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DOE OSTI2025

Discovery of FoTO1 and Taxol genes enables biosynthesis of baccatin III

Abstract Plants make complex and potent therapeutic molecules 1,2 , but sourcing these molecules from natural producers or through chemical synthesis is difficult, which limits their use in the clinic. A prominent example is the anti-cancer therapeutic paclitaxel (sold under the brand name Taxol), which is derived from yew trees (Taxusspecies) 3 . Identifying the full paclitaxel biosynthetic pathway would enable heterologous production of the drug, but this has yet to be achieved despite half a century of research 4 . WithinTaxus’ large, enzyme-rich genome 5 , we suspected that the paclitaxel pathway would be difficult to resolve using conventional RNA-sequencing and co-expression analyses. Here, to improve the resolution of transcriptional analysis for pathway identification, we developed a strategy we term multiplexed perturbation × single nuclei (mpXsn) to transcriptionally profile cell states spanning tissues, cell types, developmental stages and elicitation conditions. Our data show that paclitaxel biosynthetic genes segregate into distinct expression modules that suggest consecutive subpathways. These modules resolved seven new genes, allowing a de novo 17-gene biosynthesis and isolation of baccatin III, the industrial precursor to Taxol, inNicotiana benthamianaleaves, at levels comparable with the natural abundance inTaxusneedles. Notably, we found that a nuclear transport factor 2 (NTF2)-like protein, FoTO1, is crucial for promoting the formation of the desired product during the first oxidation, resolving a long-standing bottleneck in paclitaxel pathway reconstitution. Together with a new β-phenylalanine-CoA ligase, the eight genes discovered here enable the de novo biosynthesis of 3’-N-debenzoyl-2’-deoxypaclitaxel. More broadly, we establish a generalizable approach to efficiently scale the power of co-expression analysis to match the complexity of large, uncharacterized genomes, facilitating the discovery of high-value gene sets.

Science & Technology - Other Topics↗

DOE OSTI2025

LC-Opt: Benchmarking Reinforcement Learning and Agentic AI for End-to-End Liquid Cooling Optimization in Data Centers

Liquid cooling is critical for thermal management in high-density data centers with the rising AI workloads. However, machine learning-based controllers are essential to unlock greater energy efficiency and reliability, promoting sustainability. We present LC-Opt, a Sustainable Liquid Cooling (LC) benchmark environment, for reinforcement learning (RL) control strategies in energy-efficient liquid cooling of high-performance computing (HPC) systems. Built on the baseline of a high-fidelity digital twin of Oak Ridge National Lab's Frontier Supercomputer cooling system, LC-Opt provides detailed Modelica-based end-to-end models spanning site-level cooling towers to data center cabinets and server blade groups. RL agents optimize critical thermal controls like liquid supply temperature, flow rate, and granular valve actuation at the IT cabinet level, as well as cooling tower (CT) setpoints through a Gymnasium interface, with dynamic changes in workloads. This environment creates a multi-objective real-time optimization challenge balancing local thermal regulation and global energy efficiency, and also supports additional components like a heat recovery unit (HRU). We benchmark centralized and decentralized multi-agent RL approaches, demonstrate policy distillation into decision and regression trees for interpretable control, and explore LLM-based methods that explain control actions in natural language through an agentic mesh architecture designed to foster user trust and simplify system management. LC-Opt democratizes access to detailed, customizable liquid cooling models, enabling the ML community, operators, and vendors to develop sustainable data center liquid cooling control solutions.

Naug, Avisek [Hewlett Packard Enterprise]↗

NASA NTRS2019

Editorial: North Pacific Environment and Paleoclimate from the Late Pleistocene to Present

The vast area of the North Pacific, spanning ~55° longitude, represents a challenge for documenting and understanding the geologic history of ocean, atmosphere, and terrestrial environmental change. This special issue highlights site-specific analyses to address various questions and provides clues that arise in response to continued North Pacific warming today in a rapidly changing climate (Figure 1). The emergence of new methods and novel application of existing methods serve to enhance our fundamental understanding of natural modes of climate variability driven by ocean and atmospheric circulation patterns, including the role of external (e.g., insolation) vs. internal forcing [e.g., El Niño Southern Oscillation (ENSO) and the Pacific Decadal Oscillation (PDO)]. Included in this volume are geographically diverse studies that present new and traditional methods for the interpretation of climate records drawn from pollen, macrofossils, tree rings, diatoms, grain size, and glacial studies. Many provide new geographic comparisons, such as Kamchatka and Hawaii, or emerge from novel geologic archives and environments, such as the marine shelf, a thermokarst lake, and a fossil forest.

Jones, Miriam C.↗

DOE OSTI2025

Litter Production and Foliar Nutrient Resorption in Pioneer and Non-Pioneer Species in a Selective Logging Experiment in the Central Amazon, BIONTE, ZF-2, Manaus, 2022-23

This dataset was collected near the city of Manaus, Brazil, at the Experimental Station of Tropical Forestry (EEST, aka “ZF2”), inside the BIONTE (BIOmass and NuTrient Experiment). The experiment included three levels of increasing selective logging intensity, along with control, with 1-hectare permanent plots (12 total) located at the center of 4-hectare treatment plots. The vegetation has a high floristic diversity, the soils of the region are poor in nutrients, and the topography is characterized by plateaus (where BIONTE is located), and also valley bottoms and slopes. Three treatments of differing logging intensities were applied in the BIONTE experiment (T1, T2 and T3). The study was conducted in Treatment 3 (Block I – permanent plot), which represents the most intensive logging treatment, with 69% of the basal area (m²∙ha⁻¹) removed in 1988. The present dataset spans the period from May 1, 2022, to May 1, 2023. The data package includes leaf_nutrient_data, litterfall_total_data, leaf_litterfall_species_specific_data, and species_info, all provided in .csv format. These formats allow users to process and analyze the data in various software applications and programming languages, such as Python and R. This dataset was collected to advance knowledge on nutrient cycling in Amazonian forests, specifically distinguishing between species with two distinct functional traits: fast-growing and slow-growing. It also aims to improve Earth System Models, such as the E3SM Functionally Assembled Terrestrial Ecosystem Simulator (FATES). Additionally, it was used in a paper currently in preparation (Carvalho et al., in prep.), which aims to quantify seasonal litter production and foliar nutrient resorption in pioneer (fast-growing) and non-pioneer (slow-growing) tree species in the central Amazon. Specifically, it seeks to answer two key questions: 1) Is there a difference in leaf litter production, leaf nutrient flux and leaf nutrient concentration between pioneers and non-pioneers species? Is there a difference in the efficiency of foliar nutrient resorption between pioneers and non-pioneers species?

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2000

Fusion of AIRSAR and TM Data for Parameter Classification and Estimation in Dense and Hilly Forests

The expanded remotely sensed data space consisting of coincident radar backscatter and optical reflectance data provides for a more complete description of the Earth surface. This is especially useful where many parameters are needed to describe a certain scene, such as in the presence of dense and complex-structured vegetation or where there is considerable underlying topography. The goal of this paper is to use a combination of radar and optical data to develop a methodology for parameter classification for dense and hilly forests, and further, class-specific parameter estimation. The area to be used in this study is the H. J. Andrews Forest in Oregon, one of the Long-Term Ecological Research (LTER) sites in the US. This area consists of various dense old-growth conifer stands, and contains significant topographic relief. The Andrews forest has been the subject of many ecological studies over several decades, resulting in an abundance of ground measurements. Recently, biomass and leaf-area index (LAI) values for approximately 30 reference stands have also become available which span a large range of those parameters. The remote sensing data types to be used are the C-, L-, and P-band polarimetric radar data from the JPL airborne SAR (AIRSAR), the C-band single-polarization data from the JPL topographic SAR (TOPSAR), and the Thematic Mapper (TM) data from Landsat, all acquired in late April 1998. The total number of useful independent data channels from the AIRSAR is 15 (three frequencies, each with three unique polarizations and amplitude and phase of the like-polarized correlation), from the TOPSAR is 2 (amplitude and phase of the interferometric correlation), and from the TM is 6 (the thermal band is not used). The range pixel spacing of the AIRSAR is 3.3m for C- and L-bands and 6.6m for P-band. The TOPSAR pixel spacing is 10m, and the TM pixel size is 30m. To achieve parameter classification, first a number of parameters are defined which are of interest to ecologists for forest process modeling. These parameters include total biomass, leaf biomass, LAI, and tree height. The remote sensing data from radar and TM are used to formulate a multivariate analysis problem given the ground measurements of the parameters. Each class of each parameter is defined by a probability density function (pdf), the spread of which defines the range of that class. High classification accuracy results from situations in which little overlap occurs between pdfs. Classification results provide the basis for the future work of class-specific parameter estimation using radar and optical data. This work was performed in part by the Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, and in part by the NASA Ames Research Center, Moffett Field, CA, both under contract from the National Aeronautics and Space Administration.

Moghaddam, Mahta↗

NASA NTRSDate not supplied

Mass-Specific Power at the Organism and Biosphere Level

The concept of mass-specific power (MSP) quantitatively relates energy flux to the biomass that flux can sustain. We sought to assess the range and distribution of MSP as expressed at both the organism and biosphere level. The former serves to establish what is possible, and what predominates, in physiological terms; the latter reflects the expression of that physiological potential in an environmental context. To assess the potential range of MSP across a diversity of organisms and physiological states, we compiled a data set of more than 10,000 individual MSP measurements, encompassing more than 2900 unique species and spanning 22 orders of magnitude in body mass. Across the data set, MSP varies over six orders of magnitude, from 3 x 10-5 to 49 Watts per gram biomass carbon (W/gC), but the majority of measured values fall within a relatively narrow range of 0.018 ± 6.4-fold W/gC. It is well documented, and clearly expressed in the data set, that MSP exhibits a strong mass dependence within specific taxa (e.g., birds, mammals, and many others); however, MSP exhibits no mass dependence when considering the data set overall. To assess the expression of MSP in environmental context, we estimated energy utilization rates within eight distinct components of the global biosphere, and for the biosphere overall, and used recently published estimates of biomass within those components to compute MSP. We estimate MSP of 0.005 W/gC for the global biosphere as a whole. The close agreement with the organism-level all-species mean (within 4-fold) is noteworthy because the organism-level data set is dominated in statistical terms by animals, while the global biosphere is dominated in mass terms by trees and microorganisms. The various components of the microbe-dominated marine biosphere exhibit a systematic 5 order of magnitude decrease in MSP from the top of the water column (marine primary producers: 0.9 W/gC) to the depths of the sediment column (> 1m sediment biota: 3 x 10-6 W/gC). Biomass turnover rates, combined with the microbial capacity for both high specific growth rates and low maintenance rates, appear to underlie this large range in MSP, which is not expressed to the same extent in the terrestrial biosphere.

Tori M Hoehler↗

NASA NTRS2024

Testing of Advanced Capabilities to Enable In-time Safety Management and Assurance for Future Flight Operations

In order to refine an initial Concept of Operations, explore Concepts of Use, and expose/validate requirements for future In-Time Aviation Safety Management Systems (IASMS), testing architectures were created, along with a set of capabilities and underlying information exchange protocols. These systems were conceived and developed based on hazards associated with two envisioned urban area flight domains: (1) highly autonomous small uncrewed aerial systems (sUAS) operating at low altitudes, and (2) highly autonomous air taxis. The initial scope of this development is described in [1]; this report provides an update, focusing on the subsequent developments and test activities. As stated in [1], it is important to note that there are many capabilities already in use by the industry (or soon to be in use) that will play critical roles in future IASMS designs. Those reported here were developed to address a gap in the current state-of-the-art regarding specific hazards/risks, and/or to allow for investigation of the interplay between and across hazard types — particularly regarding how overall safety risk can be reduced or managed effectively. Results of testing and development activities are organized by the operational phase wherein a particular capability would be employed (i.e., preflight, in-flight, and post-flight/off-line). Pre-flight: A set of capabilities were developed to help mitigate safety risk prior to flight (e.g., during flight and mission planning). Results of testing summarize (1) validation activities to raise the Technology Readiness Level (TRL) and (2) evaluation activities where the capabilities were applied to flight/mission planning procedures and used by operators/pilots. For the latter, flight plans were automatically assessed, and operators/pilots were notified of hazardous flight segments so as to enable adjustment of the flight plan and re-evaluation, and/or to better inform go/no-go decisions. Capabilities addressed hazards associated with power consumption, third-party risk, wind, navigation system performance, radiofrequency interference, and proximity to geo-spatial threats (e.g., buildings, trees, and no-fly zones). In-flight: Flight experiments tested capabilities that detect and respond to hazards encountered during flight. In the first series, safety hazards were monitored and assessed onboard, and system-generated mitigation maneuvers were recorded (but not acted upon by the vehicle). In the second series, mitigation maneuver commands directed the aircraft in response to safety hazards (i.e., auto-mitigation). The sUAS used for testing is described in full, as is the test architecture, which included commercial avionics, research avionics, and onboard software designed to detect, assess, and respond to hazards. The onboard system was designed as a run-time assurance framework, consistent with [2] and supportive of both supervisory and automated modes. The primary functions included: real-time risk assessment (RTRA), auto-pilot monitoring, constraint monitoring, and contingency select/triggering. RTRA performs integrated risk assessment considering data from several hazard-related monitors (e.g., battery, motors, navigation, communications, population density, and loss-of-control). Post-flight/off-line: Data monitored and recorded during flights can enable IASMS capabilities that execute after flights have completed (or “off-line”). These include: (1) the ability to identify anomalies and trends that may only be observable when comparing data spanning a number of similar flights; (2) the ability to update and validate pre-flight and in-flight capabilities and any underlying models to improve their performance; (3) the ability to report anomalies/off-nominals that may indicate design changes or maintenance actions are needed; and (4) the ability for humans involved in operations to report safety-relevant observations to help in understanding the flight data and/or the operational context of a flight. Progress on three such capabilities is summarized; the first investigates anomaly detection given a limited set of flight logs and applies an approach previously used for space operations. The second explores what could be identified using a larger set of flight logs, including from web-based forums where flight logs are posted by sUAS autopilot users. The third creates a new means of collecting information on UAS incidents and accidents via the Aviation Safety Reporting System (ASRS).

sUAS↗