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At least 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
NASA NTRSDate not supplied

The Detection of Aromatic Amino Acids in CR Chondrites Suggests They are Prebiotically Plausible

Amino acids (AAs) are the building blocks of proteins and are essential for life on Earth. Sources of AAs on early Earth range from exogenous sources such as delivery from extraterrestrial materials(i.e., meteorites, interplanetary dust particles, comets, etc.) to endogenous sources including chemical reactions in hydrothermal vents or atmospheric mixtures. Analyses of AAs of extraterrestrial origin from meteorites and laboratory studies of simulated prebiotic environments revealed that a diverse set of abiotically produced AAs may have been present on early Earth. However only a fraction of these AAs is found within the proteins of living organisms. Of the22 genetically encoded (proteinogenic) AAs, 20 occur in the standard genetic code (SGC) and are used by nearly all living organisms to build proteins. The universality of this AA alphabet suggests the presence and incorporation of these specific AAs occurred early in the evolution of life.

A. S. Burton↗
DOE OSTI2022

13 C NMR study of amino acid salts in facilitated transport membranes for post-combustion carbon capture

Some of amino acid salts (AASs) have been demonstrated to be effective mobile carriers in facilitated transport membranes (FTMs) to achieve superior CO 2 permeance and CO 2 /N 2 selectivity for CO 2 capture from flue gas. Understandings of how the structures of different AASs affect the chemistry of the amine–CO 2 reaction are essential for the future development of more efficient AAS mobile carriers. In this study, the reaction chemistry of selected AASs with CO 2 was investigated by 13 C nuclear magnetic resonance (NMR) spectroscopy. The CO 2 loading and the distribution of major reaction products, including carbamate and bicarbonate products of each studied AAS were quantitatively analyzed. The positive correlation between the CO 2 loading of AAS (mol CO 2 /g AAS) and the CO 2 permeance of FTMs suggested that AAS with a higher CO 2 loading may improve the performance of FTMs. Our results also showed that increasing the steric hindrance of AAS could be a practical way to promote the bicarbonate reaction pathway and thus potentially increase the CO 2 loading (mol CO 2 /mol AAS). Moreover, 2-(1-piperazinyl)ethylamine (PZEA) was found to be a more effective multi-amine than piperazine (PZ) for synthesizing AASs due to the presence of more effective nitrogen sites per molecule. The superior CO 2 permeance of the PZEA-Sar membrane is also attributed to its more uniform membrane formation. As a result, the knowledge gained from this study will inform the rational design of more effective AAS carriers for CO 2 capture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1987

Energy yields for hydrogen cyanide and formaldehyde syntheses - The HCN and amino acid concentrations in the primitive ocean

Simulated prebiotic atmospheres containing either CH4, CO, or CO2, in addition to N2, H2O, and variable amounts of H2, were subjected to the spark from a high-frequency Tesla coil, and the energy yields for the syntheses of HCN and H2CO were estimated from periodic (every two days) measurements of the compound concentrations. The mixtures with CH4 were found to yield the highest amounts of HCN, whereas the CO mixtures produced the highest yields of H2CO. These results model atmospheric corona discharges. From the yearly energy yields calculated and the corona discharge available on the earth, the yearly production rate of HCN was estimated; using data on the HCN production rates and the experimental rates of decomposition of amino acids through the submarine vents, the steady state amino acid production rate in the primitive ocean was calculated to be about 10 nmoles/sq cm per year.

Stribling, Roscoe↗
NASA NTRS2009

Decomposition of Alternative Chirality Amino Acids by Alkaliphilic Anaerobe from Owens Lake, California

The study of alkaliphilic microbial communities from anaerobic sediments of Owens and Mono Lakes in California led to the isolation of a bacterial strain capable of metabolizing amino acids with alternative chirality. According to the phylogenetic analysis, the anaerobic strain BK1 belongs to the genus Tindallia; however, despite the characteristics of other described species of this genus, the strain BK1 was able to grow on D-arginine and Dlysine. Cell morphology of this strain showed straight, motile, non-spore-forming rods with sizes 0.45 x 1.2-3 microns. Physiological characteristics of the strain showed that it is catalase negative, obligately anaerobic, mesophilic, and obligately alkaliphilic. This isolate is unable to grow at pH 7 and requires CO3 (2-) ions for growth. The strain has chemo-heterotrophic metabolism and is able to ferment various proteolysis products and some sugars. It plays the role of a primary anaerobe within the trophic chain of an anaerobic microbial community by the degradation of complex protein molecules to smaller and less energetic molecules. The new isolate requires NaCl for growth, and can grow within the range of 0.5-13 %, with the optimum at 1 % NaCl (w/v). The temperature range for the growth of the new isolate is 12-40 C with optimum at 35 C. The pH range for the growth of strain BK1 occurs between 7.8 and 11.0 with optimum at 9.5. This paper presents detailed physiological characteristics of the novel isolate from Owens Lake, a unique relic ecosystem of Astrobiological significance, and makes an accent on the ability of this strain to utilize L-amino acids.

Townsend, Alisa↗
DOE OSTI2023

Snekmer: a scalable pipeline for protein sequence fingerprinting based on amino acid recoding

Abstract Motivation The vast expansion of sequence data generated from single organisms and microbiomes has precipitated the need for faster and more sensitive methods to assess evolutionary and functional relationships between proteins. Representing proteins as sets of short peptide sequences (kmers) has been used for rapid, accurate classification of proteins into functional categories; however, this approach employs an exact-match methodology and thus may be limited in terms of sensitivity and coverage. We have previously used similarity groupings, based on the chemical properties of amino acids, to form reduced character sets and recode proteins. This amino acid recoding (AAR) approach simplifies the construction of protein representations in the form of kmer vectors, which can link sequences with distant sequence similarity and provide accurate classification of problematic protein families. Results Here, we describe Snekmer, a software tool for recoding proteins into AAR kmer vectors and performing either (i) construction of supervised classification models trained on input protein families or (ii) clustering for de novo determination of protein families. We provide examples of the operation of the tool against a set of nitrogen cycling families originally collected using both standard hidden Markov models and a larger set of proteins from Uniprot and demonstrate that our method accurately differentiates these sequences in both operation modes. Availability and implementation Snekmer is written in Python using Snakemake. Code and data used in this article, along with tutorial notebooks, are available at http://github.com/PNNL-CompBio/Snekmer under an open-source BSD-3 license. Supplementary information Supplementary data are available at Bioinformatics Advances online.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2004

The Effect of Salts on Electrospray Ionization of Amino Acids in the Negative Mode

The continued search for organics on Mars will require the development of simplified procedures for handling and processing of soil or rock core samples prior to analysis by onboard instrumentation. Extraction of certain organic molecules such as amino acids from rock and soil samples using a liquid solvent (H2O) has been shown to be more efficient (by approximately an order of magnitude) than heat extraction methods. As such, liquid extraction (using H2O) of amino acid molecules from rock cores or regolith material is a prime candidate for the required processing. In this scenario, electrospray ionization (ESI) of the liquid extract would be a natural choice for ionization of the analyte prior to interrogation by one of a variety of potential analytical separation techniques (mass spectroscopy, ion mobility spectroscopy, etc.). Aside from the obvious compatibility of ESI and liquid samples, ESI offers simplicity and a soft ionization capability. In order to demonstrate that liquid extraction and ESI can work as part of an in situ instrument on Mars, we must better understand and quantify the effect salts have on the ESI process. In the current work, we have endeavored to investigate the feasibility and limitations of negative mode ESI of Martian surface samples in the context of sample salt content using ion mobility spectroscopy (IMS).

H I Kim↗
NASA NTRS2018

Indigenous Amino Acids in Iron Meteorites

Understanding the organic content of meteorites and the potential delivery of molecules relevant to the origin of life on Earth is an important area of study in astrobiology. There have been many studies of meteoritic organics, with much focus on amino acids as monomers of proteins and enzymes essential to terrestrial life. The majority of these studies have involved analysis of carbonaceous chondrites, primitive meteorites containing approx. 3-5 wt% carbon. Amino acids have been observed in varying abundances and distributions in representatives of all eight carbonaceous chondrite groups, as well as in ungrouped carbonaceous chondrites, ordinary and R chondrites, ureilites, and planetary achondrites [1 and references therein].

carbonaceous chondrites↗
NASA NTRS2003

Amino acid chiral recognition using X-ray diffraction of thin films

The astrobiological search for life, both extinct and extant, on other solar system bodies will take place via several planned lander missions to Mars, Europa and Titan. The detection and identification of organic molecules that have been associated with life is a major technical achievement. Terrestrial life utilizes organic molecules, such as amino acids, as its basic building block. Detection of an entometeric excess of L over D forms of amino acids would be a powerful sign that life had existed on Mars at one time.

ESI/IMS/CIT↗
DOE OSTI2020

Comprehensive Detection of Single Amino Acid Variants and Evaluation of Their Deleterious Potential in a PANC-1 Cell Line

Identifying single amino acid variants (SAAVs) in cancer is critical for precision oncology. Several advanced algorithms are now available to identify SAAVs but attempts to combine different algorithms and optimize them on large datasets to achieve a more comprehensive coverage of SAAVs have not been implemented. Herein we report an expanded detection of SAAVs in the PANC-1 cell line using three different strategies, which results in identification of 540 SAAVs in the mass spectrometry data, the most comprehensive coverage yet reported. Among the set of 540 SAAVs, 79 are evaluated as deleterious SAAVs based on analysis using novel AssVar software in which one of the driver mutations found in each protein of KRAS, TP53 and SLC37A4 is further validated using independent selected reaction monitoring (SRM) analysis. Our study represents the most comprehensive discovery of SAAVs to date and the first large-scale detection of deleterious SAAVs in the PANC-1 cell line. This work may serve as the basis for future research in pancreatic cancer and personal immunotherapy and treatment.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1971

Effects of hydrostatic pressure and temperature on the uptake and respiration of amino acids by a facultatively psychrophilic marine bacterium.

Studies of pressure and temperature effects on glutamic acid transport and utilization indicated that hydrostatic pressure and low temperature inhibit glutamate transport more than glutamate respiration. The effects of pressure on transport were reduced at temperatures near the optimum. Similar results were obtained for glycine, phenylalanine, and proline. Pressure effects on the transport systems of all four amino acids were reversible to some degree. Both proline and glutamic acid were able to protect their transport proteins against pressure damage. The data presented indicate that the uptake of amino acids by cells under pressure is inhibited, which is the cause of their inability to grow under pressure.

Paul, K. L.↗