitated remarkable insights into the diversity and functioning of naturally occurring microbes; however, current sequencing strategies are insufficient to reveal physiological states of microbial communities associated with protein translation dynamics. Transfer RNAs (tRNAs) are core components of protein synthesis machinery, present in all living cells, and are phylogenetically tractable, which make them ideal targets to gain physiological insights into environmental microbes. Here we report a direct sequencing approach, tRNA-seq, and a software suite, tRNA-seq-tools, to recover sequences, abundance profiles, and post-transcriptional modifications of microbial tRNA transcripts. Our analysis of cecal samples using tRNA-seq distinguishes high-fat-and low-fat-fed mice in a comparable fashion to 16S ribosomal RNA gene amplicons, and reveals taxon- and diet-dependent variations in tRNA modifications. Our results provide taxon-specific in situ insights into the dynamics of tRNA gene expression and post-transcriptional modifications within complex environmental microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate

The development of model systems requires a detailed assessment of standing genetic variation across natural populations. The Brachypodium species complex has been promoted as a plant model for grass genomics with translation to small grain and biomass crops. To capture the genetic diversity within this species complex, thousands of Brachypodium accessions from around the globe were collected and genotyped by sequencing. Overall, 1897 samples were classified into two diploid or allopolyploid species, and then further grouped into distinct inbred genotypes. A core set of diverse B. distachyon diploid lines was selected for whole genome sequencing and high resolution phenotyping. Genome-wide association studies across simulated seasonal environments was used to identify candidate genes and pathways tied to key life history and agronomic traits under current and future climatic conditions. A total of 8, 22, and 47 QTL were identified for flowering time, early vigor, and energy traits, respectively. The results highlight the genomic structure of the Brachypodium species complex, and the diploid lines provided a resource that allows complex trait dissection within this grass model species.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1994

The initial mass function for massive stars in the Magellanic Clouds. 3: Luminosity and mass functions for 14 OB associations

We have used UBV photometry of stars in 14 associations in the Large and Small Magellanic Clouds (LMC/SMS) (Hill, Madore, & Freedman) to derive luminosity and mass functions for the most massive stars. The main-sequence luminosity functions for the associations are quite similar, having an average slope of s = 0.03 +/- 0.06. The mass functions for the associations have slopes that span similar ranges about a common mean for both the LMC and SMC and there is no strong evidence for a significant variation in the slopes from one association to another. Accordingly, metal abundance does not appear to have a strong effect on the initial mass function (IMF), at least for the range in metallicity observed between the Magellanic Clouds. The average slope of the IMF for the Magellanic Cloud associations is Gamma = -2.0 +/- 0.5 for M greater than 9 Solar Masses. The range in the derived slopes is more likely due to the large uncertainties associated with the calculations of the mass functions, rather than to real variations in the IMF. There may be some evidence for a decrease in the slope of the IMF at masses below 9 Solar Masses, but incompleteness and the larger photometric errors associated with the faintest stars make this conclusion tentative.

Hill, Robert J.↗
NASA NTRS2003

RNA Crystallization

RNA molecules may be crystallized using variations of the methods developed for protein crystallography. As the technology has become available to syntheisize and purify RNA molecules in the quantities and with the quality that is required for crystallography, the field of RNA structure has exploded. The first consideration when crystallizing an RNA is the sequence, which may be varied in a rational way to enhance crystallizability or prevent formation of alternate structures. Once a sequence has been designed, the RNA may be synthesized chemically by solid-state synthesis, or it may be produced enzymatically using RNA polymerase and an appropriate DNA template. Purification of milligram quantities of RNA can be accomplished by HPLC or gel electrophoresis. As with proteins, crystallization of RNA is usually accomplished by vapor diffusion techniques. There are several considerations that are either unique to RNA crystallization or more important for RNA crystallization. Techniques for design, synthesis, purification, and crystallization of RNAs will be reviewed here.

Golden, Barbara L.↗