Evolution: a molecular point of view. Proceedings of a workshop. Woods Hole, Massachusetts, USA. 24-26 October 1997
No abstract available
NASA Discipline General Space Life Sciences↗
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Results for “molecular evolution”
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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Molecular cloud evolution and star formation
The present state of knowledge of the relationship between molecular clouds and young stars is reviewed. The determination of physical parameters from molecular line observations is summarized, and evidence for fragmentation of molecular clouds is discussed. Hierarchical fragmentation is reviewed, minimum fragment scales are derived, and the stability against fragmentation of both spherically and anisotropically collapsing clouds is discussed. Observational evidence for high-velocity flows in clouds is summarized, and the effects of winds from pre-main sequence stars on molecular gas are discussed. The triggering of cloud collapse by enhanced pressure is addressed, as is the formation of dense shells by spherical outflows and their subsequent breakup. A model for low-mass star formation is presented, and constraints on star formation from the initial mass function are examined. The properties of giant molecular clouds and massive star formation are described. The implications of magnetic fields for cloud evolution and star formation are addressed.
Silk, J.↗
Proceedings of the Astrobiology Science Conference 2010. Evolution and Life: Surviving Catastrophes and Extremes on Earth and Beyond
The Program of the 2010 Astrobiology Science Conference: Evolution and Life: Surviving Catastrophes and Extremes on Earth and Beyond, included sessions on: 50 Years of Exobiology and Astrobiology: Greatest Hits; Extraterrestrial Molecular Evolution and Pre-Biological Chemistry: From the Interstellar Medium to the Solar System I; Human Exploration, Astronaut Health; Diversity in Astrobiology Research and Education; Titan: Past, Present, and Future; Energy Flow in Microbial Ecosystems; Extraterrestrial Molecular Evolution and Prebiological Chemistry: From the Interstellar Medium to the Solar System II; Astrobiology in Orbit; Astrobiology and Interdisciplinary Communication; Science from Rio Tinto: An Acidic Environment; Can We Rule Out Spontaneous Generation of RNA as the Key Step in the Origin of Life?; How Hellish Was the Hadean Earth?; Results from ASTEP and Other Astrobiology Field Campaigns I; Prebiotic Evolution: From Chemistry to Life I; Adaptation of Life in Hostile Space Environments; Extrasolar Terrestrial Planets I: Formation and Composition; Collaborative Tools and Technology for Astrobiology; Results from ASTEP and Other Astrobiology Field Campaigns II; Prebiotic Evolution: From Chemistry to Life II; Survival, Growth, and Evolution of Microrganisms in Model Extraterrestrial Environments; Extrasolar Terrestrial Planets II: Habitability and Life; Planetary Science Decadal Survey Update; Astrobiology Research Funding; Bioessential Elements Through Space and Time I; State of the Art in Life Detection; Terrestrial Evolution: Implications for the Past, Present, and Future of Life on Earth; Psychrophiles and Polar Environments; Life in Volcanic Environments: On Earth and Beyond; Geochronology and Astrobiology On and Off the Earth; Bioessential Elements Through Space and Time II; Origins and Evolution of Genetic Systems; Evolution of Advanced Life; Water-rich Asteroids and Moons: Composition and Astrobiological Potential; Impact Events and Evolution; A Warm, Wet Mars?; Titan Versus Europa - Potential for Astrobiology; Habitability Potential of Mars; Biosignatures: Tools and Development I; Origins of Molecular Asymmetry, Homochirality, and Life Detection; Deserts and Evaporite Basins and Associated Microbialite Systems; Ancient Life and Synthetic Biology: Crossroad of the Past and Future; Biosignatures: Tools and Development II; Free Oxygen: Proxies, Causes, and Consequences; Life in Modern Microbialite Systems - Function and Adaptation; Hydrothermal Systems and Organosynthesis Processes: Origin and Evolution of Life; Where Should We Go on Mars to Seek Signs of Life?; Search for Intelligent Life I. Innovative SETI Observing Programs and Future Directions; Integrating Astrobiology Research Across and Beyond the Community; Education in Astrobiology in K-12; Search for Intelligent Life II. Global Engagement and Interstellar Message Construction; Poster sessions included: Extraterrestrial Molecular Evolution and Pre-Biological Chemistry; Prebiotic Evolution: From Chemistry to Life; RNA World; Terrestrial Evolution: Implications for the Past, Present, and Future of Life on Earth; Hydrothermal Systems and Organosynthesis Processes: Origin and Evolution of Life; Virology and Astrobiology; Horizontal Genetic Transfer and Properties of Ancestral Organisms; Life in Volcanic Environments: On Earth and Beyond; Impact Events and Evolution; Evolution of Advanced Life; Evolution of Intelligent Life; Education in Astrobiology in K-12; Origins of Molecular Asymmetry, Homochirality, and Life Detection; Astrobiology and Interdisciplinary Communication; Diversity in Astrobiology Research and Education; Integrating Astrobiology Research Across and Beyond the Community; Policy and Societal Issues: Dealing with Potential Bumps in the Astrobiology Road Ahead; Results from ASTEP and Other Astrobiology Field Campaigns; Energy Flow in Microbial Ecosystems; Psychrophiles and Polar Environments; Deserts and Evaporite Basins and Associated Microbialite stems; Life in Modern Microbialite Systems - Function and Adaptation; Free Oxygen: Proxies, Causes, and Consequences; Bioessential Elements Through Space and Time; Water-rich Asteroids and Moons: Composition and Astrobiological Potential; Biosignatures: Tools and Developments; Robotics and Instrumentation for Astrobiology; State of the Art in Life Detection; Astrobiology in Orbit; Survival, Growth, and Evolution of Microrganisms in Model Extraterrestrial Evolution; Search for Intelligent Life; Habitability Potential of Mars; How and Where Should We Seek Signs of Life on Mars?; Titan: Past, Present, and Future; Extrasolar Terrestrial Planets: Formation, Composition, Diversity, Habitability and Life; Human Exploration, Astronaut Health; Science from Rio Tinto: An Acidic Environment and Adaptation of Life in Hostile Space Environments;
Source record↗
Probing molecular wavepacket evolution using multidimensional coherent spectroscopy (Final Report)
The goal of this project was to develop and demonstrate multidimensional coherent spectroscopy (MDCS) techniques to fully map wave-packet dynamics in simple molecules. MDCS correlates excitation and emis sion frequencies, enabling continuous tracking of wave-packet evolution even when multiple wave-packets evolve simultaneously. The initial experiments were to be performed using the MDCS apparatus in the PI’s laboratory to record the evolution of the wave-packet’s energy in molecular iodine. A longer-term goal was to develop a version compatible with using an X-ray Free Electron Laser (XFEL) as a probe, which would allow the evolution of the internuclear distance of the wave-packet—not just its energy—to be determined.
74 ATOMIC AND MOLECULAR PHYSICS↗
The chemical evolution of molecular clouds
The nonequilibrium chemistry of dense molecular clouds (10,000 to 1 million hydrogen molecules per cu cm) is studied in the framework of a model that includes the latest published chemical data and most of the recent theoretical advances. In this model the only important external source of ionization is assumed to be high-energy cosmic-ray bombardment; standard charge-transfer reactions are taken into account as well as reactions that transfer charge from molecular ions to trace-metal atoms. Schemes are proposed for the synthesis of such species as NCO, HNCO, and CN. The role played by adsorption and condensation of molecules on the surface of dust grains is investigated, and effects on the chemical evolution of a dense molecular cloud are considered which result from varying the total density or the elemental abundances and from assuming negligible or severe condensation of gaseous species on dust grains. It is shown that the chemical-equilibrium time scale is given approximately by the depletion times of oxygen and nitrogen when the condensation efficiency is negligible; that this time scale is probably in the range from 1 to 4 million years, depending on the elemental composition and initial conditions in the cloud; and that this time scale is insensitive to variations in the total density.
Iglesias, E.↗
Protobiological informatoin, bidirectional recognition and reverse translation
Emergence of protobiological information has been suggested by experiments in which heated mixtures of alpha-amino acids order themselves into a self limited array of thermal proteins. The polymers display selective catalytic, hormonal, and other activities. Interactions of varied cationic thermal proteins with polynucleotides indicate selective recognition in both directions. Reverse translation is partly a missing link in the molecular evolution flowsheet. The self ordering of amino acids serves conceptually as a deterministic evolutionary precursor of the modern coding mechanism. The possibility for the evolution of information at an early nontemplated protein stage is supported by findings of electrical signals from proteinoid microspheres prepared with no DNA/RNA in their history. The deposition of thermal copolyamino acids on lipid membranes in the Mueller-Rudin apparatus has here been found to produce electrical behavior like that evoked by bacterial EIM polypeptide. A new procedure is to make a film of membrane on the electrode; the results provide maximal repeatability. The principle of nonrandom biomacromolecular specificity identified by these studies in molecular evolution have been extrapolated to principles of evolution of advanced organisms.
Fox, S. W.↗
Dynamical evolution and molecular abundances of interstellar clouds
Dynamical models are presented that start with interstellar gas in an initial diffuse state and consider their gravitational collapse and the formation of dense cores. Frozen-in tangled magnetic fields are included to mimic forces that might oppose gravitational contraction and whose effectiveness may increase with increasing core densities. Results suggest the possibility that dense cloud cores may be dynamically evolving ephemeral objects, such that their lifespan at a given core density decreases as that density increases.
Prasad, Sheo S.↗
Automatic Evolution of Molecular Nanotechnology Designs
This paper describes strategies for automatically generating designs for analog circuits at the molecular level. Software maps out the edges and vertices of potential nanotechnology systems on graphs, then selects appropriate ones through evolutionary or genetic paradigms.
Globus, Al↗
Quantifying the Evolution of Molecular Production Rates of Comet 21P/Giacobini–Zinner with iSHELL/NASA-IRTF
This paper presents results from our molecular characterization of comet 21P/Giacobini–Zinner during its 2018 apparition. We followed the comet during four observing runs, for a total of eight nights. The high-resolution spectra of 21P were acquired using iSHELL—the near-infrared high-resolution immersion echelle spectrograph on NASA/IRTF (Maunakea, Hawaii). We detected many cometary emission lines across four customized iSHELL settings in the (2.9–5.2) μm range. CO abundances relative to water displayed a relatively constant behavior during the observing campaign, suggesting a possible correlation between the outgassing of water and CO. While CO mixing ratios in 21P are consistent with the reference median value for Jupiter family comets (JFCs), ethane was depleted relative to the reference median value for JFCs, except for one observing run (August 8 and 9) in which ethane appeared overabundant. We consider several possible causes: an ethane outburst, decreasing outgassing of water, or a seasonal effect owing to nucleus rotation. In the pre-perihelion runs, methanol was overabundant compared with the reference median value for JFCs, however it decreased steadily to a depleted value during 21P’s post-perihelion phase, suggesting a possible seasonal effect. We report 3σ upper limits for acetylene, formaldehyde, ammonia, and methane. The ratios of our measured 3σ upper limits for acetylene and detections of hydrogen cyanide are consistent with the depletion of C2 relative to CN in 21P observed at optical wavelengths. This result confirms that 21P is depleted in the carbon-chain primary volatile responsible for C2.
Faggi, S.↗
Quantifying the Evolution of Molecular Production Rates of Comet 21P/Giacobini–Zinner with iSHELL/NASA-IRTF
This paper presents results from our molecular characterization of comet 21P/Giacobini-Zinner during its 2018 apparition. We followed the comet during four observing runs, for a total of 8 nights. The high-resolution spectra of 21P were acquired using iSHELL - the near-IR high resolution immersion echelle spectrograph on NASA/IRTF (Mauna Kea, Hawaii). We detected many cometary emission lines across four customized iSHELL settings in the (2.9 – 5.2) μm range. CO abundances relative to water displayed a relatively constant behavior during the observing campaign, suggesting a possible correlation between the outgassing of water and CO. While CO mixing ratios in 21P are consistent with the reference median value for Jupiter Family comets (JFCs), ethane was depleted relative to the reference median value for JFCs, excepting one observing run (8th and 9th Aug) in which ethane appeared overabundant. We consider several possible causes: an ethane outburst, decreasing outgassing of water, or a seasonal effect owing to nucleus rotation. In the pre-perihelion runs, methanol was overabundant compared with the reference median value for JFCs, however it decreased steadily to a depleted value during 21P’s post-perihelion phase, suggesting a possible seasonal effect. We report 3-s upper limits for acetylene, formaldehyde, ammonia and methane. The ratios of our measured 3-s upper limits for acetylene and detections of hydrogen cyanide are consistent with the depletion of C2 relative to CN in 21P observed at optical wavelengths. This result confirms that 21P is depleted in the carbon chain primary volatile responsible for C2 production.
Faggi S.↗
Cosmic evolution of molecular gas mass density from an empirical relationship between L 1.4 GHz and L ′CO
Explore the source record for details and available documents.
G Orellana-González↗
Molecular diversity and evolution of far-red light-acclimated photosystem I
The need to acclimate to different environmental conditions is central to the evolution of cyanobacteria. Far-red light (FRL) photoacclimation, or FaRLiP, is an acclimation mechanism that enables certain cyanobacteria to use FRL to drive photosynthesis. During this process, a well-defined gene cluster is upregulated, resulting in changes to the photosystems that allow them to absorb FRL to perform photochemistry. Because FaRLiP is widespread, and because it exemplifies cyanobacterial adaptation mechanisms in nature, it is of interest to understand its molecular evolution. Here, we performed a phylogenetic analysis of the photosystem I subunits encoded in the FaRLiP gene cluster and analyzed the available structural data to predict ancestral characteristics of FRL-absorbing photosystem I. The analysis suggests that FRL-specific photosystem I subunits arose relatively late during the evolution of cyanobacteria when compared with some of the FRL-specific subunits of photosystem II, and that the order Nodosilineales, which include strains like Halomicronema hongdechloris and Synechococcus sp. PCC 7335, could have obtained FaRLiP via horizontal gene transfer. We show that the ancestral form of FRL-absorbing photosystem I contained three chlorophyll f-binding sites in the PsaB2 subunit, and a rotated chlorophyll a molecule in the A0B site of the electron transfer chain. Along with our previous study of photosystem II expressed during FaRLiP, these studies describe the molecular evolution of the photosystem complexes encoded by the FaRLiP gene cluster.
ancestral sequence reconstruction↗
Evolution of the SARS-CoV -2 proteome in three dimensions (3D) during the first 6 months of the COVID -19 pandemic
Understanding the molecular evolution of the SARS-CoV-2 virus as it continues to spread in communities around the globe is important for mitigation and future pandemic preparedness. Three-dimensional structures of SARS-CoV-2 proteins and those of other coronavirusess archived in the Protein Data Bank were used to analyze viral proteome evolution during the first 6 months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48 000 viral isolates revealed how each one of 29 viral proteins have undergone amino acid changes. Catalytic residues in active sites and binding residues in protein–protein interfaces showed modest, but significant, numbers of substitutions, highlighting the mutational robustness of the viral proteome. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Here detailed results are presented for potential drug discovery targets and the four structural proteins that comprise the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and protein–protein and protein–nucleic acid interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.
59 BASIC BIOLOGICAL SCIENCES↗
On the origin and early evolution of biological catalysis and other studies on chemical evolution
One of the lines of research in molecular evolution which we have developed for the past three years is related to the experimental and theoretical study of the origin and early evolution of biological catalysis. In an attempt to understand the nature of the first peptidic catalysts and coenzymes, we have achieved the non-enzymatic synthesis of the coenzymes ADPG, GDPG, and CDP-ethanolamine, under conditions considered to have been prevalent on the primitive Earth. We have also accomplished the prebiotic synthesis of histidine, as well as histidyl-histidine, and we have measured the enhancing effects of this catalytic dipeptide on the dephosphorylation of deoxyribonucleotide monophosphates, the hydrolysis of oligo A, and the oligomerization 2', 3' cAMP. We reviewed and further developed the hypothesis that RNA preceded double stranded DNA molecules as a reservoir of cellular genetic information. This led us to undertake the study of extant RNA polymerases in an attempt to discover vestigial sequences preserved from early Archean times. In addition, we continued our studies of on the chemical evolution of organic compounds in the solar system and beyond.
Oro, J.↗
Preservation of corneous β-proteins in Mesozoic feathers
Fossil proteins are valuable tools in evolutionary biology. Recent technological advances and better integration of experimental methods have confirmed the feasibility of biomolecular preservation in deep time, yielding new insights into the timing of key evolutionary transitions. Keratins (formerly α-keratins) and corneous β-proteins (CBPs, formerly β-keratins) are of particular interest as they define tissue structures that underpin fundamental physiological and ecological strategies and have the potential to inform on the molecular evolution of the vertebrate integument. Reports of CBPs in Mesozoic fossils, however, appear to conflict with experimental evidence for CBP degradation during fossilization. Further, the recent model for molecular modification of feather chemistry during the dinosaur–bird transition does not consider the relative preservation potential of different feather proteins. Here we use controlled taphonomic experiments coupled with infrared and sulfur X-ray spectroscopy to show that the dominant β-sheet structure of CBPs is progressively altered to α-helices with increasing temperature, suggesting that (α-)keratins and α-helices in fossil feathers are most likely artefacts of fossilization. Our analyses of fossil feathers shows that this process is independent of geological age, as even Cenozoic feathers can comprise primarily α-helices and disordered structures. Critically, our experiments show that feather CBPs can survive moderate thermal maturation. Importantly, as predicted by our experiments, analyses of Mesozoic feathers confirm that evidence of feather CBPs can persist through deep time.
59 BASIC BIOLOGICAL SCIENCES↗
The influence of UV radiation on protistan evolution
Ultraviolet radiation has provided an evolutionary challenge to life on Earth. Recent increases in surficial ultraviolet B fluxes have focused attention on the role of UV radiation in protistan ecology, cancer, and DNA damage. Exploiting this new wealth of data, I examine the possibility that ultraviolet radiation may have played a significant role in the evolution of the first eukaryotes, that is, protists. Protists probably arose well before the formation of a significant ozone shield, and thus were probably subjected to substantial ultraviolet A, ultraviolet B, and ultraviolet C fluxes early in their evolution. Evolution consists of the generation of heritable variations and the subsequent selection of these variants. Ultraviolet radiation has played a role both as a mutagen and as a selective agent. In its role as a mutagen, it may have been crucial in the origin of sex and as a driver of molecular evolution. As a selective agent, its influence has been broad. Discussed in this paper are the influence of ultraviolet radiation on biogeography, photosynthesis, and desiccation resistance.
NASA Center ARC↗
A molecular description of the evolution of resistance
BACKGROUND: In vitro evolution has been used to obtain nucleic acid molecules with interesting functional properties. The evolution process usually is carried out in a stepwise manner, involving successive rounds of selection, amplification and mutation. Recently, a continuous in vitro evolution system was devised for RNAs that catalyze the ligation of oligonucleotide substrates, allowing the evolution of catalytic function to be studied in real time. RESULTS: Continuous in vitro evolution of an RNA ligase ribozyme was carried out in the presence of a DNA enzyme that was capable of cleaving, and thereby inactivating, the ribozyme. The DNA concentration was increased steadily over 33.5 hours of evolution, reaching a final concentration that would have been sufficient to inactivate the starting population in one second. The evolved population of ribozymes developed resistance to the DNA enzyme, reducing their vulnerability to cleavage by 2000-fold but retaining their own catalytic function. Based on sequencing and kinetic analysis of the ribozymes, two mechanisms are proposed for this resistance. One involves three nucleotide substitutions, together with two compensatory mutations, that alter the site at which the DNA enzyme binds the ribozyme. The other involves enhancement of the ribozyme's ability to bind its own substrate in a way that protects it from cleavage by the DNA enzyme. CONCLUSIONS: The ability to direct the evolution of an enzyme's biochemical properties in response to the behavior of another macromolecule provides insight into the evolution of resistance and may be useful in developing enzymes with novel or enhanced function.
Non-NASA Center↗
Parallel molecular mechanisms for enzyme temperature adaptation
The mechanisms that underly the adaptation of enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Here, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis, and we establish the underlying physical mechanisms. This residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. Furthermore, we identify residues associated with organismal growth temperature across 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation to temperature. We assess the residue properties, molecular interactions, and interaction networks that appear to underly temperature adaptation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗