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Results for “molecular evolution”

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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
NASA NTRS1993

Structure and function of the homeotic gene complex (HOM-C) in the beetle, Tribolium castaneum

The powerful combination of genetic, developmental and molecular approaches possible with the fruit fly, Drosophila melanogaster, has led to a profound understanding of the genetic control of early developmental events. However, Drosophila is a highly specialized long germ insect, and the mechanisms controlling its early development may not be typical of insects or Arthropods in general. The beetle, Tribolium castaneum, offers a similar opportunity to integrate high resolution genetic analysis with the developmental/molecular approaches currently used in other organisms. Early results document significant differences between insect orders in the functions of genes responsible for establishing developmental commitments.

NASA Program NSCORT↗
DOE OSTI2021

Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions

Abstract Early evolution of mutualism is characterized by big and predictable adaptive changes, including the specialization of interacting partners, such as through deleterious mutations in genes not required for metabolic cross-feeding. We sought to investigate whether these early mutations improve cooperativity by manifesting in synergistic epistasis between genomes of the mutually interacting species. Specifically, we have characterized evolutionary trajectories of syntrophic interactions of Desulfovibrio vulgaris (Dv) with Methanococcus maripaludis (Mm) by longitudinally monitoring mutations accumulated over 1000 generations of nine independently evolved communities with analysis of the genotypic structure of one community down to the single-cell level. We discovered extensive parallelism across communities despite considerable variance in their evolutionary trajectories and the perseverance within many evolution lines of a rare lineage of Dv that retained sulfate-respiration (SR+) capability, which is not required for metabolic cross-feeding. An in-depth investigation revealed that synergistic epistasis across pairings of Dv and Mm genotypes had enhanced cooperativity within SR− and SR+ assemblages, enabling their coexistence within the same community. Thus, our findings demonstrate that cooperativity of a mutualism can improve through synergistic epistasis between genomes of the interacting species, enabling the coexistence of mutualistic assemblages of generalists and their specialized variants.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2000

A DNA enzyme with N-glycosylase activity

In vitro evolution was used to develop a DNA enzyme that catalyzes the site-specific depurination of DNA with a catalytic rate enhancement of about 10(6)-fold. The reaction involves hydrolysis of the N-glycosidic bond of a particular deoxyguanosine residue, leading to DNA strand scission at the apurinic site. The DNA enzyme contains 93 nucleotides and is structurally complex. It has an absolute requirement for a divalent metal cation and exhibits optimal activity at about pH 5. The mechanism of the reaction was confirmed by analysis of the cleavage products by using HPLC and mass spectrometry. The isolation and characterization of an N-glycosylase DNA enzyme demonstrates that single-stranded DNA, like RNA and proteins, can form a complex tertiary structure and catalyze a difficult biochemical transformation. This DNA enzyme provides a new approach for the site-specific cleavage of DNA molecules.

Non-NASA Center↗
NASA NTRS1984

Quantum chemical studies of a model for peptide bond formation. 3. Role of magnesium cation in formation of amide and water from ammonia and glycine

The SN2 reaction between glycine and ammonia molecules with magnesium cation Mg2+ as a catalyst has been studied as a model reaction for Mg(2+)-catalyzed peptide bond formation using the ab initio Hartree-Fock molecular orbital method. As in previous studies of the uncatalyzed and amine-catalyzed reactions between glycine and ammonia, two reaction mechanisms have been examined, i.e., a two-step and a concerted reaction. The stationary points of each reaction including intermediate and transition states have been identified and free energies calculated for all geometry-optimized reaction species to determine the thermodynamics and kinetics of each reaction. Substantial decreases in free energies of activation were found for both reaction mechanisms in the Mg(2+)-catalyzed amide bond formation compared with those in the uncatalyzed and amine-catalyzed amide bond formation. The catalytic effect of the Mg2+ cation is to stabilize both the transition states and intermediate, and it is attributed to the neutralization of the developing negative charge on the electrophile and formation of a conformationally flexible nonplanar five-membered chelate ring structure.

Magnesium/chemistry↗
DOE OSTI2022

Knockout of ABC transporter gene ABCA2 confers resistance to Bt toxin Cry2Ab in Helicoverpa zea

Evolution of pest resistance reduces the benefits of widely cultivated genetically engineered crops that produce insecticidal proteins derived from Bacillus thuringiensis (Bt). Better understanding of the genetic basis of pest resistance to Bt crops is needed to monitor, manage, and counter resistance. Previous work shows that in several lepidopterans, resistance to Bt toxin Cry2Ab is associated with mutations in the gene encoding the ATP-binding cassette protein ABCA2. The results here show that mutations introduced by CRISPR/Cas9 gene editing in the Helicoverpa zea (corn earworm or bollworm) gene encoding ABCA2 (HzABCA2) can cause resistance to Cry2Ab. Disruptive mutations in HzABCA2 facilitated the creation of two Cry2Ab-resistant strains. A multiple concentration bioassay with one of these strains revealed it had > 200-fold resistance to Cry2Ab relative to its parental susceptible strain. All Cry2Ab-resistant individuals tested had disruptive mutations in HzABCA2. We identified five disruptive mutations in HzABCA2 gDNA. The most common mutation was a 4-bp deletion in the expected Cas9 guide RNA target site. The results here indicate that HzABCA2 is a leading candidate for monitoring Cry2Ab resistance in field populations of H. zea.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

The role of zinc in the adaptive evolution of polar phytoplankton

Zinc is an essential trace metal for oceanic primary producers with the highest concentrations in polar oceans. However, its role in the biological functioning and adaptive evolution of polar phytoplankton remains enigmatic. Here, we have applied a combination of evolutionary genomics, quantitative proteomics, co-expression analyses and cellular physiology to suggest that model polar phytoplankton species have a higher demand for zinc because of elevated cellular levels of zinc-binding proteins. We propose that adaptive expansion of regulatory zinc-finger protein families, co-expanded and co-expressed zinc-binding proteins families involved in photosynthesis and growth in these microalgal species and their natural communities were identified to be responsible for the higher zinc demand. The expression of their encoding genes in eukaryotic phytoplankton metatranscriptomes from pole-to-pole was identified to correlate not only with dissolved zinc concentrations in the upper ocean but also with temperature, suggesting that environmental conditions of polar oceans are responsible for an increased demand of zinc. Furthermore, these results suggest that zinc plays an important role in supporting photosynthetic growth in eukaryotic polar phytoplankton and that this has been critical for algal colonization of low-temperature polar oceans.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1999

Life: past, present and future

Molecular methods of taxonomy and phylogeny have changed the way in which life on earth is viewed; they have allowed us to transition from a eukaryote-centric (five-kingdoms) view of the planet to one that is peculiarly prokarote-centric, containing three kingdoms, two of which are prokaryotic unicells. These prokaryotes are distinguished from their eukaryotic counterparts by their toughness, tenacity and metabolic diversity. Realization of these features has, in many ways, changed the way we feel about life on earth, about the nature of life past and about the possibility of finding life elsewhere. In essence, the limits of life on this planet have expanded to such a degree that our thoughts of both past and future life have been altered. The abilities of prokaryotes to withstand many extreme conditions has led to the term extremophiles, used to describe the organisms that thrive under conditions thought just a few years ago, to be inconsistent with life. Perhaps the most extensive adaptation to extreme conditions, however, is represented by the ability of many bacteria to survive nutrient conditions not compatible with eukaryotic life. Prokaryotes have evolved to use nearly every redox couple that is in abundance on earth, filling the metabolic niches left behind by the oxygen-using, carbon-eating eukaryotes. This metabolic plasticity leads to a common feature in physically stratified environments of layered microbial communities, chemical indicators of the metabolic diversity of the prokaryotes. Such 'metabolic extremophily' forms a backdrop by which we can view the energy flow of life on this planet, think about what the evolutionary past of the planet might have been, and plan ways to look for life elsewhere, using the knowledge of energy flow on earth.

NASA Discipline Developmental Biology↗
NASA NTRS2003

Impacts and evolution: future prospects

The discipline of astrobiology includes the dynamics of biological evolution. One of the major ways that the cosmos influences life is through the catastrophic environmental disruptions caused when comets and asteroids collide with a planet. We now recognize that such impacts have caused mass extinctions and played a major role in determining the evolution of life on Earth. The time-averaged impact flux as a function of projectile energy can be derived from lunar cratering statistics as well as the current population of near Earth asteroids (NEAs). Effects of impacts of various energies can be modeled, using data from historic impacts [such as the Cretaceous-Tertiary (KT) impactor 65 million years ago] and the observed 1994 bombardment of Jupiter by fragments of Comet Shoemaker-Levy 9. It is of particular interest to find from such models that the terrestrial environment is highly vulnerable to perturbation from impacts, so that even such a small event as the KT impact (by a projectile 10-15 km in diameter) can lead to a mass extinction. Similar considerations allow us to model the effects of still smaller (and much more likely) impacts, down to the size of the asteroid that exploded over Tunguska in 1908 (energy approximately 10 megatons). Combining the impact flux with estimates of environmental and ecological effects reveals that the greatest contemporary hazard is associated with impactors near 1 million megatons in energy (approximately 2 km in diameter for an asteroid). The current impact hazard is significant relative to other natural hazards, and arguments can be developed to illuminate a variety of public policy issues. The first priority in any plan for defense against impactors is to survey the population of Earth-crossing NEAs and project their orbits forward in time. This is the purpose of the Spaceguard Survey, which has already found more than half of the NEAs >1 km in diameter. If there is an NEA on a collision course with Earth, it can be discovered and the impact predicted with decades or more of warning. It is then possible to consider how to deflect or disrupt the NEA. Unlike other natural hazards, the impact risk can be largely eliminated, given sufficient advanced knowledge to take action against the threatening projectile.

Directed Molecular Evolution↗
DOE OSTI2023

Progressive evolutions of non-fused ring electron acceptors toward efficient organic solar cells with improved photocurrent and reduced energy loss

Resolving competitive counterbalance between high external quantum efficiency (EQE) response and low energy loss is critical for achieving efficient organic solar cells (OSCs), including those based on low-cost non-fused-ring electron acceptor (NFREA). In this work, we performed a comparable study by utilizing four NFREAs with progressive evolutions in molecular structures, energetic levels, spectral coverages, crystallinity, etc, to pair with polymer donor J52. By regulating the terminal and side chains of NFREAs, the enhanced intramolecular charge transfer (ICT) effect allows O-PC-EH possessing the broader spectral coverage for higher photocurrent, the reduced energetic offset enables O-PC-EH-based device owning higher luminescence property for lower energy loss, the strengthened crystallinity endows O-PC-EH-based blend better charge transport property for less charge recombination. With those comprehensive managements from molecule to blend properties, the J52:O-PC-EH-based OSCs achieved the best efficiency of 14.4% (certified: 14.1%) with benefits in all the three device parameters. Here, this work reveals the importance of fine-tuning molecular structures of NFREAs according to paired polymer donor for maximizing the device performances.

14 SOLAR ENERGY↗
DOE OSTI2020

Spatially Offset Femtosecond Stimulated Raman Spectroscopy: Observing Exciton Transport through a Vibrational Lens

To design better molecular electronic devices, we need a strong understanding of how charges or excitons propagate, as many efficiency losses arise during transport. Exciton transport has been difficult to study because excitons tend to be short-lived, have short diffusion lengths, and can easily recombine. Here, we debut spatially offset femtosecond stimulated Raman spectroscopy (SO-FSRS), a three-pulse ultrafast microscopy technique. By offsetting the photoexcitation beam, we can monitor Raman spectral changes as a function of both time and position. We used SO-FSRS on 6,13-bis(triisopropylsilylethynyl) pentacene, a well-studied organic semiconductor used in photovoltaics and field-effect transistors. Furthermore, we demonstrated that the fast exciton and free charge carrier transport axes are identical and observed that exciton transport is less anisotropic by a factor of ~3. SO-FSRS is the first technique that directly tracks molecular structural evolution during exciton transport, which can provide roadmaps for tailor-making molecules for specific electronic devices.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Nanobubble Formation and Coverage during High Current Density Alkaline Water Electrolysis

Gas bubbles are a necessary byproduct of water electrolysis whereby hydrogen and oxygen are produced from water. These attached gases reduce the electrode’s active area, which necessitates a deep understanding of the bubble life cycle starting from nanobubbles. Synchronized with the electrochemistry, the time evolution of the surface nanobubble size and coverage is resolved using grazing incidence small-angle X-ray scattering (GISAXS) and correlated with optical microscopy and theoretical calculations to show that a significant portion of the surface is covered in nanobubbles after larger micron-sized bubbles are observed. Further, these nanobubbles increase in number and decrease in size, toward 2 nm diameter, with the charge passed. The trend in size and number is consistent with an increase in supersaturation, which reduces the nascent bubble size. Altogether, this study suggests a significant portion of the surface contains nanobubbles and that strategies to reduce the dissolved hydrogen would be effective at reducing the nanobubble surface coverage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Unraveling Triplet Formation Mechanisms in Acenothiophene Chromophores

The evolution of molecular platforms for singlet fission (SF) chromophores has fueled the quest for new compounds capable of generating triplets quantitatively at fast time scales. As the exploration of molecular motifs for SF has diversified, a key challenge has emerged in identifying when the criteria for SF have been satisfied. Here, we show how covalently bound molecular dimers uniquely provide a set of characteristic optical markers that can be used to distinguish triplet pair formation from processes that generate an individual triplet. These markers are contained within (i) triplet charge-transfer excited state absorption features, (ii) kinetic signatures of triplet-triplet annihilation processes, and (iii) the modulation of triplet formation rates using bridging moieties between chromophores. Our assignments are verified by time-resolved electron paramagnetic resonance (EPR) measurements, which directly identify triplet pairs by their electron spin and polarization patterns. Here we apply these diagnostic criteria to dimers of acenothiophene derivatives in solution that were recently reported to undergo efficient intermolecular SF in condensed media. While the electronic structure of these heteroatom-containing chromophores can be broadly tuned, the effect of their enhanced spin-orbit coupling and low-energy nonbonding orbitals on their SF dynamics has not been fully determined. We find that SF is fast and efficient in tetracenothiophene but that anthradithiophene exhibits fast intersystem crossing due to modifications of the singlet and triplet excited state energies upon functionalization of the heterocycle. We conclude that it is not sufficient to assign SF based on comparisons of the triplet formation kinetics between monomer and multichromophore systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Common origin of sterol biosynthesis points to a feeding strategy shift in Neoproterozoic animals

Steranes preserved in sedimentary rocks serve as molecular fossils, which are thought to record the expansion of eukaryote life through the Neoproterozoic Era (~1000-541 Ma). Scientists hypothesize that ancient C 27 steranes originated from cholesterol, the major sterol produced by living red algae and animals. Similarly, C 28 and C 29 steranes are thought to be derived from the sterols of prehistoric fungi, green algae, and other microbial eukaryotes. However, recent work on annelid worms–an advanced group of eumetazoan animals–shows that they are also capable of producing C 28 and C 29 sterols. In this paper, we explore the evolutionary history of the 24-C sterol methyltransferase (smt) gene in animals, which is required to make C 28+ sterols. We find evidence that the smt gene was vertically inherited through animals, suggesting early eumetazoans were capable of C 28+ sterol synthesis. Our molecular clock of the animal smt gene demonstrates that its diversification coincides with the rise of C 28 and C 29 steranes in the Neoproterozoic. This study supports the hypothesis that early eumetazoans were capable of making C 28+ sterols and that many animal lineages independently abandoned its biosynthesis around the end-Neoproterozoic, coinciding with the rise of abundant eukaryotic prey.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Ultrahigh-pressure crystallographic passage towards metallic hydrogen

The structural evolution of molecular hydrogen H 2 under multi-megabar compression and its relation to atomic metallic hydrogen is a key unsolved problem in condensed-matter physics. Although dozens of crystal structures have been proposed by theory, only one, the simple hexagonal-close-packed (hcp) structure of only spherical disordered H 2 , has been previously confirmed in experiments. Through advancing nano-focused synchrotron X-ray probes, here we report the observation of the transition from hcp H 2 to a post-hcp structure with a six-fold larger supercell at pressures above 212 GPa, indicating the change of spherical H 2 to various ordered configurations. Theoretical calculations based on our XRD results found a time-averaged structure model in the space group $P\bar{6}2c$ with alternating layers of spherically disordered H 2 and new graphene-like layers consisting of H 2 trimers (H 6 ) formed by the association of three H 2 molecules. Here, this supercell has not been reported by any previous theoretical study for the post-hcp phase, but is close to a number of theoretical models with mixed-layer structures. The evidence of a structural transition beyond hcp establishes the trend of H 2 molecular association towards polymerization at extreme pressures, giving clues about the nature of the molecular-to-atomic transition of metallic hydrogen. Considering the spectroscopic behaviours that show strong vibrational and bending peaks of H 2 up to 400 GPa, it would be prudent to speculate the continuation of hydrogen molecular polymerization up to its metallization.

Ji, Cheng [Center for High Pressure Science and Te↗
DOE OSTI2020

Anoxic photogeochemical oxidation of manganese carbonate yields manganese oxide

The oxidation states of manganese minerals in the geological record have been interpreted as proxies for the evolution of molecular oxygen in the Archean eon. In this paper we report that an Archean manganese mineral, rhodochrosite (MnCO 3 ), can be photochemically oxidized by light under anoxic, abiotic conditions. Rhodochrosite has a calculated bandgap of about 5.4 eV, corresponding to light energy centering around 230 nm. Light at that wavelength would have been present on Earth’s surface in the Archean, prior to the formation of stratospheric ozone. We show experimentally that the photooxidation of rhodochrosite in suspension with light centered at 230 nm produced H 2 gas and manganite (γ-MnOOH) with an apparent quantum yield of 1.37 × 10 –3 moles hydrogen per moles incident photons. Our results suggest that manganese oxides could have formed abiotically on the surface in shallow waters and on continents during the Archean eon in the absence of molecular oxygen.

58 GEOSCIENCES↗
DOE OSTI2024

Evolution and persistence of SiO emission in nanosecond laser ablation plumes

Analyzing laser-produced plasmas in a controlled oxygen-containing environment provides insight into the formation and evolution of molecular species through gas-phase oxidation. This study explores the role of ambient pressure and oxygen availability in forming SiO molecular species in laser ablation plumes. The self-emission emanating during the reactive ablation of Si targets was characterized by optical emission spectroscopy and optical time-of-flight techniques. Our results showed that the SiO species formation was greatly influenced by both the ambient pressure and oxygen availability. The intensity and the persistence of SiO emission bands are lower at higher oxygen concentrations, indicating they are depopulated by the formation of more complex silicon oxides. The oxygen partial pressure effects on plume chemistry showed that SiO formation is favored even with a minimal oxygen concentration in the environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Genomic factors shaping codon usage across the Saccharomycotina subphylum

Codon usage bias, or the unequal use of synonymous codons, is observed across genes, genomes, and between species. It has been implicated in many cellular functions, such as translation dynamics and transcript stability, but can also be shaped by neutral forces. We characterized codon usage across 1,154 strains from 1,051 species from the fungal subphylum Saccharomycotina to gain insight into the biases, molecular mechanisms, evolution, and genomic features contributing to codon usage patterns. We found a general preference for A/T-ending codons and correlations between codon usage bias, GC content, and tRNA-ome size. Codon usage bias is distinct between the 12 orders to such a degree that yeasts can be classified with an accuracy >90% using a machine learning algorithm. We also characterized the degree to which codon usage bias is impacted by translational selection. We found it was influenced by a combination of features, including the number of coding sequences, BUSCO count, and genome length. Our analysis also revealed an extreme bias in codon usage in the Saccharomycodales associated with a lack of predicted arginine tRNAs that decode CGN codons, leaving only the AGN codons to encode arginine. Analysis of Saccharomycodales gene expression, tRNA sequences, and codon evolution suggests that avoidance of the CGN codons is associated with a decline in arginine tRNA function. Consistent with previous findings, codon usage bias within the Saccharomycotina is shaped by genomic features and GC bias. However, we find cases of extreme codon usage preference and avoidance along yeast lineages, suggesting additional forces may be shaping the evolution of specific codons.

59 BASIC BIOLOGICAL SCIENCES↗