SEARCH · Search NASA

Results for “Recovery Testing”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 991 records · Page 55

All sources NASA NTRS DOE OSTI

NASA NTRS2014

Inflight Treadmill Exercise Can Serve as Multi-Disciplinary Countermeasure System

The goals of the Functional Task Test (FTT) study were to determine the effects of space flight on functional tests that are representative of high priority exploration mission tasks and to identify the key underlying physiological factors that contribute to decrements in performance. Ultimately this information will be used to assess performance risks and inform the design of countermeasures for exploration class missions. We have previously shown that for Shuttle, ISS and bed rest subjects, functional tasks requiring a greater demand for dynamic control of postural equilibrium (i.e. fall recovery, seat egress/obstacle avoidance during walking, object translation, jump down) showed the greatest decrement in performance. Functional tests with reduced requirements for postural stability (i.e. hatch opening, ladder climb, manual manipulation of objects and tool use) showed little reduction in performance. These changes in functional performance were paralleled by similar decrements in sensorimotor tests designed to specifically assess postural equilibrium and dynamic gait control. The bed rest analog allows us to investigate the impact of axial body unloading in isolation on both functional tasks and on the underlying physiological factors that lead to decrements in performance and then compare them with the results obtained in our space flight study. These results indicate that body support unloading experienced during space flight plays a central role in postflight alteration of functional task performance. These data also support the concept that space flight may cause central adaptation of converging body-load somatosensory and vestibular input during gravitational transitions [1]. Therefore, we conclude that providing significant body-support loading during inflight treadmill along with balance training is necessary to mitigate decrements in critical mission tasks that require dynamic postural stability and mobility. Data obtained from space flight and bed rest support the notion that in-flight treadmill exercise, in addition to providing aerobic exercise and mechanical stimuli to the bone, also has a number of sensorimotor benefits by providing: 1) A balance challenge during locomotion requiring segmental coordination in response to a downward force. 2) Body-support loading during performance of a full-body active motor task. 3) Oscillatory stimulation of the otoliths and synchronized periodic foot impacts that facilitate the coordination of gait motions and tune the full-body gaze control system. 4) Appropriate sensory input (foot tactile input, muscle and tendon stretch input) to spinal locomotor central pattern generators required for the control of locomotion. Forward work will focus on a follow-up bed rest study that incorporates aerobic and resistance exercise with a treadmill balance and gait training system that can serve as an integrated interdisciplinary countermeasure system for future exploration class missions.

Bloomberg, J. J.↗

NASA NTRS2011

The Functional Task Test (FTT): An Interdisciplinary Testing Protocol to Investigate the Factors Underlying Changes in Astronaut Functional Performance

Exposure to space flight causes adaptations in multiple physiological systems including changes in sensorimotor, cardiovascular, and neuromuscular systems. These changes may affect a crewmember s ability to perform critical mission tasks immediately after landing on a planetary surface. The overall goal of this project is to determine the effects of space flight on functional tests that are representative of high priority exploration mission tasks and to identify the key underlying physiological factors that contribute to decrements in performance. To achieve this goal we developed an interdisciplinary testing protocol (Functional Task Test, FTT) that evaluates both astronaut functional performance and related physiological changes. Functional tests include ladder climbing, hatch opening, jump down, manual manipulation of objects and tool use, seat egress and obstacle avoidance, recovery from a fall and object translation tasks. Physiological measures include assessments of postural and gait control, dynamic visual acuity, fine motor control, plasma volume, orthostatic intolerance, upper- and lower-body muscle strength, power, endurance, control, and neuromuscular drive. Crewmembers perform this integrated test protocol before and after short (Shuttle) and long-duration (ISS) space flight. Data are collected on two sessions before flight, on landing day (Shuttle only) and 1, 6 and 30 days after landing. Preliminary results from both Shuttle and ISS crewmembers indicate decrement in performance of the functional tasks after both short and long-duration space flight. On-going data collection continues to improve the statistical power required to map changes in functional task performance to alterations in physiological systems. The information obtained from this study will be used to design and implement countermeasures that specifically target the physiological systems most responsible for the altered functional performance associated with space flight.

Bloomberg, J. J.↗

NASA NTRS1982

V/STOL Tandem Fan transition section model test

An approximately 0.25 scale model of the transition section of a tandem fan variable cycle engine nacelle was tested in the NASA Lewis Research Center 10-by-10 foot wind tunnel. Two 12-inch, tip-turbine driven fans were used to simulate a tandem fan engine. Three testing modes simulated a V/STOL tandem fan airplane. Parallel mode has two separate propulsion streams for maximum low speed performance. A front inlet, fan, and downward vectorable nozzle forms one stream. An auxilliary top inlet provides air to the aft fan - supplying the core engine and aft vectorable nozzle. Front nozzle and top inlet closure, and removal of a blocker door separating the two streams configures the tandem fan for series mode operations as a typical aircraft propulsion system. Transition mode operation is formed by intermediate settings of the front nozzle, blocker door, and top inlet. Emphasis was on the total pressure recovery and flow distortion at the aft fan face. A range of fan flow rates were tested at tunnel airspeeds from 0 to 240 knots, and angles-of-attack from -10 to 40 deg for all three modes. In addition to the model variables for the three modes, model variants of the top inlet were tested in the parallel mode only. These lip variables were: aft lip boundary layer bleed holes, and Three position turning vane. Also a bellmouth extension of the top inlet side lips was tested in parallel mode.

Simpkin, W. E.↗

NASA NTRS1990

Development of a fuel cell for the EMU

The fuel cell technology for the advanced portable life support system is reviewed, using the breadboard test data, and the design concepts are presented for the development of the improved preprototype fuel cell. Subscale test results confirm the suitability of the solid polymer electrolyte fuel cell fueled by hydride stored hydrogen and oxygen for extravehicular mobility unit (EMU) power generation. Issues verified include passive, zero-G product water removal, nonventing operation in the EMU duty cycle, and complete recovery of product water in potable form. The long cycle life and quick rechargeability are confirmed in 600 h of testing including 150 deep discharge cycles.

Beckstrom, Paula↗

NASA NTRS1975

Space shuttle solid rocket booster processing and recovery operations at Kennedy Space Center

This paper describes the processing and recovery operations at Kennedy Space Center as applied to the Space Shuttle Solid Rocket Booster. The introductory portion covers the overall Space Shuttle launch vehicle with a description of the Solid Rocket Boosters and explanations of their functions. Processing operations begin with the arrival of the new or refurbished Solid Rocket Motor segments by rail cars from the manufacturer. Segment buildup is performed on the Mobile Launch Platform, and the completed major booster elements are functionally tested prior to their integration with other prime elements that comprise a complete Shuttle launch vehicle. The recovery operations following launch include Solid Rocket Booster separation, parachute deployment, splashdown, and the activities associated with retrieval of the reusable components of the Solid Rocket Boosters. Subsequently, the paper describes the processing required to thoroughly clean the retrieved items, the disassembly activities, and refurbishment steps planned for restoration of the hardware components to usable condition.

Dickinson, W. J.↗

NASA NTRS1985

Catalytic distillation water recovery subsystem

An integrated engineering breadboard subsystem for the recovery of potable water from untreated urine based on the vapor phase catalytic ammonia removal was designed, fabricated and tested. Unlike other evaporative methods, this process catalytically oxidizes ammonia and volatile hydrocarbons vaporizing with water to innocuous products; therefore, no pretreatment of urine is required. Since the subsystem is fabricated from commercially available components, its volume, weight and power requirements are not optimized; however, it is suitable for zero-g operation. The testing program consists of parametric tests, one month of daily tests and a continuous test of 168 hours duration. The recovered water is clear, odorless, low in ammonia and organic carbon, and requires only an adjustment of its pH to meet potable water standards. The obtained data indicate that the vapor phase catalytic ammonia removal process, if further developed, would also be competitive with other water recovery systems in weight, volume and power requirements.

Budininkas, P.↗

NASA NTRS2001

Recovery from vestibular ototoxicity

OBJECTIVE: Determine whether subjects with documented vestibular ototoxicity recover vestibular function and, if so, investigate the recovery dynamics. STUDY DESIGN: Prospective and retrospective reviews and repeated measures. SETTING: Clinical research and technology center. SUBJECTS: Twenty-eight subjects who received vestibulotoxic medications were followed for at least 12 months after initial treatment. CONTROLS: Our subject sample was compared with a published database of normal individuals. INTERVENTIONS: All 28 subjects received systemically administered medications known to be ototoxic. The subjects' treating physicians controlled medication, dosage, and administration schedules. MAIN OUTCOME MEASURES: Tests of horizontal canal vestibulo-ocular function were performed. Subjects' auditory and vestibular symptoms were recorded. RESULTS: Eleven subjects (39%) showed changes in horizontal canal vestibulo-ocular gain constant (GC) and/or time constant (TC) consistent with vestibular ototoxicity. When tested 1 year after ototoxic drug administration, eight of the nine subjects who experienced ototoxic decrease in GC showed a recovery of GC to normal limits. Only one of the eight subjects who experienced ototoxic decrease in TC showed recovery of TC to within normal limits. Ototoxicity onset and recovery were independent of baseline vestibular function, and ototoxicity onset did not correlate with cumulative dose of ototoxic medication. There was no relationship between subjective symptoms and ototoxicity onset. CONCLUSIONS: Recovery of GC after vestibular ototoxicity is more commonly observed than recovery of TC. Because ototoxic changes developed and continued in an unpredictable time and manner in relation to ototoxic drug administration, we propose that once ototoxic changes in vestibulo-ocular reflex are detected, ototoxic medications should be discontinued as soon as possible.

NASA Discipline Neuroscience↗

NASA NTRS1958

Free-Spinning-Tunnel Investigation of a 1/28-Scale Model of the North American FJ-4 Airplane with External Fuel Tanks, TED No. NACA AD 3112

A supplementary investigation to determine the effect of external fuel tanks on the spin and recovery characteristics of a l/28-scale model of the North American FJ-4 airplane has been conducted in the Langley 20-foot free-spinning tunnel. The model had been extensively tested previously (NACA Research Memorandum SL38A29) and therefore only brief tests were made to evaluate the effect of tank installation. Erect spin tests of the model indicate that flat-type spins-are more prevalent with 200-gallon external fuel tanks than with tanks not installed. The recovery technique determined for spins without tanks, rudder reversal to full against the spin accompanied by simultaneous movement of ailerons to full with the spin, is recommended for spins encountered with external tanks installed. If inverted spins are encountered with external tanks installed, the tanks should be jettisoned and recovery attempted by rudder reversal to full against the spin with ailerons maintained at neutral.

Healy, Frederick M.↗

NASA NTRS1976

Remotely piloted research vehicle evaluation of advanced control system effects on spins

Special functions of an advanced control system were investigated for effects on spin entries and recoveries utilizing a 3/8-scale model of the F-15 airplane as a remotely piloted research vehicle (RPRV). Telemetry uplinks and downlinks were used with a ground-based digital computer to mechanize the RPRV control system for spin tests in flight. Results from the model RPRV flight tests and from a real time digital spin simulation were used to evaluate the F-15 stall inhibiter and an automatic spin recovery system developed for the RPRV model

Petersen, K. L.↗

NASA NTRS2008

Ares I-X Flight Test - On the Fast Track to the Future

In less than two years, the National Aeronautics and Space Administration (NASA) will launch the Ares I-X mission. This will be the first flight of the Ares I crew launch vehicle, which, together with the Ares V cargo launch vehicle, will send humans to the Moon and beyond. Personnel from the Ares I-X Mission Management Office (MMO) are finalizing designs and fabricating vehicle hardware for an April 2009 launch. Ares I-X will be a suborbital development flight test that will gather critical data about the flight dynamics of the integrated launch vehicle stack; understand how to control its roll during flight; better characterize the severe stage separation environments that the upper stage engine will experience during future flights; and demonstrate the first stage recovery system. NASA also will modify the launch infrastructure and ground and mission operations. The Ares I-X Flight Test Vehicle (FTV) will incorporate flight and mockup hardware similar in mass and weight to the operational vehicle. It will be powered by a four-segment Solid Rocket Booster (SRB), which is currently in Shuttle inventory, and will include a fifth spacer segment and new forward structures to make the booster approximately the same size and weight as the five-segment SRB. The Ares I-X flight profile will closely approximate the flight conditions that the Ares I will experience through Mach 4.5, up to approximately130,OOO feet and through maximum dynamic pressure ("Max Q") of approximately 800 pounds per square foot. Data from the Ares I-X flight will support the Ares I Critical Design Review (CDR), scheduled for 2010. Work continues on Ares I-X design and hardware fabrication. All of the individual elements are undergoing CDRs, followed by an integrated vehicle CDR in March 2008. The various hardware elements are on schedule to begin deliveries to Kennedy Space Center (KSC) in early September 2008.

Davis, Stephan R.↗

NASA NTRS2008

Ares I-X Flight Test--The Future Begins Here

In less than one year, the National Aeronautics and Space Administration (NASA) will launch the Ares I-X mission. This will be the first flight of the Ares I crew launch vehicle, which, together with the Ares V cargo launch vehicle, will send humans to the Moon and beyond. Personnel from the Ares I-X Mission Management Office (MMO) are finalizing designs and fabricating vehicle hardware for a 2009 launch. Ares I-X will be a suborbital development flight test that will gather critical data about the flight dynamics of the integrated launch vehicle stack; understand how to control its roll during flight; better characterize the severe stage separation environments that the upper stage engine will experience during future flights; and demonstrate the first stage recovery system. NASA also will modify the launch infrastructure and ground and mission operations. The Ares I-X Flight Test Vehicle (FTV) will incorporate flight and mockup hardware similar in mass and weight to the operational vehicle. It will be powered by a four-segment Solid Rocket Booster (SRB), which is currently in Shuttle inventory, and will include a fifth spacer segment and new forward structures to make the booster approximately the same size and weight as the five-segment SRB. The Ares I-X flight profile will closely approximate the flight conditions that the Ares I will experience through Mach 4.5, up to approximately 130,000 feet (39,600 meters (m)) and through maximum dynamic pressure ('Max Q') of approximately 800 pounds per square foot (38.3 kilopascals (kPa)). Data from the Ares I-X flight will support the Ares I Critical Design Review (CDR), scheduled for 2010. Work continues on Ares I-X design and hardware fabrication. All of the individual elements are undergoing CDRs, followed by a two-part integrated vehicle CDR in March and July 2008. The various hardware elements are on schedule to begin deliveries to Kennedy Space Center (KSC) in early September 2008. Ares I-X is the first step in the long journey to the Moon and farther destinations. This suborbital test will be NASA's first flight of a new human-rated launch vehicle in more than a generation. This promises to be an exciting time for NASA and the nation, as we reach for new goals in space exploration. A visual presentation is included.

Davis, Stephan R.↗

NASA NTRS2006

The Use of Dynamic Visual Acuity as a Functional Test of Gaze Stabilization Following Space Flight

After prolonged exposure to a given gravitational environment the transition to another is accompanied by adaptations in the sensorimotor subsystems, including the vestibular system. Variation in the adaptation time course of these subsystems, and the functional redundancies that exist between them make it difficult to accurately assess the functional capacity and physical limitations of astro/cosmonauts using tests on individual subsystems. While isolated tests of subsystem performance may be the only means to address where interventions are required, direct measures of performance may be more suitable for assessing the operational consequences of incomplete adaptation to changes in the gravitational environment. A test of dynamic visual acuity (DVA) is currently being used in the JSC Neurosciences Laboratory as part of a series of measures to assess the efficacy of a countermeasure to mitigate postflight locomotor dysfunction. In the current protocol, subjects visual acuity is determined using Landolt ring optotypes presented sequentially on a computer display. Visual acuity assessments are made both while standing and while walking at 1.8 m/s on a motorized treadmill. The use of a psychophysical threshold detection algorithm reduces the required number of optotype presentations and the results can be presented immediately after the test. The difference between the walking and standing acuity measures provides a metric of the change in the subject s ability to maintain gaze fixation on the visual target while walking. This functional consequence is observable regardless of the underlying subsystem most responsible for the change. Data from 15 cosmo/astronauts have been collected following long-duration (approx. 6 months) stays in space using a visual target viewing distance of 4.0 meters. An investigation of the group mean shows a change in DVA soon after the flight that asymptotes back to baseline approximately one week following their return to earth. The performance of some subjects nicely parallels the stereotypical recovery curve observed in the group mean data. Others show dramatic changes in DVA from one test day to another. These changes may be indicative of a re-adaptation process that is not characterized by a steady improvement with the passage of time, but is instead a dynamic search for appropriate coordinative strategy to achieve the desired gaze stabilization goal. Ground-based data have been collected in our lab using DVA with one of the goals being to improve the DVA test itself. In one of these studies, the DVA test was repeated using a visual target viewing distance of 0.5 meters. While walking, the relative contributions of the otoliths and semi-circular canals that are required to stabilize gaze are affected by visual target viewing distance. It may be possible to exploit this using the current treadmill DVA test to differentially assess changes in these vestibular subsystems. The postflight DVA evaluations currently used have been augmented to include the near target version of the test. Preliminary results from these assessments, as well as the results from the ground-based tests will also be reported. DVA provides a direct measure of a subject's ability to see clearly in the presence of self-motion. The use of the current tests for providing a functionally relevant metric is evident. However, it is possible to expand the scope of DVA testing to include scenarios other than walking. A facility for measuring DVA in the presence of passive movements is being created. Using a mechanized platform to provide the perturbation, it should be possible to simulate aircraft and automobile vibration profiles. Used in conjunction with the far and near visual displays this facility should be able to assess a subject s ability to clearly see distant objects as well as those that appear on the dashboard or instrument control panel during functionally relevant situations.

Peters, B. T.↗

DOE OSTI2021

Heavy Oil Polymer EOR in the Challenging Alaskan Arctic - It Works!

Under co-sponsorship of the US Department of Energy and Hilcorp Alaska LLC the first ever polymer field pilot commenced on 8/28/2018 in the Schrader Bluff heavy oil reservoir at the Milne Point Field on Alaska North Slope (ANS). The primary objective of the pilot is to prove the efficacy of polymer Enhanced Oil Recovery (EOR) to unlock the vast heavy oil resources on ANS. More than two and half years after startup, the polymer injection, supporting laboratory experiments and simulation studies steadily continue. The pilot started injecting hydrolyzed polyacrylamide (HPAM), at a concentration of 1,750 ppm to achieve a target viscosity of 45 cP, into the two horizontal injectors in the flood pattern. Production is monitored in the two horizontal producers. Based on laboratory measurements of polymer viscosity at reservoir conditions, the team decided to reduce polymer concentration to 1,200 ppm since July 2020 in an effort to control injection pressure and optimize polymer utilization. Quality control (QC) on the field ensures uniform polymer solution properties. Representative rock and fluid systems and test conditions are utilized in the corefloods on polymer retention, effect of injection water salinity, polymer loading, and their combinations on oil recovery. A history matched reservoir simulation model for forecasting oil recovery was developed on the basis of all the available field data. Field concerns related to the post-polymer breakthrough impact on flow assurance is addressed via specialized laboratory tests. Notwithstanding early operational disruptions and hydration issues, continuous polymer injection in both injectors has been achieved. To date, 950,000 lbs of polymer or 2 million barrels of polymer solution, equating to 13% of total pore volume (PV), has been placed in the flood pattern, serving as an effective indicator of adequate polymer injectivity. So far, the success of polymer EOR is evident from drastically reduced water cut in the producers, an estimated incremental 1,000 bopd over waterflood, and a favorable polymer utilization of 1.7 lbs/barrel of incremental oil. Polymer breakthrough was observed 26 months after the start of polymer injection. Main observations from corefloods are unusually high polymer retention values in some cases and a positive response to low salinity water. Although the heterogeneity in the flood pattern and exceptionally low water cut pose some challenges, persistent novel and justifiable simulation approaches have resulted in a robust history matched model. Experimental results on produced fluids treatment provide operational guidance for improved oil-water separation and mitigation of heater tube fouling. The ongoing success of the pilot is a key indicator of bringing the team ever closer to meeting the project’s primary objective. The encouraging results of the pilot is one of the drivers that has provided the impetus to apply polymer EOR throughout the Milne Point Field, which would increase oil recovery and extend the economic life of the Trans Alaska Pipeline System. The scientific knowledge, including the many lessons learned from this pilot also has referential value for other potential heavy oil EOR projects throughout the world. The collected data, operational lessons learned, and the overall success of the pilot are summarized in the paper.

None, None↗

DOE OSTI2020

Performance of sweeping gas membrane distillation for treating produced water: Modeling and experiments

Membrane distillation (MD) has shown promise for desalination of produced water (PW), but there are very few studies reported on the performance of MD with real PW and the characteristics of the fouling and scaling in MD. Among different MD configurations, sweeping gas MD (SGMD) is the least studied configuration. Here we report the application of SGMD for treating high-salinity PW (123 g L -1 ). The SGMD operating conditions were first carefully optimized through pure water MD experiments by varying operating conditions. The flux evaluation was accompanied by a detailed Aspen Custom Modeler simulation based on the electrolyte-NRTL thermodynamic model to better understand the heat and mass transfer in the feed and permeate channel. Supported by experiments, modeling results confirmed the partial condensation of the vapor in the permeate channel. Furthermore, it was concluded that the saturation of the sweeping gas is controlling the overall mass transfer through the membrane. Selected membranes and optimized conditions were then used to conduct short-term and long-term performance tests with PW. In long-term MD test, the concentration of the PW increased by a factor of two (50% water recovery), while the membrane exhibited small flux decline. Elemental analysis showed that strontium and sodium were the major scalant compounds.

42 ENGINEERING↗

DOE OSTI2020

What can the GRACE seasonal cycle tell us about lake-aquifer interactions?

Lake-aquifer interactions have been the subject of investigation and debate for decades. Traditional investigation methods include measurement of water flux across the groundwater-surface water interface, application of heat and environmental tracer methods, conducting numerical simulations of the water flow, and mass balance-based approaches. We first review, evaluate and describe the different approaches that have been applied for examining lake-aquifer interactions and propose an additional complementary approach. While the leakage from lakes and its slow movement through porous media (laminar flow) is well characterized by existing methods, modeling the rapid and turbulent flow through preferred pathways (faults/karst) remains a challenging task. To better understand the nature, and the full scale, of the lake aquifer interactions, and using Lake Nasser and the underlying Dakhla subbasin of the Nubian Sandstone Aquifer System (NSAS) in the Western Desert of Egypt (area: 0.66 x 10 6 km 2 ) as a test site, we examine, model, and correlate temporally and spatially, the variations in Gravity Recovery and Climate Experiment terrestrial water storage (GRACE TWS ) solutions, with precipitation, lake levels, area, and water volume. We review current GRACE applications in hydrology and present our novel approach. Findings include: firstly, large seasonal fluctuations (peak: Nov./Dec.; trough: July/Aug.) in Lake Nasser's surface water levels (average annual fluctuations: from 3.7 m to 7.5 m), area (average area: 3622 km 2 but up to 4530 km 2 ), and volume (annual average: 13.4 km 3 , and up to 34 km 3 ) are observed throughout years 2006 to 2015. These fluctuations are accompanied by an increase in GRACE TWS (average: 50 ± 13 mm/yr, up to 77 ± 18 mm/yr) over Lake Nasser and by a progression of a front of increasing GRACE TWS values (> 50 ± 13 mm) away from the lake reaching distances of up to 700 km some 3 to 5 months following peak lake level periods. The areas witnessing the seasonal increase in GRACE TWS display a progressive increase in phase and decrease in amplitude with distance from the lake. Secondly, the negligible precipitation over the Dakhla subbasin cannot account for the observed seasonal GRACE TWS patterns and neither can the leakage signal from Lake Nasser. Thirdly, overall similarities in the distribution of GRACE TWS seasonal spatial patterns are observed. During high lake level periods (e.g., Dec. 2007; Feb. 2015) additional, and more distant, areas from Lake Nasser saw increases in GRACE TWS and vice versa during low lake level periods (e.g., July 2006; Aug. 2010). These observations are consistent with Lake Nasser being the main source of modern recharge for the Dakhla subbasin and suggest a new conceptual model for the subbasin: a slow groundwater flow through a porous matrix and a rapid groundwater flow along a network of faults, fractures, and karst topography across the matrix. We suggest that the proposed conceptual model for the interaction between Lake Nasser and the Dakhla subbasin could be applicable to aquifers of similar geologic, climatic, and hydrologic settings worldwide and that approaches similar to those advocated here could be used to investigate the validity of this suggestion.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

efam: an e xpanded, metaproteome-supported HMM profile database of viral protein fam ilies

Viruses infect, reprogram and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. Here, we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240 311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from ‘conservative’ to ‘eXtremely Conservative’ resulted in 37 841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by ~24% on average (up to ~42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Protoplast fusion as a strategy to increase ploidy in Rhodotorula toruloides for strain development

Rhodotorula toruloides is a red oleaginous yeast with growing commercial interest because of its hardiness and exceptional lipid production capacity. Because it is a basidiomycete yeast with a complex life cycle, many of the classical breeding methods used with ascomycetes are unavailable for strain improvement. However, we have been able to construct polyploid yeast by fusing protoplasts of parents with the same mating type. Fusing of Y-6985 (A2) and Y-48190 (A2), which had been transformed with complementary antibiotic markers, led to the recovery of two diploids and one triploid. The stability of the fusion yeasts was tested by plating them on non-selective medium after several growth cycles under antibiotics and then testing five colonies per strain for nuclear DNA contents using flow cytometry and standard cell cycle analysis: the triploid and one diploid were stable. Fusants inherited their mitochondria from a single parent, which was demonstrated using restriction fragment length polymorphism (RFLP) of mitochondrial DNA. The phenotypic properties of the parents and fusants were compared in glucose fed-batch bioreactor studies and cellulosic sugar batch cultures. The final lipid titers for the fed-batch cultures were 24.9–39.7 g/L with Y-6985 and the diploid and triploid performing the best and worst, respectively. The fusants demonstrated intermediate hardiness for growth on hydrolysate prepared with dilute-acid pretreated switchgrass and were outperformed by Y-48190. Unlike one of the haploid parents, the fusants grew in 70% v/v concentrated hydrolysate. Furthermore, they did not grow as fast as the other haploid. In this study, a modernized protoplast fusion method is resurrected a useful tool for strain development in this yeast, which is complementary with other available methods.

Lignocellulose↗

DOE OSTI2018

Genome-reconstruction for eukaryotes from complex natural microbial communities

Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k-mer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential. We used this approach to test the effect of addition of organic carbon on a geyser-associated microbial community and detected a substantial change of the community metabolism, with selection against almost all candidate phyla bacteria and archaea and for eukaryotes. Near complete genomes were reconstructed for three fungi placed within the Eurotiomycetes and an arthropod. While carbon fixation and sulfur oxidation were important functions in the geyser community prior to carbon addition, the organic carbon-impacted community showed enrichment for secreted proteases, secreted lipases, cellulose targeting CAZymes, and methanol oxidation. We demonstrate the broader utility of EukRep by reconstructing and evaluating relatively high-quality fungal, protist, and rotifer genomes from complex environmental samples. This approach opens the way for cultivation-independent analyses of whole microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗