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NASA NTRS1991

Macromolecular recognition: Structural aspects of the origin of the genetic system

Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of evolution of life. Using computational and modeling techniques and guided by analogies from present day systems we, seek to understand the emergence of genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. In one possible scenario, the RNA enzymatic reaction plays a key role in the emergence of the self-replicating and offers a clue to the onset of enzymatic catalysis prior to the existence of the protein biosynthetic machinery. Our ultimate goal is to propose a simple RNA segment which contains the specificity and catalytic activity of the contemporary RNA enzyme and which could emerge in a primordial chemical environment. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation have been studied. Another important aspect of this reaction is the identity of the functional groups which are essential for the acid base catalysis. The structural characteristics of the target helices, particularly a possible role of G center dot T pair, is under examination by molecular dynamics (MD) simulation technique. Modeling of the ancestral aminoacyl-tRNA synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. Assuming that the catalytic function evolved before the elements of specific recognition of a particular amino acid, we are exploring the minimal structural requirements for the catalysis of tRNA aminoacylation. The molecular modeling system SYBYL was used for this study based on the high resolution crystallographic structures of the present day tyrosyl-adenylate:tyrRS and tRNA(Gln): ATP:glnRS complexes. The trinucleotide CCA of the 3'-end tRNA is placed into the active site pocket of tyrRS, based on the scheme of interaction between tRNA(Gln) and glnRS, and upon the stereochemistry of the tyrRS:tRNA:Tyr-AMP transition state. This provides a model of the non-specific recognition of a tRNA's 3'-end by an aRS, which might be similar to that of the ancestral aRS's. In the next step, modeling of the rest of the acceptor stem of tRNA (Tyr) with tyrRS is carried out.

Rein, Robert↗

NASA NTRS2020

Effects of Long-Duration Space Flight on Training Retention and Transfer

The space environment imposes on the astronaut crew significant physiological, psycho-social, and cognitive loads that can not be replicated on the ground. These loads likely impact crew performance. To date, no systematic data collection has taken place to understand the effects of such loads on crew members ability to retain trained knowledge and skills, and to transfer such knowledge and skills to novel situations. The research described here was originally requested by HRP management to be the first such study to systematically collect data on the effects of long duration space flight on training retention and transfer. Because current theories of retention and transfer are based on results obtained in university laboratories using undergraduate students as research participants, and because crew time in space is very expensive, this study was designed to compare the performance of 4 groups of subjects: crew members in space, crew members on the ground, crew-like subjects, and university undergraduate students. Results from the ground-phase of the study reported here demonstrate that crew members performance under cognitive load can not be predicted from the performance of university undergraduate students. It is still an open question the extent to which crew members cognitive performance in space can be predicted from the performance of crew members on the ground.

Barshi, Immanuel↗

NASA NTRS2020

Effects of Long-Duration Space Flight on Training Retention and Transfer

The space environment imposes on the astronaut crew significant physiological, psycho-social, and cognitive loads that can not be replicated on the ground. These loads likely impact crew performance. To date, no systematic data collection has taken place to understand the effects of such loads on crew members’ ability to retain trained knowledge and skills, and to transfer such knowledge and skills to novel situations. The research described here was originally requested by HRP management to be the first such study to systematically collect data on the effects of long duration space flight on training retention and transfer. Because current theories of retention and transfer are based on results obtained in university laboratories using undergraduate students as research participants, and because crew time in space is very expensive, this study was designed to compare the performance of 4 groups of subjects: crew members in space, crew members on the ground, crew-like subjects, and university undergraduate students. Results from the ground-phase of the study reported here demonstrate that crew members’ performance under cognitive load can not be predicted from the performance of university undergraduate students. It is still an open question the extent to which crew members’ cognitive performance in space can be predicted from the performance of crew members on the ground.

training↗

NASA NTRSDate not supplied

Astronauts' Performance: The Retention and Transfer of Training

The space environment imposes on the astronaut crew significant physiological, psycho-social, and cognitive loads that can not be replicated on the ground. These loads likely impact crew performance. To date, no systematic data collection has taken place to understand the effects of such loads on crew members’ ability to retain trained knowledge and skills, and to transfer such knowledge and skills to novel situations. The research described here was originally designed to be the first such study to systematically collect data on the effects of long duration space flight on training retention and transfer. Because current theories of retention and transfer are based on results obtained in university laboratories using undergraduate students as research participants, and because crew time in space is very expensive, this study was designed to compare the performance of 4 groups of subjects: crew members in space, crew members on the ground, crew-like subjects, and university undergraduate students. Results from the ground-phase of the study reported here demonstrate that crew members’ performance under cognitive load can not be predicted from the performance of university undergraduate students. It is still an open question the extent to which crew members’ cognitive performance in space can be predicted from the performance of crew members on the ground.

training↗

DOE OSTI2023

Identification of hidden N4-like viruses and their interactions with hosts

The N4-like viruses, which were recently assigned to the novel viral family Schitoviridae in 2021, belong to a podoviral-like viral lineage and possess conserved genomic characteristics and a unique replication mechanism. Despite their significance, our understanding of N4-like viruses is primarily based on viral isolates. To address this knowledge gap, this study has established a comprehensive N4-like viral data sets comprising 342 high-quality N4-like viruses/proviruses (144 viral isolates, 158 uncultured viruses, and 40 integrated N4-like proviruses). These viruses were classified into 97 subfamilies (89 of which are newly identified), 148 genera (100 of which are newly identified), and 253 species (177 of which are newly identified). The study reveals that N4-like viruses inhibit the polar region, oligotrophic open oceans, and the human gut, where they infect various bacterial lineages, such as Alpha/Beta/Gamma/Epsilon-proteobacteria in the Proteobacteria phylum. Although N4-like viral endogenization appears to be prevalent in Proteobacteria, it has also been observed in Firmicutes. Additionally, the phylogenetic analysis has identified evolutionary divergence within the hallmark genes of N4-like viruses, indicating a complex origin of the different conserved parts of viral genomes. Moreover, 1,101 putative auxiliary metabolic genes (AMGs) were identified in the N4-like viral pan-proteome, which mainly participate in nucleotide and cofactor/vitamin metabolisms. Of these AMGs, 27 were found to be associated with virulence, suggesting their potential involvement in the spread of bacterial pathogenicity. The findings of this study are significant, as N4-like viruses represent a unique viral lineage with a distinct replication mechanism and a conserved core genome. This work has resulted in a comprehensive global map of the entire N4-like viral lineage, including information on their distribution in different biomes, evolutionary divergence, genomic diversity, and the potential for viral-mediated host metabolic reprogramming. As such, this work significantly contributes to our understanding of the ecological function and viral-host interactions of bacteriophages.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Measurement of Plutonium Ratios for CRM 137A Recertification

This report documents the analytical methodologies used by the Chemical and Isotopics Mass Spectrometry (CIMS) Group at the US Department of Energy’s Oak Ridge National Laboratory (ORNL) for plutonium isotopic ratio characterizations on purified ~1 mg units prepared by Lawrence Livermore National Laboratory (LLNL) from a mother solution created from an existing 250 mg unit of certified reference material (CRM) 137. The analytical processes described are designed to maintain traceability of the final certified attributes and to eliminate sources of systematic bias for the measurements described. The measurands for certification are the plutonium isotope ratios: 238 Pu/ 239 Pu, 240 Pu/ 239 Pu, 241 Pu/ 239 Pu, and 242 Pu/ 239 Pu. The preparation and analytical process included the following activities: Preparation of reference materials to be used as calibrants to establish traceability to the SI unit of mass for the isotopic analyses and quality controls. For the plutonium isotopic analyses, CRM 128 (a CRM comprising equal atoms of 239 Pu and 242 Pu) was used as the primary calibrant; Each CRM 137A unit was reconstituted using dilute high-purity HNO3. From each, seven replicates were distributed for the isotopic characterizations by thermal ionization mass spectrometry (TIMS) using the total evaporation (TE) method for isotope ratio measurements and MC-ICP-MS using a dynamic peak hooping method for secondary isotope ratio measurements; Due to time delay in the analyses from the last purification of the original CRM 137 mother solution by LLNL, an aliquot of the three provided plutonium units was purified using Eichrom TEVA separation methods to remove americium in-growth and uranium impurities; Minimally corrected data were reported from each analysis using reporting templates provided by the New Brunswick Laboratory Program Office (NBL PO) for the specific methods used for isotopic measurements. In addition, a copy of the instrument exports, Excel templates for isotopic data corrections, and the uncertainty budgets completed with the GUM Workbench software package were submitted to NBL PO.

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2021

Extreme dimensions — how big (or small) can tailed phages be?

Bacteriophages (phages), that is, viruses that infect bacteria, represent an extremely diverse, yet under-characterized, group of viruses. Although most known phages harbour genomes that are shorter than 200 kb packaged into capsids with a diameter under 100 Å, more and more ‘extremely large’ phages are being discovered. Early reports of phages with genomes larger than 200 kb defined them as ‘jumbo phages’1. Phylogenetic analysis of these jumbo phages revealed that they form distinct and cohesive groups with multiple independent origins. This suggested that jumbo phages are not merely mistakes or aberrations of smaller phages that got too big, but that large genome size is generally a stable trait. In fact, a larger genome can be advantageous; almost all jumbo phages encode their own specific transcription factors, at least some parts of the replication machinery, and many also have their own tRNA genes, which enables increased independence from their host. Here, large genomes also provide more flexibility in terms of transcription strategy; smaller phage genomes tend to have a strict modular genome structure to increase efficiency, whereas jumbo phage genomes may be much less organized in the absence of a strong selection pressure to maintain a compact genome.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1988

Continuing the biological exploration of Mars

Mars has been an object of interest for the better part of this century. To a biologist, Mars assumes special importance because many aspects of the theory of chemical evolution for the origin of life can be tested there. The central idea of this theory is that life on a suitable planet arises through a process in which the so-called biogenic elements combine to form increasingly more complex molecules under the influence of naturally-occurring energy sources ultimately resulting in the formation of replicating organic molecules. The biogenic elements are present on Mars today. Furthermore, the available evidence also strongly suggests that Mars may have had an early history similar to that of the Earth, including a period in which large amounts of liquid water once flowed on its surface and a denser atmosphere and higher global temperatures prevailed. This is important since many lines of evidence indicate that living organisms were already present on the Earth within the first billion years after its formation at a time when the environment on Mars may have closely resembled that of Earth. Our current knowledge of the state of chemical evolution on Mars can best be described as paradoxical. Most of what we have learned has come from experiments performed on the Viking landers. The combination of planned investigations covered a broad range of techniques to detect signs of chemical evolution. The most surprising data from all of these was the absence of any detectable quantities of organic compounds at the two landing sites. On the other hand, the Viking experiments did indicate that the Martian surface samples contained unidentified strong oxidant(s) that could account for their absence.

Klein, Harold P.↗

NASA NTRS2005

Gesture Based Control and EMG Decomposition

This paper presents two probabilistic developments for use with Electromyograms (EMG). First described is a new-electric interface for virtual device control based on gesture recognition. The second development is a Bayesian method for decomposing EMG into individual motor unit action potentials. This more complex technique will then allow for higher resolution in separating muscle groups for gesture recognition. All examples presented rely upon sampling EMG data from a subject's forearm. The gesture based recognition uses pattern recognition software that has been trained to identify gestures from among a given set of gestures. The pattern recognition software consists of hidden Markov models which are used to recognize the gestures as they are being performed in real-time from moving averages of EMG. Two experiments were conducted to examine the feasibility of this interface technology. The first replicated a virtual joystick interface, and the second replicated a keyboard. Moving averages of EMG do not provide easy distinction between fine muscle groups. To better distinguish between different fine motor skill muscle groups we present a Bayesian algorithm to separate surface EMG into representative motor unit action potentials. The algorithm is based upon differential Variable Component Analysis (dVCA) [l], [2] which was originally developed for Electroencephalograms. The algorithm uses a simple forward model representing a mixture of motor unit action potentials as seen across multiple channels. The parameters of this model are iteratively optimized for each component. Results are presented on both synthetic and experimental EMG data. The synthetic case has additive white noise and is compared with known components. The experimental EMG data was obtained using a custom linear electrode array designed for this study.

Wheeler, Kevin R.↗

NASA NTRS2011

An Analysis of Database Replication Technologies with Regard to Deep Space Network Application Requirements

The Deep Space Network (DSN) has three communication facilities which handle telemetry, commands, and other data relating to spacecraft missions. The network requires these three sites to share data with each other and with the Jet Propulsion Laboratory for processing and distribution. Many database management systems have replication capabilities built in, which means that data updates made at one location will be automatically propagated to other locations. This project examines multiple replication solutions, looking for stability, automation, flexibility, performance, and cost. After comparing these features, Oracle Streams is chosen for closer analysis. Two Streams environments are configured - one with a Master/Slave architecture, in which a single server is the source for all data updates, and the second with a Multi-Master architecture, in which updates originating from any of the servers will be propagated to all of the others. These environments are tested for data type support, conflict resolution, performance, changes to the data structure, and behavior during and after network or server outages. Through this experimentation, it is determined which requirements of the DSN can be met by Oracle Streams and which cannot.

Oracle Database File System↗

NASA NTRSDate not supplied

Comparison of Dynamic Stability Testing Techniques with Magnetic Suspension Wind Tunnel

Dynamic stability testing techniques currently utilized at NASA Langley Research Center (LaRC) are conducted in multiple facilities and consists of free flight, forced oscillation, and free-to-oscillate tests. The MIT/NASA/ODU Magnetic Suspension and Balance System (MSBS) has been recommissioned to explore its utility as an additional facility to expand the dynamic stability test capabilities currently available at NASA LaRC. Simulations were created to replicate each current test facility and method as closely as possible. Data collected from the simulated environments was corrupted with replicated noise sources of the different testing environments and then compared to real data collected during tests when such data was available. The corrupted data was then passed through data reduction and System Identification (SID) to estimate the accuracy of the results with the known aerodynamic model that was utilized within the simulation to generate the original data. Magnitudes of noise were varied utilizing Monte Carlo analysis to perform sensitivity analysis of each noise source on the extracted dynamic stability coefficients. Some preliminary results will be presented.

Otoniel Ramirez↗

NASA NTRSDate not supplied

Comparison of Dynamic Stability Testing Techniques with Magnetic Suspension Wind Tunnel

Otoniel Ramirez↗

NASA NTRS2003

Non-Genomic Origins of Proteins and Metabolism

It is proposed that evolution of inanimate matter to cells endowed with a nucleic acid- based coding of genetic information was preceded by an evolutionary phase, in which peptides not coded by nucleic acids were able to self-organize into networks capable of evolution towards increasing metabolic complexity. Recent findings that truly different, simple peptides (Keefe and Szostak, 2001) can perform the same function (such as ATP binding) provide experimental support for this mechanism of early protobiological evolution. The central concept underlying this mechanism is that the reproduction of cellular functions alone was sufficient for self-maintenance of protocells, and that self- replication of macromolecules was not required at this stage of evolution. The precise transfer of information between successive generations of the earliest protocells was unnecessary and, possibly, undesirable. The key requirement in the initial stage of protocellular evolution was an ability to rapidly explore a large number of protein sequences in order to discover a set of molecules capable of supporting self- maintenance and growth of protocells. Undoubtedly, the essential protocellular functions were carried out by molecules not nearly as efficient or as specific as contemporary proteins. Many, potentially unrelated sequences could have performed each of these functions at an evolutionarily acceptable level. As evolution progressed, however proteins must have performed their functions with increasing efficiency and specificity. This, in turn, put additional constraints on protein sequences and the fraction of proteins capable of performing their functions at the required level decreased. At some point, the likelihood of generating a sufficiently efficient set of proteins through a non-coded synthesis was so small that further evolution was not possible without storing information about the sequences of these proteins. Beyond this point, further evolution required coupling between proteins and informational polymers that is characteristic to all known forms of life. The emergence of such coupling must be postulated in any scenario of the origin of life, no matter whether it starts with RNA or proteins. To examine the evolutionary potential of non-genomic systems, a simple, computationally tractable model, which is still capable of capturing the essential features of the real system, has been studied computationally. Both constructive and destructive processes have been introduced into the model in a stochastic manner. Instead of assuming random reaction sets, only a suite of protobiologically plausible reactions has been considered. Peptides have been explicitly considered as protoenzymes and their catalytic efficiencies have been assigned on the basis of biochemical principles and experimental estimates. Simulations have been carried out using a novel approach (The Next Reaction Method) that is appropriate even for very low concentrations of reactants. Studies have focused on global autocatalytic processes and their diversity.

Pohorille, Andrew↗

NASA NTRS1990

A verified model of fault-tolerance

The main objectives are: a model of a replicated system with exact-match voting; a fault model that includes transients; a theorem that establishes the conditions under which the system provides fault tolerance; a formal specification of the model; and a mechanically checked verification of the theorem that is consonant with the journal-level presentation. Formal specification and verification revealed typos in the original report, exposed omission in original proof, led to the stronger theorem and more elegant proof, and confirmed that Enhanced Hierarchical Development Methodology (EHDM) has the capability to specify interesting and useful properties in a direct, natural, and readable manner.

Rushby, John↗

NASA NTRS1980

How many theories for the origin of /proto/life

The sequence of primordial chemical events leading to contemporary metabolism is considered, taking into account primordial reactants, amino acids, proteinoid, protocells, ATP, polynucleotides, and protein. The right kind of matter, thermal copolyamino acids, can organize itself into cell-like structures, in the absence of discrete lipid, when triggered to do so by water. Another unpredicted result of examination of the microsystems formed was the step-by-step realization that the component processes of a primitive form of replication were latent in the proteinoid microsystems. At the present time, four modes of primitive replication of proteinoid microsystems have been identified, plus one that has the appearance of protosexual reproduction. Two main conceptual pathways have received attention. One is the proteinoid theory, derived from experiments. The other is the DNA-first theory, for which attempts at conceptual construction and experimental support continue to be sought.

Fox, S. W.↗

NASA NTRS2017

Towards a Universal Biology: Is the Origin and Evolution of Life Predictable?

The origin and evolution of life seems an unpredictable oddity, based on the quirks of contingency. Celebrated by the late Stephen Jay Gould in several books, "evolution by contingency" has all the adventure of a thriller, but lacks the predictive power of the physical sciences. Not necessarily so, replied Simon Conway Morris, for convergence reassures us that certain evolutionary responses are replicable. The outcome of this debate is critical to Astrobiology. How can we understand where we came from on Earth without prophesy? Further, we cannot design a rational strategy for the search for life elsewhere - or to understand what the future will hold for life on Earth and beyond - without extrapolating from pre-biotic chemistry and evolution. There are several indirect approaches to understanding, and thus describing, what life must be. These include philosophical approaches to defining life (is there even a satisfactory definition of life?), using what we know of physics, chemistry and life to imagine alternate scenarios, using different approaches that life takes as pseudoreplicates (e.g., ribosomal vs non-ribosomal protein synthesis), and experimental approaches to understand the art of the possible. Given that: (1) Life is a process based on physical components rather than simply an object; (2). Life is likely based on organic carbon and needs a solvent for chemistry, most likely water, and (3) Looking for convergence in terrestrial evolution we can predict certain tendencies, if not quite "laws", that provide predictive power. Biological history must obey the laws of physics and chemistry, the principles of natural selection, the constraints of an evolutionary past, genetics, and developmental biology. This amalgam creates a surprising amount of predictive power in the broad outline. Critical is the apparent prevalence of organic chemistry, and uniformity in the universe of the laws of chemistry and physics. Instructive is the widespread occurrence of convergent or parallel evolution, which suggests that under certain conditions similar solutions are arrived at independently.

Universal biology; life everywhere↗

DOE OSTI2020

Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA

The recently characterized mammalian writer (methyltransferase) and eraser (demethylase) of the DNA N6-methyladenine (N6mA) methyl mark act on single-stranded (ss) and transiently-unpaired DNA. As YTH domain-containing proteins bind N6mA-containing RNA in mammalian cells, we investigated whether mammalian YTH domains are also methyl mark readers of N6mA DNA. Here, we show that the YTH domain of YTHDC1 (known to localize in the nucleus) binds ssDNA containing N6mA, with a 10 nM dissociation constant. This binding is stronger by a factor of 5 than in an RNA context, tested under the same conditions. However, the YTH domains of YTHDF2 and YTHDF1 (predominantly cytoplasmic) exhibited the opposite effect with ~1.5–2× stronger binding to ssRNA containing N6mA than to the corresponding DNA. We determined two structures of the YTH domain of YTHDC1 in complex with N6mA-containing ssDNA, which illustrated that YTHDC1 binds the methylated adenine in a single-stranded region flanked by duplexed DNA. We discuss the hypothesis that the writer-reader-eraser of N6mA-containining ssDNA is associated with maintaining genome stability. Structural comparison of YTH and SRA domains (the latter a DNA 5-methylcytosine reader) revealed them to be diverse members of a larger family of DNA/RNA modification readers, apparently having originated from bacterial modification-dependent restriction enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Development and Validation of Physics-Based Sub-Models of High-Pressure Supercritical Fuel Injection at Diesel Conditions Insert

The project sought to develop and validate accurate, physics-based, numerical submodels and implement them in computational fluid dynamics (CFD) software codes to enable accurate predictions of diesel sprays at pressures higher than the current systems. The combined experimental-computational effort has four main objectives: (1) acquire spatially and temporally resolved scalar measurements of fuel-oxidizer mixing in the near field of the fuel jet, (2) develop software modules to calculate thermo-physical properties of diesel surrogates and their mixtures with oxidizer of interest in real-gas operating regime, (3) integrate the real-fluid model into a commercial and an open-source CFD code to simulate fuel-air mixing in high-pressure diesel sprays, and (4) assess the robustness, accuracy, and uncertainty of the integrated CFD solvers in computing diesel sprays. Project accomplishments are consistent with the original goals of the project. Although we acquired spatially and temporally resolved scalar measurements, they were limited to refractive index difference and not to thermodynamic properties such as temperature and equivalence ratio. However, we successfully developed the theoretical background needed to acquire such measurements at diesel conditions and demonstrated the capability of the RSD for scalar measurements in a canonical turbulent jet flow replicating features of the diesel jet. Additional work will be needed to implement these procedures at high-pressure, high-temperature engine-like conditions of the CPFR. Mainly, we did not anticipate the need to find the liquid boundary and its statistical features or the state relationships between refractive index and thermodynamic properties, assuming the widely known Dale-Gladstone equation would suffice. Still, efforts devoted to these tasks were essential to fulfil the goals of the project and serves as the foundation on which many of the conclusions and key contributions of this project are based. Further assessment and application of the developed CFD codes is recommended to fully realize the benefits of this research.

33 ADVANCED PROPULSION SYSTEMS↗