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445 records · Page 25

GL4U: Training the next generation of bioinformaticians, one omics datatype at a time

Spaceflight modifies gene expression in every organism examined to date, including humans. Understanding how these gene expression changes affect physiology is crucial for the development of countermeasures to enable long-duration manned missions. NASA’s GeneLab project provides researchers open access to multi-omics data, including genetic and gene expression data, from spaceflight experiments that can be mined to understand the effects of spaceflight on biological systems. To ensure new knowledge generation through data re-use, it is important to maximize the number of scientists who utilize GeneLab data. Training students on the GeneLab platform is the best way to create long-term adopters of this NASA database and its tools. Turning students into future instructors and advocates will also accelerate the dissemination of these data and tools to the broader scientific community. Therefore, in collaboration with the GeneLab Educational Working Group (EWG), GeneLab has created GeneLab for Colleges and Universities (GL4U). GL4U provides space biology-relevant training in bioinformatics to the next generation of scientists through direct and indirect approaches. The GeneLab team plans to host two annual data processing bootcamps, one for college-level students (direct) and one for college educators (indirect – training of trainers), in which participants learn to analyze GeneLab’s space-relevant omics data. During the bootcamp, educators will receive materials and training to enable them to run the bootcamp at their home institutions or alternatively to adapt the content to implement within existing courses, thereby extending the reach of this initiative. The GL4U direct training pilot program was conducted in June 2021 in collaboration with USRA and San Jose State University (SJSU). During the pilot, SJSU students participated in a week-long bootcamp consisting of space biology-specific lectures and hands-on instruction using Jupyter Notebooks to analyze RNA sequence data. This pilot demonstrates the capacity of GL4U for training young scientists and encouraging data re-use.

Jonathan Matthew Galazka↗

Development of an inexpensive matrix-assisted laser desorption—time of flight mass spectrometry method for the identification of endophytes and rhizobacteria cultured from the microbiome associated with maize

Many endophytes and rhizobacteria associated with plants support the growth and health of their hosts. The vast majority of these potentially beneficial bacteria have yet to be characterized, in part because of the cost of identifying bacterial isolates. Matrix-assisted laser desorption-time of flight (MALDI-TOF) has enabled culturomic studies of host-associated microbiomes but analysis of mass spectra generated from plant-associated bacteria requires optimization. In this study, we aligned mass spectra generated from endophytes and rhizobacteria isolated from heritage and sweet varieties of Zea mays. Multiple iterations of alignment attempts identified a set of parameters that sorted 114 isolates into 60 coherent MALDI-TOF taxonomic units (MTUs). These MTUs corresponded to strains with practically identical (>99%) 16S rRNA gene sequences. Mass spectra were used to train a machine learning algorithm that classified 100% of the isolates into 60 MTUs. These MTUs provided >70% coverage of aerobic, heterotrophic bacteria readily cultured with nutrient rich media from the maize microbiome and allowed prediction of the total diversity recoverable with that particular cultivation method. Acidovorax sp., Pseudomonas sp. and Cellulosimicrobium sp. dominated the library generated from the rhizoplane. Relative to the sweet variety, the heritage variety contained a high number of MTUs. The ability to detect these differences in libraries, suggests a rapid and inexpensive method of describing the diversity of bacteria cultured from the endosphere and rhizosphere of maize.

dereplication↗

Comparing Galaxy Morphology at Ultraviolet and Optical Wavelengths

We have undertaken an imaging survey of 34 nearby galaxies in far-ultraviolet (FUV, - 1500A) and optical (UBVRI) passbands to characterize galaxy morphology as a function of wavelength. This sample, which includes a range of classical Hubble types from elliptical to irregular with emphasis on spirals at low inclination angle, provides a valuable database for comparison with images of high-z galaxies whose FUV light is redshifted into the optical and, near-infrared bands. Ultraviolet data are from the UIT Astro-2 mission. We present images and surface brightness profiles for each galaxy, and we discuss the wavelength-dependence of morphology for different Hubble types in the context of understanding high-z objects. In general, the dominance of young stars in the FUV produces the patchy appearance of a morphological type later than that inferred from optical images. Prominent rings and circumnuclear star formation regions are clearly evident in FUV images of spirals, while bulges, bars, and old, red stellar disks are faint to invisible at these short wavelengths. However, the magnitude of the change in apparent morphology ranges from dramatic in early-type spirals with prominent optical bulges to slight in late-type spirals and irregulars, in which young stars dominate both the UV and optical emission. Starburst galaxies with centrally concentrated, symmetric bursts display an apparent "E/SO" structure in the FUV, while starbursts associated with rings or mergers produce a peculiar morphology. We briefly discuss the inadequacy of the optically-defined Hubble sequence to describe FUV galaxy images and estimate morphological k-corrections, and we suggest some directions for future research with this dataset.

Stecher, Theodore↗

In search of Nemesis

The parallax of all stars of visual magnitude greater than about 6.5 has already been measured. If Nemesis is a main-sequence star 1 parsec away, this requires Nemesis's mass to be less than about 0.4 solar masses. If it were less than about 0.05 solar masses its gravity would be too weak to trigger a comet storm. If Nemesis is on the main sequence, this mass range requires it to be a red dwarf. A red dwarf companion would probably have been missed by standard astronomical surveys. Nearby stars are usually found because they are bright or have high proper motion. However, Nemesis's proper motion would now be 0.01 arcsec/yr, and if it is a red dwarf its magnitude is about 10 - too dim to attract attention. Unfortunately, standard four-color photometry does not distinguish between red dwarfs and giants. So although surveys such as the Dearborn Red Star Catalog list stars by magnitude and spectral type, they do not identify the dwarfs. Every star of the correct spectral type and magnitude must be scrutinized. Our candidate list is a hybrid; candidate red stars are identified in the astrometrically poor Dearborn Red Star Catalog and their positions are corrected using the Hubble Guide Star Catalog. When errors in the Dearborn catalog make it impossible to identify the corresponding Hubble star, the fields are split so that we have one centering on each possible candidate. We are currently scrutinizing 3098 fields, which we believe contain all possible red dwarf candidates in the northern hemisphere. Since our last report the analysis and database software has been completely rebuilt to take advantage of updated hardware, to make the data more accessible, and to implement improved methods of data analysis. The software is now completed and we are eliminating stars every clear night.

Carlson, S.↗

A Tool for Automatic Data Distribution for CFD Applications on Structured Grids

Development of HPF versions of NPB and ARC3D has shown that HPF provides an efficient, concise way to express parallelism and to organize data traffic. The use of HPF, as noted in the papers, requires an intimate knowledge of the applications and a detailed analysis of data affinity, data movement, and data granularity. To simplify and accelerate the task of developing HPF versions of existing CFD applications we have designed and implemented ADAPT (Automatic Data Alignment and Placement Tool). ADAPT analyzes a CFD application working on a single structured grid and generates HPF TEMPLATE, (RE)DISTRIBUTION, ALIGNMENT, and INDEPENDENT directives. The directives can be generated on the nest level, subroutine level, application level, or on the application interface level. ADAPT annotates an existing CFD FORTRAN application, performing computations on single or multiple grids. On each grid the application is considered as a sequence of operators, each applied to a set of variables defined in a particular grid domain. ADAPT automatically detects implicit operators (i.e., having data dependences) and explicit operators (without data dependences). For parallelization of an explicit operator ADAPT creates a template for the operator domain, aligns arrays used in the operator with the template, distributes the template, and declares the loops over the distributed dimensions as INDEPENDENT. For parallelization of an implicit operator, the distribution of the operator's domain should be consistent with the operator's dependences. Any dependence between sections distributed on different processors would preclude parallelization if the compiler does not have an ability to pipeline computations. If a data distribution is "orthogonal" to the dependences of an implicit operator, then the loop which implements the operator can be declared as INDEPENDENT. ADAPT starts with an analysis of array index expressions of the loop nests. For each pair of arrays referenced in an assignment statement, it generates an arc in the alignment graph and annotates it with an affinity relation. The template, alignment, and distribution directives for a particular loop nest are then derived from a transitive closure of the affinity relation. A compromise of data distributions in different nests and subroutines is achieved by merging annotated alignment graphs for adjacent nests/stibroutine calls in the nest/call graph of the application in the process called distribution lifting. ADAPT has been implemented as a C++ program running in conjunction with a parallelization tool called CAPTools. ADAPT uses the parse tree, interprocedural analysis and application database generated by CAPTools. It also uses the Directed Graph class, initially implemented in p2d2 (parallel debugger oi distributed programs), and some other classes supporting symbolic computations. ADAPT uses data distribution techniques described. ADAPT was tested with ARC3D and the FT benchmark and has demonstrated a code performance within a factor of 1.5 of handwritten versions.

Frumkin, Michael↗

Spherical Coordinate Systems for Streamlining Suited Mobility Analysis

Introduction: When describing human motion, biomechanists generally report joint angles in terms of Euler angle rotation sequences. However, there are known limitations in using this method to describe complex motions such as the shoulder joint during a baseball pitch. Euler angle notation uses a series of three rotations about an axis where each rotation is dependent upon the preceding rotation. As such, the Euler angles need to be regarded as a set to get accurate angle information. Unfortunately, it is often difficult to visualize and understand these complex motion representations. It has been shown that using a spherical coordinate system allows Anthropometry and Biomechanics Facility (ABF) personnel to increase their ability to transmit important human mobility data to engineers, in a format that is readily understandable and directly translatable to their design efforts. Objectives: The goal of this project was to use innovative analysis and visualization techniques to aid in the examination and comprehension of complex motions. Methods: This project consisted of a series of small sub‐projects, meant to validate and verify a new method before it was implemented in the ABF's data analysis practices. A mechanical test rig was built and tracked in 3D using an optical motion capture system. Its position and orientation were reported in both Euler and spherical reference systems. In the second phase of the project, the ABF estimated the error inherent in a spherical coordinate system, and evaluated how this error would vary within the reference frame. This stage also involved expanding a kinematic model of the shoulder to include the rest of the joints of the body. The third stage of the project involved creating visualization methods to assist in interpreting motion in a spherical frame. These visualization methods will be incorporated in a tool to evaluate a database of suited mobility data, which is currently in development. Results: Initial results demonstrated that a spherical coordinate system is helpful in describing and visualizing the motion of a space suit. The system is particularly useful in describing the motion of the shoulder, where multiple degrees of freedom can lead to very complex motion paths.

Benson, Elizabeth↗

Phylogenetic mapping of bacterial morphology

The availability of a meaningful molecular phylogeny for bacteria provides a context for examining the historical significance of various developments in bacterial evolution. Herein, the classical morphological descriptions of selected members of the domain Bacteria are mapped upon the genealogical ancestry deduced from comparison of small-subunit rRNA sequences. For the species examined in this study, a distinct pattern emerges which indicates that the coccus shape has arisen and accumulated independently multiple times in separate lineages and typically survived as a persistent end-state morphology. At least two other morphologies persist but have evolved only once. This study demonstrates that although bacterial morphology is not useful in defining bacterial phylogeny, it is remarkably consistent with that phylogeny once it is known. An examination of the experimental evidence available for morphogenesis as well as microbial fossil evidence corroborates these findings. It is proposed that the accumulation of persistent morphologies is a result of the biophysical properties of peptidoglycan and their genetic control, and that an evolved body-plan strategy based on peptidoglycan may have been a fate-sealing step in the evolution of Bacteria. More generally, this study illustrates that significant evolutionary insights can be obtained by examining biological and biochemical data in the context of a reliable phylogenetic structure.

NASA Discipline Exobiology↗

Theory and Simulation of Ultrafast Multidimensional Nonlinear X-ray Spectroscopy of Molecules (Final Report)

Emerging X-ray free electron laser (XFEL) beam sources offer new types of probes of matter with unprecedented spatial and temporal resolutions. These experimental advances must be met by robust theoretical and computational tools that provide predictive modeling capacity of the underlining electronic and structural dynamics. The latter will be essential for the design of sophisticated multi-pulse experiments and for their interpretation. The proposed research effort will focus on developing cutting- edge simulation tools for nonlinear multidimensional X-ray/optical spectroscopies and aims to address key questions in Priority Research Opportunities 1 (Probing and controlling electron motion within a molecule) and 3 (Capturing rare events and intermediate states in the transformation of matter) as mentioned in the BES Roundtable Report “Opportunities for Basic Research at the Frontiers of XFEL Ultrafast Science”. XFEL multidimensional nonlinear techniques, which combine sequences of X-ray and possibly optical pulses, provide a unique experimental toolbox for probing the dynamics of core and valence electronic excitations, as well as material structure. Predictive modeling of these dynamical processes requires the combination of analytical theory for nonlinear interactions of light and matter, robust quantum-chemical methodologies for the accurate description of electronic structure of various materials, and multiscale ab initio electron and nuclear dynamics techniques operating beyond Born-Oppenheimer approximation. These challenges will be addressed with three research thrusts (i) Develop and implement theoretical apparatus for modeling a broad range of multidimensional spectroscopic techniques enabled by present and upcoming XFEL facilities. This thrust also includes the incorporation of a computational module in the DOE supported open-source NWChem computational chemistry package as well as the development of other open-source codes ready for dissemination across a broad user base; (ii) Propose and design new multi-pulse experiments that make use of the capabilities of the incoming LCLS-II facility; (iii) Perform selected applications to specific molecular systems that can be carried out at LCLS-II and demonstrate how these X-ray sources may be used to study nonadiabatic dynamics through conical interactions, electronic correlations in multi-core excitons, and charge transfer/energy transfer processes. The proposed research will be carried out by a multi-disciplinary four-institution research team which combines academia and national laboratories and spans the broad and necessary expertise in theoretical spectroscopy, nonlinear optics, quantum chemistry, molecular non-adiabatic dynamics and code development. The work will be performed in a highly interactive team environment with junior researchers shared between institutions thus cementing cross- disciplinary interactions. The developed simulation tools will be immediately deployed for XFEL facility users, both experimentalists and theorists, via freely distributed codes and databases. Altogether, this project will facilitate establishing XFEL-based multidimensional spectroscopies as a novel diagnostic tool for monitoring electronic and structural dynamics in molecular materials.

74 ATOMIC AND MOLECULAR PHYSICS↗

Addressing the pervasive scarcity of structural annotation in eukaryotic algae

Abstract Despite a continuous increase in algal genome sequencing, structural annotations of most algal genome assemblies remain unavailable. This pervasive scarcity of genome annotation has restricted rigorous investigation of these genomic resources and may have precipitated misleading biological interpretations. However, the annotation process for eukaryotic algal species is often challenging as genomic resources and transcriptomic evidence are not always available. To address this challenge, we benchmark the cutting-edge gene prediction methods that can be generalized for a broad range of non-model eukaryotes. Using the most accurate methods selected based on high-quality algal genomes, we predict structural annotations for 135 unannotated algal genomes. Using previously available genomic data pooled together with new data obtained in this study, we identified the core orthologous genes and the multi-gene phylogeny of eukaryotic algae, including of previously unexplored algal species. This study not only provides a benchmark for the use of structural annotation methods on a variety of non-model eukaryotes, but also compensates for missing data in the current spectrum of algal genomic resources. These results bring us one step closer to the full potential of eukaryotic algal genomics.

59 BASIC BIOLOGICAL SCIENCES↗

Integrating biological knowledge for mechanistic inference in the host-associated microbiome

Advances in high-throughput technologies have enhanced our ability to describe microbial communities as they relate to human health and disease. Alongside the growth in sequencing data has come an influx of resources that synthesize knowledge surrounding microbial traits, functions, and metabolic potential with knowledge of how they may impact host pathways to influence disease phenotypes. These knowledge bases can enable the development of mechanistic explanations that may underlie correlations detected between microbial communities and disease. In this review, we survey existing resources and methodologies for the computational integration of broad classes of microbial and host knowledge. We evaluate these knowledge bases in their access methods, content, and source characteristics. We discuss challenges of the creation and utilization of knowledge bases including inconsistency of nomenclature assignment of taxa and metabolites across sources, whether the biological entities represented are rooted in ontologies or taxonomies, and how the structure and accessibility limit the diversity of applications and user types. We make this information available in a code and data repository at: https://github.com/lozuponelab/knowledge-source-mappings. Addressing these challenges will allow for the development of more effective tools for drawing from abundant knowledge to find new insights into microbial mechanisms in disease by fostering a systematic and unbiased exploration of existing information.

59 BASIC BIOLOGICAL SCIENCES↗

Spherical Coordinate Systems for Streamlining Suited Mobility Analysis

When describing human motion, biomechanists generally report joint angles in terms of Euler angle rotation sequences. However, there are known limitations in using this method to describe complex motions such as the shoulder joint during a baseball pitch. Euler angle notation uses a series of three rotations about an axis where each rotation is dependent upon the preceding rotation. As such, the Euler angles need to be regarded as a set to get accurate angle information. Unfortunately, it is often difficult to visualize and understand these complex motion representations. One of our key functions is to help design engineers understand how a human will perform with new designs and all too often traditional use of Euler rotations becomes as much of a hindrance as a help. It is believed that using a spherical coordinate system will allow ABF personnel to more quickly and easily transmit important mobility data to engineers, in a format that is readily understandable and directly translatable to their design efforts. Objectives: The goal of this project is to establish new analysis and visualization techniques to aid in the examination and comprehension of complex motions. Methods: This project consisted of a series of small sub‐projects, meant to validate and verify the method before it was implemented in the ABF's data analysis practices. The first stage was a proof of concept, where a mechanical test rig was built and instrumented with an inclinometer, so that its angle from horizontal was known. The test rig was tracked in 3D using an optical motion capture system, and its position and orientation were reported in both Euler and spherical reference systems. The rig was meant to simulate flexion/extension, transverse rotation and abduction/adduction of the human shoulder, but without the variability inherent in human motion. In the second phase of the project, the ABF estimated the error inherent in a spherical coordinate system, and evaluated how this error would vary within the reference frame. This stage also involved expanding a kinematic model of the shoulder, to include the torso, knees, ankle, elbows, wrists and neck. Part of this update included adding a representation of 'roll' about an axis, for upper arm and lower leg rotations. The third stage of the project involved creating visualization methods to assist in interpreting motion in a spherical frame. This visualization method will be incorporated in a tool to evaluate a database of suited mobility data, which is currently in development.

Benson, Elizabeth↗

Flight Mechanics Modeling and Simulation of the Earth Entry System

Introduction: The Mars Sample Return (MSR) Campaign being planned by NASA and ESA has the ambitious goal to return Mars samples back to Earth. This international collaboration had developed a concept of operations that included a ESA-designed Earth Return Orbiter (ERO) and NASA-designed Capture, Containment, and Return System (CCRS). The Earth Entry System (EES), consisting of a protective aeroshell that houses the samples as well as sample containment vessels, would conduct entry, descent, and landing (EDL) on a direct Earth trajectory. The EES would enter on a spin-stabilized ballistic trajectory with the goal to passively achieve aerodynamic stability throughout all regions of flight. The EDL sequence would end with the EES impacting the soft playa soil of the Utah Test and Training Range (UTTR). As of the submission of this abstract, the MSR campaign is undergoing a re-architecture leading to a pause in EES development. However, the novel approaches developed in flight mechanics modeling and simulation can significantly benefit the greater IPPW community in the development of Earth return vehicles. This paper will present the latest state of EES flight mechanics modeling and simulation. The paper will highlight the simulation architecture developed and key lessons learned from understanding of EDL trajectory sensitivities. Modeling and Simulation: Figure 1 provides a high-level concept of operations for the approach, entry, descent, and landing (AEDL) phase of the CCRS-portion of MSR. The objective of EES flight mechanics is to model and simulate the EES trajectory from ERO separation to ground impact at UTTR. A variety of flight mechanics simulation models were utilized to model both exo-atmopsheric and atmospheric portions of flight. 42, a 6-DOF simulation developed at Goddard Space Flight Center, is utilized for propagating the attitude of EES during exo-atmospheric flight. 42 allows for a variety of spin eject mechanism scenarios to be simulated for analysis. 10 minutes prior to entry, the 42 states are handed off to the EDL sims. The prime EDL sim utilized by EES is the Program to Optimize Simulated Trajectories II (POST2), a 6-DOF sim developed at Langley Research Center, and the independent verification and validation EDL sim utilized is DSENDS, a 6-DOF sim developed at Jet Propulsion Laboratory. Figure 2 provides a visualization of the flight mechanics simulation model flow through various points in the AEDL phase. Due to the existence of a variety of sim models, the EES flight mechanics team developed processes for data hand-off. These processes included the development of a centralized coordinate frame document, utilization of a single, centralized simulation input document for all sims to reference, and hand-off files containing both the technical data to be ingested by other flight mechanics sims as well as annotations of modeling assumptions utilized to generate the data. Figure~\ref{fig:post2simarchitecture} provides an overview of the POST2 sim architecture wherein POST2 ingests numerous subsystem models and input files. The dispersed state file generated by MONTE provides the position/velocity state of the trajectory while the 42 Handoff file provides the attitude. The aerodynamics database, delivered by the EES aeroscience team, is utilized to simulate the aerodynamic forces and moments experienced during EDL. A custom atmosphere model, developed by EES atmosphere team, is utilized to simulate the anticipated atmosphere environment around the region of Earth through which the EES trajectory flys. These inputs and subsystem models can be varied depending on the AEDL flight mechanics scenario being simulated. Monte Carlo simulations are utilized to generate statistical AEDL performance metrics in the form of scorecards and violin plots. Furthermore, outputs from the POST2 simulation are utilized for follow-on analyses including aerothermal and landing performance. \section{Flight Mechanics Lessons Learned} Though the EES flight mechanics team uncovered a variety of lessons learned through the analysis conducted to support CCRS through preliminary design review, this paper will highlight the most important lessons. A key AEDL performance goal is to ensure the landing footprint of EES remains on the UTTR south range. A common modeling strategy used in EDL analysis is One-Variable-At-a-Time (OVAT). OVAT analysis provides insight into the key drivers that affect AEDL performance metrics. Figure 3 shows the landing ellipses for single dispersion sources as compared to the baseline aggregate of all dispersions. The figure shows that atmosphere winds alone dominate the size of the footprint ellipse (note: EES does not use a parachute unlike previous Earth-return missions and is in wind-driven free fall for ~5min). The significance of the wind led the EES flight mechanics team to pursue the development of a Custom Atmosphere Model [4], in lieu of EarthGRAM [1], built on actual radiosonde wind measurements around the UTTR-region. This decision was driven by the realism in the generated footprint ellipses and lessons-learned from Stardust [5]. These findings will be invaluable for future Earth-return missions in providing an early understanding of the key drivers affecting footprint size and modeling considerations for which to account. Another lesson learned is tied to the AEDL performance goal of achieving passive stability throughout all regions of flight. It is well understood that blunt-body aeroshells are less stable as they transition from supersonic to subsonic. Eliminating a backshell does help improvestability; however, other phenomena such as roll-induced instability during terminal descent can still arise. The EES flight mechanics team developed stability metrics as tools to better understand the causes of and better predict the onset of dynamic instability. These tools were built upon analytical models developed by Jaffe [3] and Murphy [2]. The tools were shown to both be very accurate in correlation with actual unstable cases and useful in developing stability margin policies based on the vehicle design and simulation considerations (e.g. sphere-cone angle change, mass change, wind turbulence). These tools allowed for the current EES design to demonstrate the ability to achieve passive stability and can be an invaluable tool for consideration in the design of parachute-less Earth-return vehicles.

Rohan Deshmukh↗

A global metagenomic map of urban microbiomes and antimicrobial resistance

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.

59 BASIC BIOLOGICAL SCIENCES↗