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Integration sites for Rhodotorula toruloides strain NBRC 0880. This repository accompanies the work "Discovery, characterization, and application of chromosomal integration sites for stable heterologous gene expression in Rhodotorula toruloides". Add scripts and ifo0880 folders to code and data folder of "CRISPR-COPIES" repository.
The development of an interactive/batch gridded information system (array of cells georeferenced to USGS quad sheets) and interfacing application programs (e.g., hydrologic models) is discussed. This system allows non-programer users to request any data set(s) stored in the data base by inputing any random polygon's (watershed, political zone) boundary points. The data base information contained within this polygon can be used to produce maps, statistics, and define model parameters for the area. Present/proposed conditions for the area may be compared by inputing future usage (land cover, soils, slope, etc.). This system, known as the Hydrologic Analysis Program (HAP), is especially effective in the real time analysis of proposed land cover changes on runoff hydrographs and graphics/statistics resource inventories of random study area/watersheds.
The Integrated Propulsion Data System's (IPDS) focus is to provide technologically-advanced philosophies of doing business at SSC that will enhance the existing operations, engineering and management strategies and provide insight and metrics to assess their daily impacts, especially as related to the Propulsion Test Directorate testing scenarios for the 21st Century.
The Spacelab development program is a joint undertaking of the NASA and ESA. The paper addresses the initial concept of Spacelab payload mission management, the lessons learned, and modifications made as a result of the actual implementation of Spacelab Mission 1. The discussion covers mission management responsibilities, program control, science management, payload definition and interfaces, integrated payload mission planning, integration requirements, payload specialist training, payload and launch site integration, payload flight/mission operations, and postmission activities. After 3.5 years the outlined overall mission manager approach has proven to be most successful. The approach does allow the mission manager to maintain the lowest overall mission cost.
The concept and the responsibilities of a mission manager approach are reviewed, and some of the associated problems in implementing Spacelab mission are discussed. Consideration is given to program control, science management, integrated payload mission planning, and integration requirements. Payload specialist training, payload and launch site integration, payload flight/mission operations, and postmission activities are outlined.
Sustained human presence on the surface of the Moon and future missions to Mars require increased independence from surface crews and Earth-based mission control to operate efficiently, safely, and reliably. The time for surface crews to perform tasks will be limited. Extravehicular activities by surface personnel are burdensome and time-consuming, even when a continuous human presence on the surface occurs. Identifying and balancing human/automation roles and tasks and infusing automation and autonomy practices early in a system’s lifecycle will be essential to achieve mission objectives. Among these objectives are attaining a sustained human presence, improving performance and mission effectiveness, reducing operations and maintenance (O&M) costs, and ensuring operations that are robust to communication delays. To achieve these objectives, an operational shift toward increased automation and autonomy with less reliance on humans is needed. Uncrewed lunar surface operations and support activities occur when surface crews are not present or are independent of surface crew timeline activities requiring no surface crew oversight or intervention. These uncrewed surface opportunities can also be planned to minimize crew workload that avoids routine maintenance and support tasks, thus maximizing crew exploration time. Uncrewed preparations such as staging and prepositioning equipment and materials before the crew arrives could improve crew task efficiency. Additional opportunities exist to conduct uncrewed science, exploration, and utilization. Uncrewed surface architecture functions can include science and exploration; habitation; launch and landing support; surface communication and navigation; surface power generation and distribution; human surface mobility; lifting, handling, manipulating; excavation, construction, and site preparation; logistics management; maintenance and repair; surface resource utilization; integrated site operations and shared support services (e.g., site scheduling/prioritization, dust mitigation/contamination control, and surface safety). Early robotic lunar surface campaigns will provide information on the availability of resources, such as oxygen and water, and demonstrate surface-based technologies. After the Artemis III human lunar return mission, a series of landers will deliver surface systems, cargo, supplies, science packages, spare parts, and commodities. A balance of crewed and uncrewed surface operations will enable a sustained lunar surface presence at the South Pole of the Moon at a site that will be known as the Artemis Base Camp (ABC). It is envisioned that base camp operations on and around the Moon will then help prepare for the mission durations and activities needed to support the first human mission to Mars. Before long-duration crew missions to the base camp can occur, the necessary surface infrastructure will be pre-deployed and verified operational. Surface assets will be teleoperated and remotely managed from Earth. Additionally, robotic and short-duration crewed missions to the ABC will ensure the site’s merit to achieve long-term science objectives, availability of usable resources, and that terrain, seasonal variations, and illumination conditions are acceptable. ABC will consist of different areas where specific functions and services are rendered, including: • Launch and Landing Area • Habitation Area • Power Production Area • Resource Areas Launch and Landing Area—The launch and landing area will support associated functions for the arrival and departure of vehicles, such as crewed landing and ascent and uncrewed cargo deliveries and offloading. It will evolve from an unimproved site at the beginning of the exploration campaign to a more sustainable landing and launch area that can support repeated arrivals and departures. Initial uncrewed Lunar Terrain Vehicle (LTV) surface operations may include emplacement of navigation beacons and communication equipment, real-time video and photography of landing/liftoff events, and element repositioning, such as portable utility power (PUP) (applicable for other landed assets at other areas). Site preparations, such as surface leveling, soil compaction, and berm/path construction, may be needed for a more sustainable launch and landing area capable of accommodating vehicles that are increasingly more reusable and reduce the effects of plume surface interactions and ejecta impacts on nearby surface assets. During the ABC missions, cargo and logistics will be delivered to the lunar surface via robotic cargo landers before the crew arrives. These shipments, which can arrive in pressurized logistics carriers, will deliver the logistics necessary to support a crewed mission and include items such as food, water, equipment spares, etc. Providing the capability to retrieve, offload, and transport the logistics closer to the ABC site before the arrival of the crew will increase the overall efficiency of crew operations once they arrive. In the sustained phase of exploration, other supporting services may be needed, such as lander propellant servicing, surface power services, commodity refreshes, and additional inspection, maintenance, and repair capabilities, to sustain a cadence of extended personnel stays and cargo arrivals and departures. Habitation Area—Uncrewed support to surface habitation could involve supporting activation and pre-entry operations of the habitat while the crew is in orbit at the Gateway outpost preparing for a surface landing. Surface Habitat (SH) uncrewed operations may include bringing the cabin environment to a habitable temperature and air mix and activating other critical crew support systems. Potential crop production uncrewed tasks in the SH could also include autonomous watering and tending. Additionally, when the crew departs, the SH enters dormancy for the long period of uncrewed operation. A logistical staging area could also be collocated near the SH. If so, staging operations for crew supplies, waste re-location, and recycling operations may be opportunities for uncrewed operations. Power Production Area—The Fission Surface Power (FSP) element and its supporting distribution equipment provide power to surface elements as needed across the ABC to supplement day-to-day operations and survive lunar nights. Uncrewed support of this power system includes any initial LTV-assisted deployments of cables and other distributed equipment, associated electrical connections, and system testing and activation operations. Robotically performing some inspections, maintenance, or repair tasks on the power distribution equipment could reduce the surface crew workload. Resource Area— Uncrewed resource prospecting, mapping, and characterizing possible resource sites is likely to be time-consuming and represents an opportunity for uncrewed operations between crewed missions. Uncrewed mobile equipment operations will be needed in the extreme environments of permanently shadowed locations where resource extractions occur. As In-Situ Resource Utilization (ISRU) pilot plant operations begin, uncrewed surface support activities with available mobile and portable assets (LTV, PUP, etc.) will better support these operations. Any produced commodities can be stored at a centralized storage location for future use. Also associated with these operations is the use of mobile robotic excavators for resource acquisition and robotic/autonomous regolith processing. The waste tailings generated during excavation and regolith processing would also need to be transported and deposited at a dedicated location. Surface assets will continue operating between crew visits to maintain surface capabilities, conduct lunar surface science, technology demonstrations, and public outreach opportunities. Additionally, certain sustaining tasks that would consume valuable crew time could be performed before crew arrival, or after their departure. This capability may offer more affordable options to construct, activate, test, and maintain a broad set of surface assets. Telerobotically operated human surface mobility systems, such as the LTV and Pressurized Rover (PR), can be utilized for various tasks. Surface environmental conditions pose a distinct challenge for all these activities. Surface illumination and localized shadows are one such factor. Night-survival operations could consist of thermal management, battery pre-charging, and load shedding. Some surface systems may hibernate through the night and then awake and continue nominal operations. Uncrewed mobile assets may use a more adaptive approach to optimize their power and operations; one method is to follow the sunlight. Night-survival operations may be initiated remotely by teleoperation, automated, or accomplished by supervised autonomous operation. The ability to pre-deploy and control remote assets in orbit or on Mars before the arrival of the mission crew is a key capability that can be simulated on the moon. The base camp provides a venue where these advanced operational concepts, technologies, and autonomous methods and techniques, including the incorporation of time delays to simulate Earth-Mars latency can be replicated to help buy down future Mars mission risks. This paper will examine the evolution of uncrewed lunar surface operations and support activities. It will also discuss the lunar surface environmental conditions (thermal, lighting, terrain, topography, communications) along with the challenges they pose on uncrewed surface operations, and the performance of these activities with limited to minimal human interaction and/or teleoperation. Since lunar missions include Mars mission analogs, such investigation provides the framework for future uncrewed Mars mission support.
Transcriptomics is a powerful approach for functional genomics and systems biology, yet it can also be used for genetic part discovery. Here, we derive constitutive and light-regulated promoters directly from transcriptomics data of the basidiomycete red yeast Xanthophyllomyces dendrorhous CBS 6938 (anamorph Phaffia rhodozyma) and use these promoters with other genetic elements to create a modular synthetic biology parts collection for this organism. X. dendrorhous is currently the sole biotechnologically relevant yeast in the Tremellomycete class-it produces large amounts of astaxanthin, especially under oxidative stress and exposure to light. Thus, we performed transcriptomics on X. dendrorhous under different wavelengths of light (red, green, blue, and ultraviolet) and oxidative stress. Differential gene expression analysis (DGE) revealed that terpenoid biosynthesis was primarily upregulated by light through crtI, while oxidative stress upregulated several genes in the pathway. Further gene ontology (GO) analysis revealed a complex survival response to ultraviolet (UV) where X. dendrorhous upregulates aromatic amino acid and tetraterpenoid biosynthesis and downregulates central carbon metabolism and respiration. The DGE data was also used to identify 26 constitutive and regulated genes, and then, putative promoters for each of the 26 genes were derived from the genome. Simultaneously, a modular cloning system for X. dendrorhous was developed, including integration sites, terminators, selection markers, and reporters. Each of the 26 putative promoters were integrated into the genome and characterized by luciferase assay in the dark and under UV light. The putative constitutive promoters were constitutive in the synthetic genetic context, but so were many of the putative regulated promoters. Notably, one putative promoter, derived from a hypothetical gene, showed ninefold activation upon UV exposure. Thus, this study reveals metabolic pathway regulation and develops a genetic parts collection for X. dendrorhous from transcriptomic data. Therefore, this study demonstrates that combining systems biology and synthetic biology into an omics-to-parts workflow can simultaneously provide useful biological insight and genetic tools for nonconventional microbes, particularly those without a related model organism. This approach can enhance current efforts to engineer diverse microbes.
The electrical and thermal energy utilization efficiencies of a 500 unit apartment complex are analyzed and compared for each of three energy supply systems. Two on-site integrated energy systems, one powered by diesel engines and the other by phosphoric-acid fuel cells were compared with a conventional system which uses purchased electricity and on-site boilers for heating. All fuels consumed on-site are clean, synthetic fuels (distillate fuel oil or pipeline quality gas) derived from coal. Purchased electricity was generated from coal at a central station utility. The relative energy consumption and economics of the three systems are analyzed and compared.
While there are many tools for designing and modeling a single floating turbine, array level design and modeling has much more to consider. Designing floating wind arrays requires a coupled approach considering many variables, from bathymetry to installation and maintenance to failure and risk analysis. With all of these considerations, an array-level modeling tool is needed to quickly evaluate array designs. The Floating Array Model (FAModel) tool developed at the National Renewable Energy Laboratory was created to fill this gap in low-fidelity array modeling. FAModel is a python framework created to streamline holistic low-fidelity floating wind modeling for array-level analysis. FAModel integrates site data and models with a variety of open-source modeling tools developed by NREL, including FLORIS, RAFT, MoorPy, and anchor capacity models. The integration of these tools allows users to quickly and holistically design an array by considering forces, area analysis, visualization, annual energy production, failure modeling, and component costs.
Ionic liquids (ILs) have emerged as highly tunable sorbents and membranes for gas separation, especially in the purification of CO 2 -containing gas streams such as air, natural gas, biogas, and syngas. Their negligible volatility, high thermal stability, and chemical versatility position them as promising alternatives to conventional amine and alkaline metal derivative-based systems, effectively addressing key challenges such as volatility, stability, and high regeneration energy. Here, this Review explores IL-derived systems for CO 2 -related gas separation across dense, porous, and supported categories. At the dense liquid level, we discuss strategies for tailoring IL properties to optimize CO 2 sorption, focusing on the correlation between IL-CO 2 interaction strength, uptake capacity, and regeneration energy. Key advancements in carbon capture, including amino-functionalized (AILs) and superbase-derived ILs (SILs), are highlighted, along with strategies such as chemical structure engineering, multiple binding site integration, alternative driving force exploration, and stability enhancement. Then, the porous liquids (PLs) scale focuses on the emerging field integrating IL properties with permanent porosity engineering, spanning ultramicropores (<5 Å) to macropores (around 100 nm). These innovations improve gas uptake capacity, accelerate transport kinetics, introduce the gating effect, and enable the coexistence of active sites with antagonistic properties within a single IL medium. At the supported IL scale, the discussion shifts to IL- and ionic pair-modified sorbents and membranes, emphasizing the modulation of cations and anions, confinement effects from porous supports, and the IL–interface interaction to enhance CO 2 separation performance, particularly in diluted gas streams. Beyond separation, this Review highlights IL-based integrated processes for CO 2 capture and conversion into value-added chemicals via thermocatalytic, electrocatalytic, and photocatalytic pathways. At each scale, advanced computational and experimental tools for IL design are also discussed, providing insights into stability enhancement, sorption efficiency, and process integration. The Review concludes by addressing existing challenges and outlining future directions for IL-driven innovations in gas separation technologies.
Abstract Transfer–messenger RNA (tmRNA) contributes essential tRNA-like and mRNA-like functions during the process of trans-translation, a mechanism of quality control for the translating bacterial ribosome. Proper tmRNA identification benefits the study of trans-translation and also the study of genomic islands, which frequently use the tmRNA gene as an integration site. Automated tmRNA gene identification tools are available, but manual inspection is still important for eliminating false positives. We have increased our database of precisely mapped tmRNA sequences over 50-fold to 97 179 unique sequences. Group I introns had previously been found integrated within a single subsite within the TψC-loop; they have now been identified at four distinct subsites, suggesting multiple founding events of invasion of tmRNA genes by group I introns, all in the same vicinity. tmRNA genes were found in metagenomic archaeal genomes, perhaps a result of misbinning of bacterial sequences during genome assembly. With the expanded database, we have produced new covariance models for improved tmRNA sequence search and new secondary structure visualization tools.
From the work of Potts et al. Papelier et al. and Shi et al. it is readily apparent that the arterial (aortic and carotid) baroreflexes are reset to function at the prevailing ABP of exercise. The blood pressure of exercise is the result of the hemodynamic (cardiac output and TPR) responses, which appear to be regulated by two redundant neural control systems, "Central Command" and the "exercise pressor reflex". Central Command is a feed-forward neural control system that operates in parallel with the neural regulation of the locomotor system and appears to establish the hemodynamic response to exercise. Within the central nervous system it appears that the HLR may be the operational site for Central Command. Specific neural sites within the HLR have been demonstrated in animals to be active during exercise. With the advent of positron emission tomography (PET) and single-photon emission computed tomography (SPECT), the anatomical areas of the human brain related to Central Command are being mapped. It also appears that the Nucleus Tractus Solitarius and the ventrolateral medulla may serve as an integrating site as they receive neural information from the working muscles via the group III/IV muscle afferents as well as from higher brain centers. This anatomical site within the CNS is now the focus of many investigations in which arterial baroreflex function, Central Command and the "exercise pressor reflex" appear to demonstrate inhibitory or facilitatory interaction. The concept of whether Central Command is the prime mover in the resetting of the arterial baroreceptors to function at the exercising ABP or whether the resetting is an integration of the "exercise pressor reflex" information with that of Central Command is now under intense investigation. However, it would be justified to conclude, from the data of Bevegard and Shepherd, Dicarlo and Bishop, Potts et al., and Papelier et al. that the act of exercise results in the resetting of the arterial baroreflex. In addition, if, as we have proposed, the cardiopulmonary baroreceptors primarily monitors and reflexly regulates cardiac filling volume, it would seem from the data of Mack et al. and Potts et al. that the cardiopulmonary baroreceptor is also reset at the beginning of exercise. Therefore, investigations of the neural mechanisms of regulation involving Central Command and cardiopulmonary afferents, similar to those being undertaken for the arterial baroreflex, need to be established.
Single-species laboratory toxicity tests are a standard tool for evaluating potential impairment of freshwater systems; however, it remains uncertain how well they reflect community-level impacts in natural environments. This study presents a multi-decadal dataset (2005-2025) pairing ambient toxicity testing with macroinvertebrate surveys along Bear Creek on the Oak Ridge Reservation (Tennessee, USA) downstream of an industrial complex to assess the ability of laboratory tests using stream water to track community-level effects. Biannual three-brood Ceriodaphnia dubia tests from 2005 to 2025 often showed reduced reproduction at select sites. Integrating water quality data showed strong positive correlations between sublethal toxicity and specific conductance. Macroinvertebrate diversity metrics, family-level occurrence, and densities were also associated with conductance and contemporaneous C. dubia responses. Laboratory-measured sublethal toxicity was a stronger indicator of macroinvertebrate change than conductance alone, although responses varied among sites and seasons. At the site with the highest diversity, densities and richness of Ephemeroptera, Plecoptera, Trichoptera (EPT) and non-EPT taxa were significantly related to C. dubia reproduction, with greater toxicity corresponding to lower diversity. At the family level, some pollution-tolerant taxa were more prevalent and at higher densities during periods of sublethal toxicity, while some sensitive families were absent or reduced. These patterns may reflect site-specific mixtures of acute and chronic stressors, with laboratory toxicity tests more effectively capturing short-term impacts. Overall, these multi-decadal observations suggest that laboratory toxicity tests can help track water-quality changes linked to shifts in aquatic community diversity, despite variable responses reflecting the complexity of dynamic stressors in this impacted freshwater system.
The purpose of this groundwater sampling plan (referred to herein as “the Plan”) is to describe the approach for collecting and analyzing groundwater samples to meet the objectives of the U.S. Department of Energy (DOE), Environmental Management (EM) Nevada Program’s Underground Test Area (UGTA) Activity. The Plan is focused on the Central and Western Pahute Mesa corrective action units (CAUs 101 and 102), which are currently in the Corrective Action Decision Document (CADD)/Corrective Action Plan (CAP) stage of the Federal Facility Agreement and Consent Order (FFACO) UGTA Strategy. The remaining UGTA CAUs are in the final stage of the UGTA strategy (Closure Report [CR] stage), and monitoring requirements for these CAUs are described in the Federal Facility Agreement and Consent Order Nevada National Security Site Use Restriction Management Plan (DOE/EMNV, 2024a). The Plan supersedes the Nevada National Security Site Integrated Groundwater Sampling Plan and its ensuing Record of Technical Change (ROTC) (DOE/EMNV, 2019b).
Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete genomes. We used soil depth–resolved population metagenomic data sets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically into theAtabeyarchaeum deiterrae-1chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp ICE encodes an expressed Type IIG restriction-modification system with a sequence specificity matching an active methylation motif identified by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility.
Nearly 50% of the total energy consumed by the industrial sector in the United States is used to produce process steam with natural gas and coal-fired boilers1 . This project conducts a technoeconomic assessment of a NuScale Small Modular Reactor (SMR) coupled with a chemical plant as an Integrated Energy System (IES) where nuclear produces steam and electric power to meet the requirements of a large chemical plant. In a 2020 study, ORNL evaluated the feasibility of using advanced SMRs, including the NuScale design, to supply energy to the Eastman Chemical Plant. However, since that report was published, NuScale received NRC approval for its uprated 77 MWe design with 56% more power and has also introduced a high-temperature, high pressure, steam heat-augmentation system, a key focus of the new study. The new study also benefits from revised capital costs, a 10-day refueling outage time, reduced plant staffing, higher capacity factors, and a site boundary Emergency Planning Zone methodology. The study consists of a techno-economic assessment of two possible energy sources (nuclear and natural gas) in a number of steam and power generation configurations (NuScale Power Modules (NPMs), boilers and combinations of both) to satisfy the steam and power demand with the most reliable and cost competitive system. A total of 2,947.3 klb/hr of steam and 72.5 MWe of electricity are required for the demonstration case. A range of scenarios and solutions are explored, from a 12-NPM plant (3,000 MWth)—with excess capacity and redundancy, capable of supplying a significant amount of extra power to the grid—to a 4-NPM (1,000 MWth) plant—supplemented with existing boilers or grid power for redundancy. The study uses historical steam and power data from a chemical plant and examines the sensitivity to natural gas and grid power cost variations. Scenarios with up to two times gas and electricity costs were considered. Profitability in a 60-year time horizon was analyzed, consistent with NuScale’s design life specification. A steady-state site integration and reliability analysis was performed, and trade-offs were identified.
The Large Optical Test and Integration Site (LOTIS) at the Lockheed Martin Space Systems Company in Sunnyvale, CA is designed for the verification and testing of optical systems. The facility consists of an 88 foot temperature stabilized vacuum chamber that also functions as a class 10k vertical flow cleanroom. Many problems were encountered in the design and construction phases. The industry capability to build large chambers is very weak. Through many delays and extra engineering efforts, the final product is very good. With 11 Thermal Conditioning Units and precision RTD s, temperature is uniform and stable within 1oF, providing an ideal environment for precision optical testing. Within this chamber and atop an advanced micro-g vibration-isolation bench is the 6.5 meter diameter LOTIS Collimator and Scene Generator, LOTIS alignment and support equipment. The optical payloads are also placed on the vibration bench in the chamber for testing. This optical system is designed to operate in both air and vacuum, providing test imagery in an adaptable suite of visible/near infrared (VNIR) and midwave infrared (MWIR) point sources, and combined bandwidth visible-through-MWIR point sources, for testing of large aperture optical payloads. The heart of the system is the LOTIS Collimator, a 6.5m f/15 telescope, which projects scenes with wavefront errors <85 nm rms out to a 0.75 mrad field of view (FOV). Using field lenses, performance can be extended to a maximum field of view of 3.2 mrad. The LOTIS Collimator incorporates an extensive integrated wavefront sensing and control system to verify the performance of the system.
Cyanobacteria are promising microbial platforms for a diverse set of biotechnology applications, from living materials to photosynthetic chemical production, but are less well characterized than commonly engineered microbes such as Escherichia coli. This study facilitates genetic engineering in Synechococcus sp. PCC 7002, a fast-growing, halotolerant, and naturally competent strain, by identifying ten native methylation motifs and designing shuttle strains that mimic the native methylation state by expressing a subset of heterologous methyltransferases. DNA methylation in E. coli with as few as two active methyltransferases increased transformation efficiency up to 30-fold across four distinct integration sites in PCC 7002. This work provides an experimental framework to bypass native restriction-modification systems for efficient genome editing and metabolic engineering in nonmodel bacteria.