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At least 109 records · Page 6

Ryugu Asteroid Sample Return Provides A Natural Laboratory for Primordial Chemical Evolution

The samples returned from near-Earth asteroid (162173) Ryugu provide a pristine record of the 4.6 billion years since the birth of the Solar System. The Hayabusa2 initial analysis team has integrated a range of analytical techniques to investigate Ryugu’s organic chemistry. Here, we highlight their latest findings, the potential questions which may be answered, and provide an overview of new prospects in the decade to come.

Asteroids↗

Impacts of object-oriented technologies: Seven years of SEL studies

This paper examines the premise that object-oriented technology (OOT) is the most significant technology ever examined by the Software Engineering Laboratory. The evolution of the use of OOT in the Software Engineering Laboratory (SEL) 'Experience Factory' is described in terms of the SEL's original expectations, focusing on how successive generations of projects have used OOT. General conclusions are drawn on how the usage of the technology has evolved in this environment.

Stark, Mike↗

Search for Primitive Matter in the Solar System

Recent astronomical observations and theoretical modeling led to a consensus regarding the global scenario of the formation of young stellar objects (YSO) from a cold molecular cloud of interstellar dust (organics and minerals) and gas that, in some cases, leads to the formation of a planetary system. In the case of our Solar System, which has already evolved for approximately 4567 Ma, the quest is to access, through the investigation of planets, moons, cometary and asteroidal bodies, meteorites, micrometeorites, and interplanetary dust particles, the primitive material that contains the key information about the early Solar System processes and its evolution. However, laboratory analyses of extraterrestrial samples, astronomical observations and dynamical models of the Solar System evolution have not brought yet any conclusive evidence on the nature and location of primitive matter in the Solar System, preventing a clear understanding of its early stages.

Libourel, G.↗

Laboratory Astrophysics Studies of the Evolution of Organic Matter with the COSmIC Facility.

Understanding the origin of organic matter in astrophysical environments ranging from circumstellar (CS) outflows to diffuse and dense interstellar (IS) clouds to protoplanetary disks and planetary bodies has become a central objective in astrophysics. Experimental facilities dedicated to the formation and characterization of laboratory analogs generated under conditions relevant to the targeted environments have been developed in the past recent years. Recent advances achieved in laboratory astrophysics using COSmIC’s laboratory data in synergy with observational data will be presented. These results include the use of laboratory spectra to search for IS organic molecules and ions in astronomical spectra, the formation of laboratory analogs of CS and IS dust grains and planetary atmospheres aerosols from molecular precursors.

Salama, Farid↗

Laboratory for Atmospheres 2002 Technical Highlights

How can we improve our ability to predict the weather-tomorrow, next week, and into the future? How is the Earth's climate changing? What causes such change? And what are its costs? What can the atmospheres of distant planets teach us about our own planet and its evolution? The Laboratory for Atmospheres is helping to answer these and other scientific questions about our planet and its neighbors. The Laboratory conducts a broad theoretical and experimental research program studying all aspects of the atmospheres of the Earth and other planets, including their structural, dynamical, radiative, and chemical properties, with the overarching goal to provide better understanding and to improve prediction of the Earth's climate. Vigorous research is central to NASA's exploration of the frontiers of knowledge. NASA scientists play a key role in conceiving new space missions, providing mission requirements, and carrying out research to explore the behavior of planetary systems, including, notably, the Earth's. Our Laboratory's scientists also supply outside scientists with technical assistance and scientific data to further investigations not immediately addressed by NASA itself. Laboratory scientists submit competitive research proposals with diverse scientific or technological approaches to NASA and other Federal agencies to acquire research support. The Laboratory management strives to provide a working environment that promotes creativity, competition, and openness. The Laboratory for Atmospheres is a vital participant in NASA's research program. Our Laboratory often has relatively large programs, sizable satellite missions, or observational campaigns that require the cooperative and collaborative efforts of many scientists. We ensure an appropriate balance between our scientists' responsibility for these large collaborative projects and their need for an active individual research agenda. This balance allows members of the Laboratory to continuously improve their scientific credentials. The Laboratory places high importance on promoting and measuring quality in its scientific research. We strive to assure high quality through peer-review funding processes that support approximately 90% of the work in the Laboratory. The overall quality of our scientific efforts is evaluated periodically by committees of advisors from the external scientific community, as detailed in Appendix 2 of this document. Members of the Laboratory interact with the general public to support a wide range of interests in the atmospheric sciences. Among other activities, the Laboratory raises the public's awareness of atmospheric science by presenting public lectures and demonstrations, by making scientific data available to wide audiences, by teaching, and by mentoring students and teachers. Section 6 presents details of the Laboratory's outreach activities during 2002. The Laboratory is also committed to addressing the demographic imbalances that exist today in the atmospheric and space sciences. We must address these imbalances for our field to enjoy the full benefit of all of the Nation's talent. The Laboratory makes substantial efforts to attract new scientists to the fields of atmospheric and space sciences. We strongly encourage the establishment of partnerships with Federal and state agencies that have operational responsibilities to promote the societal application of Earth sciences.

Steven E. Platnick↗

Foreshock properties illuminate nucleation processes of slow and fast laboratory earthquakes

Understanding the connection between seismic activity and the earthquake nucleation process is a fundamental goal in earthquake seismology with important implications for earthquake early warning systems and forecasting. We use high-resolution acoustic emission (AE) waveform measurements from laboratory stick-slip experiments that span a spectrum of slow to fast slip rates to probe spatiotemporal properties of laboratory foreshocks and nucleation processes. We measure waveform similarity and pairwise differential travel-times (DTT) between AEs throughout the seismic cycle. AEs broadcasted prior to slow labquakes have small DTT and high waveform similarity relative to fast labquakes. We show that during slow stick-slip, the fault never fully locks, and waveform similarity and pairwise differential travel times do not evolve throughout the seismic cycle. In contrast, fast laboratory earthquakes are preceded by a rapid increase in waveform similarity late in the seismic cycle and a reduction in differential travel times, indicating that AEs begin to coalesce as the fault slip velocity increases leading up to failure. These observations point to key differences in the nucleation process of slow and fast labquakes and suggest that the spatiotemporal evolution of laboratory foreshocks is linked to fault slip velocity.

58 GEOSCIENCES↗

RNAseq data for P. putida with vanillate

Illumina sequencing reads from RNA sequencing of vanillate-utilizing strains of Pseudomonas putida, described in Evolution and engineering of pathways for aromatic O-demethylation in Pseudomonas putida KT2440 by A. Bleem, et al. (2024)

Adaptive laboratory evolution↗

Rewiring yeast metabolism to synthesize products beyond ethanol

Saccharomyces cerevisiae, Baker's yeast, is the industrial workhorse for producing ethanol and the subject of substantial metabolic engineering research in both industry and academia. S. cerevisiae has been used to demonstrate production of a wide range of chemical products from glucose. However, in many cases, the demonstrations report titers and yields that fall below thresholds for industrial feasibility. Ethanol synthesis is a central part of S. cerevisiae metabolism, and redirecting flux to other products remains a barrier to industrialize strains for producing other molecules. Furthermore, removing ethanol producing pathways leads to poor fitness, such as impaired growth on glucose. Here, we review metabolic engineering efforts aimed at restoring growth in non-ethanol producing strains with emphasis on relieving glucose repression associated with the Crabtree effect and rewiring metabolism to provide access to critical cellular building blocks. Finally, substantial progress has been made in the past decade, but many opportunities for improvement remain.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Crabtree/Warburg-like aerobic xylose fermentation by engineered Saccharomyces cerevisiae

Bottlenecks in the efficient conversion of xylose into cost-effective biofuels have limited the widespread use of plant lignocellulose as a renewable feedstock. The yeast Saccharomyces cerevisiae ferments glucose into ethanol with such high metabolic flux that it ferments high concentrations of glucose aerobically, a trait called the Crabtree/Warburg Effect. In contrast to glucose, most engineered S. cerevisiae strains do not ferment xylose at economically viable rates and yields, and they require respiration to achieve sufficient xylose metabolic flux and energy return for growth aerobically. Here, we evolved respiration-deficient S. cerevisiae strains that can grow on and ferment xylose to ethanol aerobically, a trait analogous to the Crabtree/Warburg Effect for glucose. Through genome sequence comparisons and directed engineering, we determined that duplications of genes encoding engineered xylose metabolism enzymes, as well as TKL1, a gene encoding a transketolase in the pentose phosphate pathway, were the causative genetic changes for the evolved phenotype. Reengineered duplications of these enzymes, in combination with deletion mutations in HOG1, ISU1, GRE3, and IRA2, increased the rates of aerobic and anaerobic xylose fermentation. Importantly, we found that these genetic modifications function in another genetic background and increase the rate and yield of xylose-to-ethanol conversion in industrially relevant switchgrass hydrolysate, indicating that these specific genetic modifications may enable the sustainable production of industrial biofuels from yeast. We propose a model for how key regulatory mutations prime yeast for aerobic xylose fermentation by lowering the threshold for overflow metabolism, allowing mutations to increase xylose flux and to redirect it into fermentation products.

59 BASIC BIOLOGICAL SCIENCES↗

Computational Design of Synthetic Enzymes

We review the standard model for de novo computational design of enzymes, which primarily focuses on the development of an active-site geometry, composed of protein functional groups in orientations optimized to stabilize the transition state, for a novel chemical reaction not found in nature. Its emphasis is placed on the structure and energetics of the active site embedded in an accommodating protein that serves as a physical support that shields the reaction chemistry from solvent, which is typically improved upon by laboratory-directed evolution. We also provide a review of design strategies that move beyond the standard model, by placing more emphasis on the designed enzyme as a whole catalytic construct. Starting with complete de novo enzyme design examples, we consider additional design factors such as entropy of individual residues, correlated motion between side chains (mutual information), dynamical correlations of the enzyme motions that could aid the reaction, reorganization energy, and electric fields as ways to exploit the entire protein scaffold to improve upon the catalytic rate, thereby providing directed evolution with better starting sequences for increasing biocatalytic performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Solvent Entropy Contributions to Catalytic Activity in Designed and Optimized Kemp Eliminases

This work reports on the role of solvation for enzymatic catalysis in two distinct, artificially designed Kemp Eliminases, KE07 and KE70, and mutated variants that were optimized by laboratory directed evolution. Using a spatially resolved analysis of hydration patterns, intermolecular vibrations, and local solvent entropies, we identify distinct classes of hydration water and follow their changes upon substrate binding and transition state formation for the designed KE07 and KE70 enzymes and their evolved variants. We observe that differences in hydration of the enzymatic systems are concentrated in the active site and undergo significant changes during substrate recruitment. For KE07, directed evolution reduces variations in the hydration of the polar catalytic center upon substrate binding, preserving strong protein-water interactions, while the evolved enzyme variant of KE70 features a more hydrophobic reaction center for which the expulsion of low-entropy water molecules upon substrate binding is substantially enhanced. While our analysis suggests a system-dependent role of solvation for the substrate binding process, we identify more subtle changes in solvation for the transition state formation, which are less affected by directed evolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Proteomes reveal metabolic capabilities of Yarrowia lipolytica for biological upcycling of polyethylene into high-value chemicals

ABSTRACT Polyolefins derived from plastic wastes are recalcitrant for biological upcycling. However, chemical depolymerization of polyolefins can generate depolymerized plastic (DP) oil, comprising of a complex mixture of saturated, unsaturated, even, and odd hydrocarbons suitable for biological conversion. While DP oil contains a rich carbon and energy source, it is inhibitory to cells. Understanding and harnessing robust metabolic capabilities of microorganisms to upcycle the hydrocarbons in DP oil, both naturally and unnaturally occurring, into high-value chemicals are limited. Here, we discovered that an oleaginous yeast, Yarrowia lipolytica, undergoing short-term adaptation to DP oil robustly utilized a wide range of hydrocarbons for cell growth and production of citric acid and neutral lipids. When growing on hydrocarbons, Y. lipolytica partitioned into planktonic and oil-bound cells with each exhibiting distinct proteomes and amino acid distributions invested in establishing these proteomes. Significant proteome reallocation toward energy and lipid metabolism, belonging to 2 of the 23 Eukaryotic Orthologous Groups classes C and I, enabled robust growth of Y. lipolytica on hydrocarbons, with n-hexadecane as the preferential substrate. This investment was even higher for growth on DP oil where classes C and I were ranked one and two, respectively, and many associated proteins and pathways were expressed and upregulated including the hydrocarbon degradation pathway, Krebs cycle, glyoxylate shunt and, unexpectedly, propionate metabolism. However, a reduction in proteome allocation for protein biosynthesis, at the expense of the observed increase toward energy and lipid metabolisms, might have caused the inhibitory effect of DP oil on cell growth. IMPORTANCE Sustainable processes for biological upcycling of plastic wastes in a circular bioeconomy are needed to promote decarbonization and reduce environmental pollution due to increased plastic consumption, incineration, and landfill storage. Strain characterization and proteomic analysis revealed the robust metabolic capabilities of Yarrowia lipolytica to upcycle polyethylene into high-value chemicals. Significant proteome reallocation toward energy and lipid metabolisms was required for robust growth on hydrocarbons with n-hexadecane as the preferential substrate. However, an apparent over-investment in these same categories to utilize complex depolymerized plastic (DP) oil came at the expense of protein biosynthesis, limiting cell growth. Taken together, this study elucidates how Y. lipolytica activates its metabolism to utilize DP oil and establishes Y. lipolytica as a promising host for the upcycling of plastic wastes.

1-alkenes↗

From Cryogenic to High Temperatures: A Microstructural Evolution of δ-phase Pu-Ga Alloys Investigated by Time-of-Flight High-resolution Neutron Diffraction

Phase stability and phase transformations in binary Pu alloys are critical for multiple applications. Long-term phase stability affects mechanical properties, microstructure, corrosion behavior, and structural integrity. A clear and detailed understanding of phase transformations and phase stability mechanisms is necessary to assess the behavior and response to unexpected stimuli. Gaining advanced knowledge on the behavior of Pu and Pu alloys at a variety of temperatures, pressures, and time will ensure better predictions and control on evolution outside laboratory measurements.

36 MATERIALS SCIENCE↗

Applied genomics for industrially relevant microalgal strain development & optimization: characterizing genotype-phenotype relationships towards scalable environment-enhancing energy systems

Multiple planetary boundaries considered a safe operating space for humanity have been exceeded in recent years, with twice as many boundaries transgressed in 2023 as in 2009. Bioenergy systems are unique in that they can interact with and improve many of the transgressed boundaries directly, including multiple geochemical cycles, water and land use, and climate change. Among bioenergy systems, microalgae-based environment enhancing energy (E 2 -energy) are promising bioenergy systems for drop-in biofuels, valuable materials, chemicals and therapeutics, while making deep emission cuts and remediating wastewater, all without competing for agricultural resources.

09 BIOMASS FUELS↗