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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Multimodal Approaches for Leveraging Domain Knowledge with State-of-the-Art Machine Learning to Engineer Biocatalysts

This grant aimed to accelerate the development of specialized enzymes—biological catalysts essential for sustainable manufacturing and medicine—by integrating traditional laboratory evolution with cutting-edge artificial intelligence. To achieve this, we developed a suite of high-throughput sequencing tools and a centralized database to bridge the gap between a protein’s genetic "code" and its physical function. By training machine learning models on large datasets, we also demonstrated the ability to move beyond slow, trial-and-error testing to a "generative" approach, where AI can independently design new, versatile enzymes like tryptophan synthases. Ultimately, these findings demonstrate that combining laboratory data with computer-guided design enables the engineering of highly efficient biological tools with unprecedented speed and precision.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Understanding and Harnessing the Robustness of Undomesticated Yarrowia lipolytica Strains for Biosynthesis of Designer Bioesters (Final Report)

This project seeks to elucidate and harness the exceptional robustness of novel and undomesticated Y. lipolytica isolates, which were identified from a genetic diversity screening for compatibility with bioenergy development. Bioenergy-relevant isolates were further developed as microbial platforms for efficient conversion of undetoxified biomass hydrolysates into designer bio-esters continuously recovered by solvent extraction. The project has three major goals. Goal 1. Elucidate and enhance the endogenous metabolism of Y. lipolytica for superior growth, sugar utilization, and lipid accumulation in undetoxified biomass hydrolysates under hypoxic conditions. Goal 2. Understand and enhance the underlying mechanism of exceptional tolerance of Y. lipolytica to organic solvents. Goal 3. Elucidate and rewire endogenous metabolism of the most robust Y. lipolytica strains for effective conversion of accumulating lipids to designer bio-esters. Significant progress has been made toward completing all research goals. We elucidated and optimized the robustness of Y. lipolytica by utilizing mixed C5 and C6 sugars in switchgrass hydrolysates (SGH) for lipid production (Aim 1). We conducted extensive omics analysis to investigate how genetic diversity among Yarrowia strains, derived from natural isolates or developed through adaptive laboratory evolution, influences lipid production when utilizing SGH. In Aim 2, novel mechanisms and underlying genetics were discovered that enabled Yarrowia strains to thrive in cultures containing high ionic liquid (IL) concentrations. Amongst other novel findings, it was found that sterols strengthened cell membranes to confer IL toxicity resistance, specifically via increased ergosterol content upon exposure to IL. In Aim 3, mechanistic studies elucidated how Y. lipolytica utilized intracellular lipids and alkanes/alkenes, leading to our discovery of novel enzymes and pathways for making short-chain esters. Most notably, thermostable chloramphenicol transferases were repurposed to function as alcohol acetyltransferases in Y. lipolytica, as well as the Gram-negative and Gram-positive bacteria Escherichia coli and thermophile Clostridium thermocellum, respectively.

09 BIOMASS FUELS↗
DOE OSTI2025

MarK, a Novosphingobium aromaticivorans kinase required for catabolism of multiple aromatic monomers

The aromatic compounds used in a variety of industrial products are currently obtained from nonrenewable petroleum sources. Alternatively, the plant polymer lignin is an abundant renewable source of aromatics, and its depolymerization generates a variety of products that can include acetovanillone, a vanillin derivative containing an acetyl side chain. The Alphaproteobacterium Novosphingobium aromaticivorans DSM12444 can metabolize several chemically modified aromatics in deconstructed lignin, but not acetovanillone. In this work, adaptive laboratory evolution identified a single amino acid change in the previously uncharacterized gene product Saro_1862 that is necessary and sufficient for N. aromaticivorans growth with acetovanillone as a sole growth substrate, as well as other aromatic monomers not metabolized by wild-type cells. We show that a glutamate (E) to lysine (K) substitution at amino acid residue 16 of Saro_1862 results in a ~1600-fold increase in the rate of ATP-dependent acetovanillone phosphorylation. We also find that recombinant Saro_1862 E16K phosphorylates several other aromatic compounds in vitro , defining the first reported catalytic activity for the widespread UPF0261 protein domain contained in Saro_1862. Thus, we propose naming Saro_1862 MarK, for multiple aromatic kinase. A 1.57 Å crystal structure of MarK E16K predicts that the E16K substitution lies in a potential ATP binding site, suggesting how this amino acid change increased catalytic activity. A search for homologs of MarK and other proteins required for acetovanillone degradation predicts that this pathway for aromatic metabolism exists throughout the bacterial phylogeny.

Novosphingobium↗
DOE OSTI2025

Engineering controllable alteration of malonyl-CoA levels to enhance polyketide production

Heterologous expression of polyketide synthase (PKS) genes in Escherichia coli has enabled the production of various valuable natural and synthetic products. However, the limited availability of malonyl-CoA (M-CoA) in E. coli remains a substantial impediment to high-titer polyketide production. Here we address this limitation by disrupting the native M-CoA biosynthetic pathway and introducing an orthogonal pathway comprising a malonate transporter and M-CoA ligase, enabling efficient M-CoA biosynthesis under malonate supplementation. This approach substantially increases M-CoA levels, enhancing fatty acid and polyketide titers while reducing the promiscuous activity of PKSs toward undesired acyl-CoA substrates. Subsequent adaptive laboratory evolution of these strains provides insights into M-CoA regulation and identifies mutations that further boost M-CoA and polyketide production. This strategy improves E. coli as a host for polyketide biosynthesis and advances understanding of M-CoA metabolism in microbial systems.

Klass, Sarah H↗
DOE OSTI2024

Application of functional genomics for domestication of novel non-model microbes

Abstract With the expansion of domesticated microbes producing biomaterials and chemicals to support a growing circular bioeconomy, the variety of waste and sustainable substrates that can support microbial growth and production will also continue to expand. The diversity of these microbes also requires a range of compatible genetic tools to engineer improved robustness and economic viability. As we still do not fully understand the function of many genes in even highly studied model microbes, engineering improved microbial performance requires introducing genome-scale genetic modifications followed by screening or selecting mutants that enhance growth under prohibitive conditions encountered during production. These approaches include adaptive laboratory evolution, random or directed mutagenesis, transposon-mediated gene disruption, or CRISPR interference (CRISPRi). Although any of these approaches may be applicable for identifying engineering targets, here we focus on using CRISPRi to reduce the time required to engineer more robust microbes for industrial applications. One-Sentence Summary The development of genome scale CRISPR-based libraries in new microbes enables discovery of genetic factors linked to desired traits for engineering more robust microbial systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A small number of point mutations confer formate tolerance in Shewanella oneidensis

ABSTRACT Microbial electrosynthesis (MES) is a sustainable approach to chemical production from CO 2 and clean electricity. However, limitations in electron transfer efficiency and gaps in understanding of electron transfer pathways in MES systems prevent full realization of this technology. Shewanella oneidensis could serve as an MES biocatalyst because it has a well-studied, efficient transmembrane electron transfer pathway. A key first step in MES in this organism could be CO 2 reduction to formate. However, we report that wild-type S. oneidensis does not tolerate high levels of formate. In this work, we created and characterized formate-tolerant strains of S. oneidensis for further engineering and future use in MES systems through adaptive laboratory evolution. Two different point mutations in a gene encoding a predicted sodium-dependent bicarbonate transporter and a DUF2721-containing protein separately confer formate tolerance to S. oneidensis . The mutations were further evaluated to understand their role in improving formate tolerance. We also show that the wild-type and mutant versions of the putative sodium-dependent bicarbonate transporter improve formate tolerance of Zymomonas mobilis , indicating the potential of transferring this formate tolerance phenotype to other organisms. IMPORTANCE Shewanella oneidensis is a bacterium with a well-studied, efficient extracellular electron transfer pathway. This capability could make this organism a suitable host for microbial electrosynthesis using CO 2 or formate as feedstocks. However, we report here that formate is toxic to S. oneidensis , limiting the potential for its use in these systems. In this work, we evolve several strains of S. oneidensis that have improved formate tolerance, and we investigate some mutations that confer this phenotype. The phenotype is confirmed to be attributed to several single point mutations by transferring the wild-type and mutant versions of each gene to the wild-type strain. Finally, the formate tolerance mechanism of one variant is studied using structural modeling and expression in another host. This study, therefore, presents a simple method for conferring formate tolerance to bacterial hosts.

Cross, Megan C. Gruenberg (ORCID:0000000291589900)↗
DOE OSTI2024

raogroupuiuc/yl_variantcalling

NGS analysis for mutation analysis in Yarrowia lipolytica evolved strains. Yarrowia lipolytica, an oleaginous yeast, shows promise for industrial fermentation due to its robust acetyl-CoA flux and well-developed genetic engineering tools. However, its lack of an active xylose metabolism restricts the conversion of cellulosic sugars to valuable products. To address this, metabolic engineering, and adaptive laboratory evolution (ALE) were applied to the Y. lipolytica PO1f strain, resulting in an efficient xylose-assimilating strain (XEV). Whole-genome sequencing (WGS) of the XEV followed by reverse engineering revealed that the amplification of the heterologous oxidoreductase pathway and a mutation in the GTPase-activating protein gene (YALI0B12100g) might be the primary reasons for improved xylose assimilation in the XEV strain. When a sorghum hydrolysate was used, the XEV strain showed superior xylose consumption and lipid production compared to its parental strain (X123). This study advances our understanding of xylose metabolism in Y. lipolytica and proposes effective metabolic engineering strategies for optimizing lignocellulosic hydrolysates.

Deewan, Anshu↗
NASA NTRS1996

EOS Laser Atmosphere Wind Sounder (LAWS) investigation

In this final report, the set of tasks that evolved from the Laser Atmosphere Wind Sounder (LAWS) Science Team are reviewed, the major accomplishments are summarized, and a complete set of resulting references provided. The tasks included preparation of a plan for the LAWS Algorithm Development and Evolution Laboratory (LADEL); participation in the preparation of a joint CNES/NASA proposal to build a space-based DWL; involvement in the Global Backscatter Experiments (GLOBE); evaluation of several DWL concepts including 'Quick-LAWS', SPNDL and several direct detection technologies; and an extensive series of system trade studies and Observing System Simulation Experiments (OSSE's). In this report, some of the key accomplishments are briefly summarized with reference to interim reports, special reports, conference/workshop presentations, and publications.

Source record↗
NASA NTRS2010

Global Clusters as Laboratories for Stellar Evolution

Globular clusters have long been considered the closest approximation to a physicist's laboratory in astrophysics, and as such a near-ideal laboratory for (low-mass) stellar evolution, However, recent observations have cast a shadow on this long-standing paradigm, suggesting the presence of multiple populations with widely different abundance patterns, and - crucially - with widely different helium abundances as welL In this review we discuss which features of the Hertzsprung-Russell diagram may be used as helium abundance indicators, and present an overview of available constraints on the helium abundance in globular clusters,

Catelan, Marcio↗
NASA NTRS2000

NGC 1614: A Laboratory for Starburst Evolution

The modest extinction and reasonably face-on viewing geometry make the luminous infrared galaxy NGC 1614 an ideal laboratory for study of a powerful starburst. HST/NICMOS observations show: (1) deep CO stellar absorption, tracing a starburst nucleus about 45 pc in diameter; (2) surrounded by an approx. 600 pc diameter ring of supergiant H II regions revealed in Pa-alpha line emission; (3) lying within a molecular ring indicated by its extinction shadow in H - K; and (4) all at the center of a disturbed spiral galaxy. The luminosities of the giant H II regions in the ring axe extremely high, an order of magnitude brighter than 30 Doradus; very luminous H II regions, comparable with 30 Dor, are also found in the spiral arms of the galaxy. Luminous stellar clusters surround the nucleus and lie in the spiral arms, similar to clusters observed in other infrared luminous and ultraluminous galaxies. The star forming activity may have been initiated by a merger between a disk galaxy and a companion satellite, whose nucleus appears in projection about 300 pc to the NE of the nucleus of the primary galaxy. The relation of deep stellar CO bands to surrounding ionized gas ring to molecular gas indicates that the luminous starburst started in the nucleus and is propagating outward into the surrounding molecular ring. This hypothesis is supported by evolutionary starburst modeling that shows that the properties of NGC 1614 can be fitted with two short-lived bursts of star formation separated by 5 Myr (and by inference by a variety of models with a similar duration of star formation). The total dynamical mass of the starburst region of 1.3 x 10(exp 9) solar masses is mostly accounted for by the old pre-starburst stellar population. Although our starburst models use a modified Salpeter initial mass function (turning over near one solar mass), the tight mass budget suggests that the IMF may contain relatively more 10 - 30 solar masses stars and fewer low mass stars than the Salpeter function. The dynamical mass is nearly four times smaller than the mass of molecular gas estimated from the standard ratio of (C-12)O (1 - 0) to H2. A number of arguments place the mass of gas in the starburst region at approx. 25% of the dynamical mass, nominally about 1/15 and with an upper limit of 1/10 of the amount estimated from (C-12)O and the standard ratio.

Alonso-Herrero, A.↗
NASA NTRS1990

Regolith evolution in the laboratory - Scaling dissimilar comminution experiments

Repeated impacts into fragmental targets simulating unconsolidated debris on planetary surfaces have provided empirical insight into the evolution of planetary regoliths. The techniques of dimensional analysis have been employed to quantify and examine the relationships between the more important variables in the evolution of these experimental regoliths. Application of this method to the results of 10 experimental series shows that the quantity of comminuted target mass is directly proportional to (1) the number of impacts, (2) the diameter of the projectile, (3) the mean size of the crystals, (4) the mean grain size of the evolving regolith, (5) the total target mass, (6) the impactor density, and (7) the ratio of the impact velocity to the velocity of sound in the target rock. The comminuted mass is inversely proportional to the density of the target rock and the sorting of the regolith.

Cintala, Mark J.↗
NASA NTRS2019

PSR J2234+0611: A New Laboratory for Stellar Evolution

We report the timing results for PSR J2234+0611, a 3.6 ms pulsar in a 32 day, eccentric (e = 0.13) orbit with a helium white dwarf. The precise timing and eccentric nature of the orbit allow measurements of an unusual number of parameters: (a) a precise proper motion of 27.10(3) mas yr−1 and a parallax of 1.05(4) mas resulting in a pulsar distance of 0.95(4) kpc; enabling an estimate of the transverse velocity, 123(5) km s−1. Together with previously published spectroscopic measurements of the systemic radial velocity, this allows a 3D determination of the system’s velocity; (b) precise measurements of the rate of advance of periastron yields a total system mass of 1.6518 +0.0033-0.0035 Msun; (c) a Shapiro delay measurement, h3 = 82 ± 14 ns, despite the orbital inclination not being near 90°; combined with the measurement of the total mass yields a pulsar mass of 1.353 +0.014-0.017 Msun and a companion mass of 0.298 +0.015-0.0120 Msun; (d) we measure precisely the secular variation of the projected semimajor axis and detect a significant annual orbital parallax; together these allow a determination of the 3D orbital geometry of the system, including an unambiguous orbital inclination (i = 138.7 +2.5-2.2 deg) and a position angle for the line of nodes ( omega = 44 +5-4 deg). We discuss the component masses to investigate the hypotheses previously advanced to explain the origin of eccentric MSPs. The unprecedented determination of the 3D position, motion, and orbital orientation of the system, plus the precise pulsar and WD masses and the latter’s optical detection make this system a unique test of our understanding of white dwarfs and their atmospheres.

K Stovall↗
NASA NTRS2019

The Chemical Evolution of Cosmic Carbon: Laboratory Studies with the COSmIC Facility

Cosmic dust plays an essential role in our understanding of the chemical and physical evolution of the universe. Our understanding of cosmic dust relies on a combination of astronomical observations (either remote or on extraterrestrial dust samples), astrophysical modeling and laboratory studies of realistic analogs of cosmic dust grains. The COSmIC facility was developed at NASA Ames to study the evolution of cosmic carbon from circumstellar outflows to interstellar clouds to planetary atmospheres in the laboratory [1]. COSmIC stands for “Cosmic Simulation Chamber” and is dedicated to the study of neutral and ionized molecules and grain particles under the low temperature and density conditions that are required to simulate space environments. COSmIC integrates a variety of instruments that allow generating, processing, and monitoring simulated space conditions in the laboratory. It is composed of a Pulsed Discharge Nozzle (PDN) expansion that generates a plasma in a free supersonic jet expansion, coupled to high-sensitivity, complementary in situ diagnostic tools used for the detection and characterization of the species present in the expansion: Cavity Ring Down Spectroscopy (CRDS) and fluorescence spectroscopy systems for photonic detection and an orthogonal Reflectron Time-Of-Flight Mass Spectrometer (oReTOF-MS) for mass detection. Recent advances achieved in laboratory astrophysics using COSmIC’s laboratory data in synergy with observational data will be presented. These results include the formation of dust grains and aerosols from gas-phase molecular precursors in environments as varied as circumstellar outflows of late AGB stars [2] and planetary atmospheres [3] and the evolution of our understanding of the diffuse interstellar bands (DIBs) with applications to the ESO Diffuse Interstellar Bands Large Exploration Survey (EDIBLES [4, 5]). Plans for future laboratory developments and techniques to study the evolution of cosmic carbon molecules and grains (including NIR-MIR CRDS, laser induced fluorescence (LIF) and incandescence (LII)) will also be addressed as well as their astronomical applications.

Salama, F.↗
NASA NTRS1994

Open clusters as laboratories: The angular momentum evolution of young stars

This is the annual status report for the third year of our LTSA grant 'Open Clusters as Laboratories.' Because we have now had a few years to work on the project, we have started to produce and publish a large number of papers. We have been extremely successful in obtaining ROSAT observations of open clusters. With the demise of the PSPC on ROSAT, our main data source has come to an end and we will be able to concentrate on analyzing those data.

Stauffer, John R.↗
NASA NTRS1992

Evolution of catalytic RNA in the laboratory

We are interested in the biochemistry of existing RNA enzymes and in the development of RNA enzymes with novel catalytic function. The focal point of our research program has been the design and operation of a laboratory system for the controlled evolution of catalytic RNA. This system serves as working model of RNA-based life and can be used to explore the catalytic potential of RNA. Evolution requires the integration of three chemical processes: amplification, mutation, and selection. Amplification results in additional copies of the genetic material. Mutation operates at the level of genotype to introduce variability, this variability in turn being expressed as a range of phenotypes. Selection operates at the level of phenotype to reduce variability by excluding those individuals that do not conform to the prevailing fitness criteria. These three processes must be linked so that only the selected individuals are amplified, subject to mutational error, to produce a progeny distribution of mutant individuals. We devised techniques for the amplification, mutation, and selection of catalytic RNA, all of which can be performed rapidly in vitro within a single reaction vessel. We integrated these techniques in such a way that they can be performed iteratively and routinely. This allowed us to conduct evolution experiments in response to artificially-imposed selection constraints. Our objective was to develop novel RNA enzymes by altering the selection constraints in a controlled manner. In this way we were able to expand the catalytic repertoire of RNA. Our long-range objective is to develop an RNA enzyme with RNA replicase activity. If such an enzyme had the ability to produce additional copies of itself, then RNA evolution would operate autonomously and the origin of life will have been realized in the laboratory.

Joyce, Gerald F.↗
NASA NTRS1998

Open Clusters as Laboratories: The Angular Momentum Evolution of Young Stars

The core group concentrated on three primary research topics: (1) ROSAT observation of the coronal activity of low mass stars in young open clusters; (2) the determination of stellar ages and the determination of the timescale for dissipation of circumstellar disks around young stars; and (3) the determination of rotation velocities of low mass stars in young open cluster and the inferred angular momentum evolution of low mass stars. With accurate ages for the clusters, we can then derive an independent estimate of the timescale for debris disks to dissipate. As the second half of that project, we are using the Caltech/UC/NASA Keck telescopes to obtain spectra of brown dwarf candidates in a number of nearby, young open clusters, from which we can determine new and accurate cluster ages. The final primary program that we have addressed was the determination of rotational velocities for low mass stars in our target open clusters. Our group has obtained rotational velocities for a large number of stars in several open clusters during this LTSA program, and we have published the results in several papers. One particularly time-consuming aspect of our program was the development of a database of the photometry and rotational velocities for nearby open clusters, which we have made available to the community.

Stauffer, John R.↗
NASA NTRS2023

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↗