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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,009 records · Page 56
All sourcesNASA NTRSDOE OSTI
NASA NTRS2012

Automated Lab-on-a-Chip Electrophoresis System

Capillary electrophoresis is an analytical technique that can be used to detect and quantify extremely small amounts of various biological molecules. In the search for biochemical traces of life on other planets, part of this search involves an examination of amino acids, which are the building blocks of life on Earth. The most sensitive method for detecting amino acids is the use of laser induced fluorescence. However, since amino acids do not, in general, fluoresce, they first must be reacted with a fluorescent dye label prior to analysis. After this process is completed, the liquid sample then must be transported into the electrophoresis system. If the system is to be reused multiple times, samples must be added and removed each time. In typical laboratories, this process is performed manually by skilled human operators using standard laboratory equipment. This level of human intervention is not possible if this technology is to be implemented on extraterrestrial targets. Microchip capillary electrophoresis (CE) combined with laser induced fluorescence detection (LIF) was selected as an extremely sensitive method to detect amino acids and other compounds that can be tagged with a fluorescent dye. It is highly desirable to package this technology into an integrated, autonomous, in situ instrument capable of performing CE-LIF on the surface of an extraterrestrial body. However, to be fully autonomous, the CE device must be able to perform a large number of sample preparation and analysis operations without the direct intervention of a human.

Willis, Peter A.↗
NASA NTRS2009

Assessment of Nutrient Stability in Space Foods

Maintaining an intact nutrient supply in the food system flown on spacecraft is a critical issue for mission success and crew health and safety. Early polar expeditions and exploration expeditions by sailing vessels have taught us that a deficiency, or excess, of even a single vitamin in the food supply can be catastrophic. Evidence from ground-based research indicates that some vitamins are destroyed and fatty acids are oxidized (and therefore rendered dangerous or useless) by different types of radiation and by conditions of long-term storage. We hypothesize that radiation and long-term storage in the space-flight environment will affect the stability of vitamins, amino acids, and fatty acids in the space food system. The research objectives of our ongoing stability studies are to determine the stability of water- and fat-soluble vitamins, fatty acids, and amino acids in the space food supply before and after space flight on the International Space Station (ISS). Foods were analyzed after 2 weeks (a flight control), 11, 19, and 28 months of flight. Along with the space-flown foods, ground-based controls matched for time, light, and temperature are analyzed. The flight studies complement planned ground-based studies of the effects of radiation on vitamins, amino acids, and fatty acids. Flight studies are needed because a model based on ground-based data cannot predict all of the effects of the space-flight environment. Flight studies provide a more accurate test system to determine the effects on these nutrients of the temperature, and radiation conditions in the space-flight environment. Ground studies are required to evaluate longer missions and higher radiation levels expected outside low-Earth orbit. In addition to providing information about nutrient stability in space, the results of these studies will help NASA determine if a need exists to develop special packaging that can ensure stability of foods and nutrients in space, or if further studies of nutrient metabolism or nutrient requirements are needed.

Zwart, S. R.↗
NASA NTRS1978

Evaluation of compositional nonrandomness in proteins

The finite sampling component of Q, a measure of nonrandomness in the amino acid composition of proteins, is quantitatively estimated by using the natural abundances of amino acids rather than the genetic code table frequencies, and the revised value of Q implies that the value of Q(c), a measure of selective effects above and beyond those imposed by the average natural abundance of the amino acids, should be 9.7 rather than its previous value of 24.3. Individual Q(c) values are given for 81 protein families. The standard deviation of the population of Q(c) values is 12.5 but the Q(c) value differs significantly from the value of zero expected were the natural abundances of the amino acids the only selective constraint. The small value of Q(c) indicates that quantitatively minimal adjustments away from the average protein composition are necessary to maintain many different biological functions.

Holmquist, R.↗
NASA NTRS2002

Systematic Underutilization of Glutamine In Thermophile Proteins

Rapid racemization above 100 C of L-amino acids to Domino acids, as well as deamidation, is probably a hazard for high temperature life. For example, the half-life of some asparaginyl peptides can be as short as 10 minutes at 100 C. High temperature organisms could protect themselves by reducing usage of amino acids that are easily racemized/deamidazed, by having a rapid rate of protein turnover which requires energy, or by adapting special cis-peptide conformations. We have searched eight completely sequenced thermophile genomes, and compare them to mesophile genomes, in order to identify underutilized amino acids. To our surprise, asparagine, the most unstable amino acid to deamidation, is used at about the same level in thermophile proteins in comparison to mesophiles whereas it is the second most unstable amino acid, glutamine, that is underutilized in all of eight thermophile species. Glutamines are present at 2% level in a typical thermophile protein, instead of 4% in mesophile. We argue that it is easier to protect asparagines from deamidation by cis-peptide conformations. We discuss statistical as well as structural evidence in support of our conclusions.

Liang, Shoudan↗
DOE OSTI2015

Cdc6 localizes to S- and G2-phase centrosomes in a cell cycle-dependent manner

Highlights: • Cdc6 protein is a component of the pre-replicative complex required for chromosomal replication initiation. • Cdc6 localized to centrosomes of S and G2 phases in a cell cycle-dependent manner. • The centrosomal localization was governed by centrosomal localization signal sequences of Cdc6. • Deletions or substitution mutations on the centrosomal localization signal interfered with centrosomal localization of the Cdc6 proteins. - Abstract: The Cdc6 protein has been primarily investigated as a component of the pre-replicative complex for the initiation of chromosome replication, which contributes to maintenance of chromosomal integrity. Here, we show that Cdc6 localized to the centrosomes during S and G2 phases of the cell cycle. The centrosomal localization was mediated by Cdc6 amino acid residues 311–366, which are conserved within other Cdc6 homologues and contains a putative nuclear export signal. Deletions or substitutions of the amino acid residues did not allow the proteins to localize to centrosomes. In contrast, DsRed tag fused to the amino acid residues localized to centrosomes. These results indicated that a centrosome localization signal is contained within amino acid residues 311–366. The cell cycle-dependent centrosomal localization of Cdc6 in S and G2 phases suggest a novel function of Cdc6 in centrosomes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Pyrrolysyl-tRNA Synthetase, an Aminoacyl-tRNA Synthetase for Genetic Code Expansion

Genetic code expansion (GCE) has become a central topic of synthetic biology. GCE relies on engineered aminoacyl-tRNA synthetases (aaRSs) and a cognate tRNA species to allow codon reassignment by co-translational insertion of non-canonical amino acids (ncAAs) into proteins. Introduction of such amino acids increases the chemical diversity of recombinant proteins endowing them with novel properties. Such proteins serve in sophisticated biochemical and biophysical studies both in vitro and in vivo, they may become unique biomaterials or therapeutic agents, and they afford metabolic dependence of genetically modified organisms for biocontainment purposes. In the Methanosarcinaceae the incorporation of the 22nd genetically encoded amino acid, pyrrolysine (Pyl), is facilitated by pyrrolysyl-tRNA synthetase (PylRS) and the cognate UAG-recognizing tRNAPyl. This unique aaRS•tRNA pair functions as an orthogonal translation system (OTS) in most model organisms. The facile directed evolution of the large PylRS active site to accommodate many ncAAs, and the enzyme’s anticodon-blind specific recognition of the cognate tRNAPyl make this system highly amenable for GCE purposes. The remarkable polyspecificity of PylRS has been exploited to incorporate >100 different ncAAs into proteins. Here we review the Pyl-OT system and selected GCE applications to examine the properties of an effective OTS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1975

Linkages in thermal copolymers of lysine

The thermal copolymerization of lysine with other alpha-amino acids was studied. The identity of the second amino acid influences various properties of the polymer obtained, including the proportion of alpha and epsilon linkages of lysine. A review of linkages in proteinoids indicates alpha and beta linkages for aspartic acid, alpha and gamma linkages for glutamic acid, alpha and epsilon linkages for lysine, and alpha linkages for other amino acids. Thermal proteinoids are thus more complex in types of linkage than are proteins.

Fox, S. W.↗
NASA NTRS1995

Isolation, characterization, and primary structure of rubredoxin from the photosynthetic bacterium, Heliobacillus mobilis

Rubredoxin is a small nonheme iron protein that serves as an electron carrier in bacterial systems. Rubredoxin has now been isolated and characterized from the strictly anaerobic phototroph, Heliobacillus mobilis. THe molecular mass (5671.3 Da from the amino acid sequence) was confirmed and partial formylation of the N-terminal methionyl residue was established by matrix-assisted laser desorption mass spectroscopy. The complete 52-amino-acid sequence was determined by a combination of N-terminal sequencing by Edman degradation and C-terminal sequencing by a novel method using carboxypeptidase treatment in conjunction with amino acid analysis and laser desorption time of flight mass spectrometry. The molar absorption coefficient of Hc. mobilis rubredoxin at 490 nm is 6.9 mM-1 cm-1 and the midpoint redox potential at pH 8.0 is -46 mV. The EPR spectrum of the oxidized form shows resonances at g = 9.66 and 4.30 due to a high-spin ferric iron. The amino acid sequence is homologous to those of rubredoxins from other species, in particular, the gram-positive bacteria, and the phototrophic green sulfur bacteria, and the evolutionary implications of this are discussed.

NASA Discipline Number 52-30↗
DOE OSTI2013

Complete genome sequencing and evolutionary analysis of Indian isolates of Dengue virus type 2

Highlights: •Complete genome of Indian DENV-2 was deciphered for the first time in this study. •The recent Indian DENV-2 revealed presence of many unique amino acid residues. •Genotype shift (American to Cosmopolitan) characterizes evolution of DENV-2 in India. •Circulation of a unique clade of DENV-2 in South Asia was identified. -- Abstract: Dengue is the most important arboviral infection of global public health significance. It is now endemic in most parts of the South East Asia including India. Though Dengue virus type 2 (DENV-2) is predominantly associated with major outbreaks in India, complete genome information of Indian DENV-2 is not available. In this study, the full-length genome of five DENV-2 isolates (four from 2001 to 2011 and one from 1960), from different parts of India was determined. The complete genome of the Indian DENV-2 was found to be 10,670 bases long with an open reading frame coding for 3391 amino acids. The recent Indian DENV-2 (2001–2011) revealed a nucleotide sequence identity of around 90% and 97% with an older Indian DENV-2 (1960) and closely related Sri Lankan and Chinese DENV-2 respectively. Presence of unique amino acid residues and non-conservative substitutions in critical amino acid residues of major structural and non-structural proteins was observed in recent Indian DENV-2. Selection pressure analysis revealed positive selection in few amino acid sites of the genes encoding for structural and non-structural proteins. The molecular phylogenetic analysis based on comparison of both complete coding region and envelope protein gene with globally diverse DENV-2 viruses classified the recent Indian isolates into a unique South Asian clade within Cosmopolitan genotype. A shift of genotype from American to Cosmopolitan in 1970s characterized the evolution of DENV-2 in India. Present study is the first report on complete genome characterization of emerging DENV-2 isolates from India and highlights the circulation of a unique clade in South Asia.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1971

Experimental investigation on the origin of the genetic code.

A simple model of interacting complex systems of species is tested to assess the binding behavior of monomeric nucleic acid and protein components during evolution. Nine representative amino acids are immobilized by the formation of an amide linkage on a prepared chromatographic support. Selective binding of ribonucleoside 5-phosphates in these amino acids is achieved under standardized conditions, and a site-binding model is derived to characterize the binding. It is shown that the binding behavior of the reactants during nucleic acid-protein interactions depends on the nature of the base and the amino acid. The results of the study are assessed as useful for the interpretation of more complex nucleic acid-protein systems and of their role in the evolution of the cell.

Saxinger, C.↗
DOE OSTI2019

Crystal Structure of d -Ornithine/ d -Lysine Decarboxylase, a Stereoinverting Decarboxylase: Implications for Substrate Specificity and Stereospecificity of Fold III Decarboxylases

A newly discovered Fold III pyridoxal 5'-phosphate (PLP)-dependent decarboxylase, d-ornithine/lysine decarboxylase (DOKDC), catalyzes decarboxylation of d-lysine and d-ornithine with inversion of stereochemistry. The X-ray crystal structure of DOKDC has been determined to 1.72 Å. DOKDC has a low level of sequence identity (<30%) with meso-diaminopimelate decarboxylase (DAPDC) and l-lysine/ornithine decarboxylase (LODC), but its three-dimensional structure is very similar. The distal binding site of DAPDC contains a conserved arginine that forms an ion pair with the l-carboxylate end of DAP. In both LODC and DOKDC, this distal site is modified by replacement of the arginine with aspartate, changing the substrate specificity. l-Ornithine decarboxylase (ODC) and LODC have a conserved phenylalanine on the re-face of the PLP complex that has been found to play a key role in the decarboxylation mechanism. We have found that both DAPDC and DOKDC have tyrosine instead of phenylalanine at this position, which precludes the binding of l-amino acids. Because the PLP-binding lysine in ODC, LODC, DAPDC, and DOKDC is located on the re-face of the PLP, we propose that this is the acid group responsible for protonation of the product, thus resulting in the observed retention of configuration for decarboxylation of l-amino acids and inversion for decarboxylation of d-amino acids. Here, the reactions of DAPDC and DOKDC are likely accelerated by positive electrostatics on the re-face by the lysine ε-ammonium ion and on the si-face by closure of the lid over the active site, resulting in desolvation and destabilization of the d-amino acid carboxylate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Thermophilic cellobiohydrolase

The present invention provides for a composition comprising a polypeptide comprising a first amino acid sequence having at least 70% identity with the amino acid sequence of Csac GH5 wherein said first amino acid sequence has a thermostable or thermophilic cellobiohydrolase (CBH) or exoglucanase activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Enzymatic carbon–fluorine bond cleavage by human gut microbes

Fluorinated compounds are used for agrochemical, pharmaceutical, and numerous industrial applications, resulting in global contamination. In many molecules, fluorine is incorporated to enhance the half-life and improve bioavailability. Fluorinated compounds enter the human body through food, water, and xenobiotics including pharmaceuticals, exposing gut microbes to these substances. The human gut microbiota is known for its xenobiotic biotransformation capabilities, but it was not previously known whether gut microbial enzymes could break carbon-fluorine bonds, potentially altering the toxicity of these compounds. Here, through the development of a rapid, miniaturized fluoride detection assay for whole-cell screening, we identified active gut microbial defluorinases. We biochemically characterized enzymes from diverse human gut microbial classes including Clostridia, Bacilli, and Coriobacteriia, with the capacity to hydrolyze (di)fluorinated organic acids and a fluorinated amino acid. Whole-protein alanine scanning, molecular dynamics simulations, and chimeric protein design enabled the identification of a disordered C-terminal protein segment involved in defluorination activity. Domain swapping exclusively of the C-terminus conferred defluorination activity to a nondefluorinating dehalogenase. To advance our understanding of the structural and sequence differences between defluorinating and nondefluorinating dehalogenases, we trained machine learning models which identified protein termini as important features. Models trained on 41-amino acid segments from protein C termini alone predicted defluorination activity with 83% accuracy (compared to 95% accuracy based on full-length protein features). This work is relevant for therapeutic interventions and environmental and human health by uncovering specificity-determining signatures of fluorine biochemistry from the gut microbiome.

Probst, Silke I↗
NASA NTRS1970

Origins of life; Proceedings of the First Conference, Princeton, N.J., May 21-24, 1967.

The dialogs on the origin of life commence with the fossil record. They deal with the age of the earth; the primitive atmosphere; precambrian microfossils; the Fig Tree series of rocks, which is part of the Swaziland system; the Bitter Springs Formation in Australia; and simulated Precambrian microfossils. The syntheses of biologically important monomers, amino acids, and nucleic acid derivatives are discussed. Polymerization mechanisms; the thermal origin of amino acid polymers; nonnucleic acid information carriers; the relationship between amino acid and nucleic acid polymers; the origin of the triple code; early reciprocating systems; and the evolution of the ribosomal system receive attention. Some brief comments on extraterrestrial life are presented. An appendix deals with the geological evidence for the thermal origin of living systems.

Margulis, L.↗
DOE OSTI2018

Organic matter in extraterrestrial water-bearing salt crystals

Direct evidence of complex prebiotic chemistry from a water-rich world in the outer solar system is provided by the 4.5-billion-year-old halite crystals hosted in the Zag and Monahans (1998) meteorites. This study offers the first comprehensive organic analysis of the soluble and insoluble organic compounds found in the millimeter-sized halite crystals containing brine inclusions and sheds light on the nature and activity of aqueous fluids on a primitive parent body. Associated with these trapped brines are organic compounds exhibiting wide chemical variations representing organic precursors, intermediates, and reaction products that make up life’s precursor molecules such as amino acids. The organic compounds also contain a mixture of C-, O-, and N-bearing macromolecular carbon materials exhibiting a wide range of structural order, as well as aromatic, ketone, imine, and/or imidazole compounds. The enrichment in 15 N is comparable to the organic matter in pristine Renazzo-type carbonaceous chondrites, which reflects the sources of interstellar 15 N, such as ammonia and amino acids. The amino acid content of the Zag halite deviates from the meteorite matrix, supporting an exogenic origin of the halite, and therefore, the Zag meteorite contains organics synthesized on two distinct parent bodies. Lastly, our study suggests that the asteroidal parent body where the halite precipitated, potentially asteroid 1 Ceres, shows evidence for a complex combination of biologically and prebiologically relevant molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1997

An analysis of the metabolic theory of the origin of the genetic code

A computer program was used to test Wong's coevolution theory of the genetic code. The codon correlations between the codons of biosynthetically related amino acids in the universal genetic code and in randomly generated genetic codes were compared. It was determined that many codon correlations are also present within random genetic codes and that among the random codes there are always several which have many more correlations than that found in the universal code. Although the number of correlations depends on the choice of biosynthetically related amino acids, the probability of choosing a random genetic code with the same or greater number of codon correlations as the universal genetic code was found to vary from 0.1% to 34% (with respect to a fairly complete listing of related amino acids). Thus, Wong's theory that the genetic code arose by coevolution with the biosynthetic pathways of amino acids, based on codon correlations between biosynthetically related amino acids, is statistical in nature.

NASA Discipline Exobiology↗