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At least 109 records · Page 6

Automated vehicle guidance using discrete reference markers

Techniques for providing steering control for an automated vehicle using discrete reference markers fixed to the road surface are investigated analytically. Either optical or magnetic approaches can be used for the sensor, which generates a measurement of the lateral offset of the vehicle path at each marker to form the basic data for steering control. Possible mechanizations of sensor and controller are outlined. Techniques for handling certain anomalous conditions, such as a missing marker, or loss of acquisition, and special maneuvers, such as u-turns and switching, are briefly discussed. A general analysis of the vehicle dynamics and the discrete control system is presented using the state variable formulation. Noise in both the sensor measurement and in the steering servo are accounted for. An optimal controller is simulated on a general purpose computer, and the resulting plots of vehicle path are presented. Parameters representing a small multipassenger tram were selected, and the simulation runs show response to an erroneous sensor measurement and acquisition following large initial path errors.

Johnston, A. R.↗

A multilayer network analysis of Alzheimer's disease pathogenesis: Roles for p‐tau, synaptic peptides, and physical activity

INTRODUCTION: In the aging brain, cognitive abilities emerge from the coordination of complex pathways arising from a balance between protective lifestyle and environmental factors and accumulation of neuropathologies. METHODS: As part of the Rush Memory and Aging Project (n = 440), we measured accelerometer-based actigraphy, cognitive performance, and after brain autopsy, selected reaction monitoring mass spectrometry. Multilevel network analysis was used to examine the relationships among the molecular machinery of vesicular neurotransmission, Alzheimer's disease (AD) neuropathology, cognition, and late-life physical activity. RESULTS: Synaptic peptides involved in neuronal secretory function were the most influential contributors to the multilayer network, reflecting the complex interdependencies among AD pathology, synaptic processes, and late-life cognition. Older adults with lower physical activity evidenced stronger adverse relationships among phosphorylated tau peptides, markers of synaptic integrity, and tangle pathology. DISCUSSION: Network-based approaches simultaneously model interdependent biological processes and advance understanding of the role of physical activity in age-associated cognitive impairment. Highlights: Network-based approaches simultaneously model interdependent biological processes. Secretory synaptic peptides were influential contributors to the multilayer network. Older adults with lower physical activity had adverse relationships among pathology. There was interdependence among phosphorylated tau, synaptic integrity, and tangles. Network methods elucidate the role of physical activity in cognitive impairment.

60 APPLIED LIFE SCIENCES↗

Seasonal investigation of ultrafine-particle organic composition in an eastern Amazonian rainforest

Abstract. Reports on the composition of ultrafine particles (<100 nm in diameter) in the Amazon are scarce, due in part to the fact that new-particle formation has rarely been observed near ground level. Ultrafine particles near the surface have nevertheless been observed, leaving open questions regarding the sources and chemistry of their formation and growth, particularly as these vary across seasons. Here, we present measurements of the composition of ultrafine particles collected in the Tapajós National Forest (2.857° S, 54.959° W) during three different seasonal periods: 10–30 September 2016 (SEP), 18 November–23 December 2016 (DEC), and 22 May–21 June 2017 (JUN). Size-selected (5–70 nm) particles were collected daily (for 22 h each day) using an offline sampler. Samples collected during the three time periods were compiled and analyzed using liquid chromatography coupled with Orbitrap high-resolution mass spectrometry. Our findings suggest a sustained influence of isoprene organosulfate chemistry on ultrafine particles from the different periods. We present chemical evidence that indicates that biological-spore fragmentation impacted ultrafine-particle composition during the late wet season (JUN), while chemical markers for biomass burning and secondary chemistry peaked during the dry season (SEP and DEC). Higher oxidation states and degrees of unsaturation were observed for organics in the dry season (SEP and DEC), suggesting greater extents of aerosol aging. Finally, applying a volatility parameterization to the observed compounds suggests that organic sulfur species are likely key drivers of new-particle growth in the region due to their low volatility compared to other species.

54 ENVIRONMENTAL SCIENCES↗

Aging and Spaceflight: Catalase Targeted to Mitochondria Alters Skeletal Structure and Responses to Musculoskeletal Disuse

Microgravity and ionizing radiation in the spaceflight environment pose multiple challenges to homeostasis and may contribute to cellular stress. Effects may include increased generation of reactive oxygen species (ROS), DNA damage and repair error, cell cycle arrest, cell senescence or death. Our central hypothesis is that prolonged exposure to the spaceflight environment leads to excess production of ROS and oxidative damage, culminating in accelerated tissue degeneration which resembles aging. The main goal of this project is to determine the importance of cellular redox defense for physiological adaptations and tissue degeneration in the space environment. To accomplish this, we will use both wildtype (WT) mice and a well-established, genetically-engineered animal model (mCAT mice) which displays extended lifespan (Schriner et al. 2005). The animal model selected to test these ideas is engineered to quench ROS in mitochondria by targeted over-expression of the human catalase gene to the mitochondrial matrix. We showed previously that mCAT mice express the catalase transgene in skeletal tissues, bone forming osteoblasts, and bone resorbing osteoclasts. In addition, mCAT mice also display increased catalase activity in bone. Our findings revealed that exposure of adult, male, C57Bl/6J mice to simulated spaceflight (hindlimb unloading and gamma radiation) led to an increase in markers of oxidative damage (malondialdehyde, 4-hydroxynonenol) in skeletal tissue of WT mice but not mCAT mice. To extend our hypothesis to other, spaceflight-relevant tissues, we are performing a ground-based study simulating 30 days of spaceflight by hindlimb unloading to determine potential protective effects of mitochondrial catalase activity on aging of multiple tissues (cardiovascular, nervous and skeletal).

transgenic mice↗

Implementation of an extensible property modeling framework in ESPEI with applications to molar volume and elastic stiffness models

Property models are becoming more widely adopted by commercial Calphad databases, but they are not nearly as common in non-commercial or traditional academic Calphad databases. A primary driver is that user-friendly Calphad modeling tools that support property models are not widely available. Here we present new property modeling capabilities that have been implemented in ESPEI (the Extensible, Self-optimizing Phase Equilibrium Infrastructure). These capabilities include both generating property model parameters from data and improvements to the algorithmic selection of the most appropriate model from a series of candidates. Additionally, two illustrative examples are given that use ESPEI to fit different property models. First, we generate molar volume model parameters for Group IV, V, and VI refractory BCC alloys based on the model by Lu et al. (2005). Second, we demonstrate the extensibility of ESPEI’s property modeling capabilities by implementing a custom PyCalphad model for BCC elastic stiffness parameters to generate and compare parameters to the ones assessed by Marker et al. (2018) using the same data. Property models generated by ESPEI can be used in PyCalphad or further optimized with uncertainty quantification using ESPEI.

36 MATERIALS SCIENCE↗

Physical and Biological Properties of Cobalt- and Copper-Doped Calcium Phosphates as Bone Substitute Materials

Arthritis, osteoporosis, and other bone diseases and defects are common medical issues worldwide. By utilizing ceramic biomaterials as bone substitutes to treat these diseases, bone regeneration can be promoted and toxicity from the substitute material can be limited. Calcium phosphate (CaP) ceramics have become popular as bone substitutes due to their biocompatibility and similarity in composition to natural bone. The purpose of this research was to investigate the physical properties and biological responses of CaP-based bone substitutes, doped with metal ions. Some metal ions are present in natural bone in small amounts, and recent studies show they affect the biological responses of CaPs significantly. Dopants such as magnesium (Mg), strontium (Sr), silicon (Si) and iron (Fe) alter the phase composition, mechanical properties, osteogenesis and angiogenesis properties of CaPs, depending on their concentration and method of addition. In the present study, the effects of cobalt (Co) and copper (Cu) on the physical and biological properties of two main CaP materials, brushite cement (BrC) and tricalcium phosphate (TCP), have been investigated. Different concentrations of dopants in forms of oxide and/or chloride were selected and their effect on phase composition, sintering behavior, density, setting time, compressive strength and in vitro interaction with osteosarcoma and osteoblast cells were studied. Different techniques of sample preparation, challenges during cement preparation and compact sample pressing, sintering, and methods of dopant addition are discussed. The presence of Cu in tricalcium phosphate was found to increase thermal stability of the material and decrease the impact of sintering temperature on porosity. In addition, Cu caused a reduction in expression of inflammatory gene markers by human osteoblast cells and an increased expression at early time points due of osteoinductive markers.The addition of Cu and Co to brushite cement caused an increase in thermal stability of the material, and the addition of Cu caused significant increase in setting time. Small dopant amounts of Co caused decrease in setting time, but higher amounts caused an increase. In addition, Cu dopant in small amounts resulted in an increase of compressive strength. Both Cu and Co led to a decrease in expression of inflammatory gene markers by osteoblast and osteosarcoma cells respectively, and Cu also caused an increase in osteoinductive marker expression. Thus, these results indicate that Cu and Co have a positive impact on the physical, mechanical and biological properties of calcium phosphate biomaterials.

Cummings, Haley V.↗

Long-term insulin-like growth factor-I expression in skeletal muscles attenuates the enhanced in vitro proliferation ability of the resident satellite cells in transgenic mice

Insulin-like growth factor-I (IGF-I) overexpression for 1-month in mouse skeletal muscle increases satellite cell proliferation potential. However, it is unknown whether this beneficial enhancement by IGF-I expression would persist over a longer-term duration in aged mice. This is an important issue to address if a prolonged course of IGF-I is to be used clinically in muscle-wasting conditions where satellite cells may become limiting. Using the IGF-I transgenic (IGF-I Tg) mouse that selectively expresses the IGF-I transgene in striated muscles, we found that 18-months of continuous IGF-I overexpression led to a loss in the enhanced in vitro proliferative capacity of satellite cells from Tg skeletal muscles. Also 18-month-old IGF-I Tg satellite cells lost the enhanced BrdU incorporation, greater pRb and Akt phosphorylations, and decreased p27(Kip1) levels initially observed in cells from 1-month-old IGF-I Tg mice. The levels of those biochemical markers reverted to similar values seen in the 18-months WT littermates. These findings, therefore, suggest that there is no further beneficial effect on enhancing satellite cell proliferation ability with persistent long-term expression of IGF-I in skeletal muscles of these transgenic mice.

Non-NASA Center↗

Medical Data Architecture (MDA) Project Status

The Medical Data Architecture (MDA) project supports the Exploration Medical Capability (ExMC) risk to minimize or reduce the risk of adverse health outcomes and decrements in performance due to in-flight medical capabilities on human exploration missions. To mitigate this risk, the ExMC MDA project addresses the technical limitations identified in ExMC Gap Med 07: We do not have the capability to comprehensively process medically-relevant information to support medical operations during exploration missions. This gap identifies that the current in-flight medical data management includes a combination of data collection and distribution methods that are minimally integrated with on-board medical devices and systems. Furthermore, there are a variety of data sources and methods of data collection. For an exploration mission, the seamless management of such data will enable a more medically autonomous crew than the current paradigm. The medical system requirements are being developed in parallel with the exploration mission architecture and vehicle design. ExMC has recognized that in order to make informed decisions about a medical data architecture framework, current methods for medical data management must not only be understood, but an architecture must also be identified that provides the crew with actionable insight to medical conditions. This medical data architecture will provide the necessary functionality to address the challenges of executing a self-contained medical system that approaches crew health care delivery without assistance from ground support. Hence, the products supported by current prototype development will directly inform exploration medical system requirements.In fiscal year 2018, the MDA project developed Test Bed 2, the second iteration in a series of prototypes with functionality focused on data security through role-based access control and encryption, integration with One Portal exercise software and ingestion of an ultrasound Digital Imaging and Communications in Medicine (DICOM) file and image display. Test Bed 2 advances the medical data system architecture framework by providing these functionalities in a scalable system that maintained a layered, modular design. The architecture framework uses a data services approach with role-based access to data in a customized medical record system suitable for space exploration. These functionalities were demonstrated as part of the Next Space Technologies for Exploration Partnerships (NextSTEP) ground test demonstrated at the NASA Johnson Space Center Integrated Power, Avionics and Software (iPAS) facility. Interfacing to a Core Flight Software (CFS) system, the MDA system, using Consultative Committee for Space Data Systems (CCSDS) protocol, transferred an exercise file from the simulated flight MDA system to a mirrored MDA system on the ground through the CFS system. The selection of data sources and demonstrations enabled the team to address stakeholder concerns throughout the development process. In the next iteration, the MDA team will work with stakeholders to identify additional relevant functionalities to further advance system data models, standards and principles that will inform the medical system requirements development.

medical data architecture↗

Materials Combustion Testing and Combustion Product Sensor Evaluations in FY12

NASA Centers continue to collaborate to characterize the chemical species and smoke particles generated by the combustion of current space-rated non-metallic materials including fluoropolymers. This paper describes the results of tests conducted February through September 2012 to identify optimal chemical markers both for augmenting particle-based fire detection methods and for monitoring the post-fire cleanup phase in human spacecraft. These studies follow up on testing conducted in August 2010 and reported at ICES 2011. The tests were conducted at the NASA White Sands Test Facility in a custom glove box designed for burning fractional gram quantities of materials under varying heating profiles. The 623 L chamber was heavily instrumented to quantify organics (gas chromatography/mass spectrometry), inorganics by water extraction followed by ion chromatography, and select species by various individual commercially-available sensors. Evaluating new technologies for measuring carbon monoxide, hydrogen cyanide, hydrogen fluoride, hydrogen chloride and other species of interest was a key objective of the test. Some of these sensors were located inside the glovebox near the fire source to avoid losses through the sampling lines; the rest were located just outside the glovebox. Instruments for smoke particle characterization included a Tapered Element Oscillating Microbalance Personal Dust Monitor (TEOM PDM) and a TSI Dust Trak DRX to measure particle mass concentration, a TSI PTrak for number concentration and a thermal precipitator for collection of particles for microscopic analysis. Materials studied included Nomex®, M22759 wire insulation, granulated circuit board, polyvinyl chloride (PVC), Polytetrafluoroethylene (PTFE), Kapton®, and mixtures of PTFE and Kapton®. Furnace temperatures ranged from 340o to 640o C, focusing on the smoldering regime. Of particular interest in these tests was confirming burn repeatability and production of acid gases with different fuel mixture compositions, as well as the dependence of aerosol concentrations on temperature.

Smoke↗

Materials Combustion Testing and Combustion Product Sensor Evaluations in FY12

NASA Centers continue to collaborate to characterize the chemical species and smoke particles generated by the combustion of current space-rated non-metallic materials including fluoropolymers. This paper describes the results of tests conducted February through September 2012 to identify optimal chemical markers both for augmenting particle-based fire detection methods and for monitoring the post-fire cleanup phase in human spacecraft. These studies follow up on testing conducted in August 2010 and reported at ICES 2011. The tests were conducted at the NASA White Sands Test Facility in a custom glove box designed for burning fractional gram quantities of materials under varying heating profiles. The 623 L chamber was heavily instrumented to quantify organics (gas chromatography/mass spectrometry), inorganics by water extraction followed by ion chromatography, and select species by various individual commercially-available sensors. Evaluating new technologies for measuring carbon monoxide, hydrogen cyanide, hydrogen fluoride, hydrogen chloride and other species of interest was a key objective of the test. Some of these sensors were located inside the glovebox near the fire source to avoid losses through the sampling lines; the rest were located just outside the glovebox. Instruments for smoke particle characterization included a Tapered Element Oscillating Microbalance Personal Dust Monitor (TEOM PDM) and a TSI Dust Trak DRX to measure particle mass concentration, a TSI PTrak for number concentration and a thermal precipitator for collection of particles for microscopic analysis. Materials studied included Nomex(R), M22759 wire insulation, granulated circuit board, polyvinyl chloride (PVC), Polytetrafluoroethylene (PTFE), Kapton(R), and mixtures of PTFE and Kapton(R). Furnace temperatures ranged from 340 to 640 C, focusing on the smoldering regime. Of particular interest in these tests was confirming burn repeatability and production of acid gases with different fuel mixture compositions, as well as the dependence of aerosol concentrations on temperature.

Combustion↗

Pulmonary Toxicity Studies of Lunar Dust in Rodents

NASA has been contemplating returning astronauts to the moon for long-duration habitation and research and using it as a stepping-stone to Mars. Other spacefaring nations are planning to send humans to the moon for the first time. The surface of the moon is covered by a layer of fine dust. Fine terrestrial dusts, if inhaled, are known to pose a health risk to humans. Some Apollo crews briefly exposed to moon dust that adhered to spacesuits and became airborne in the Lunar Module reported eye and throat irritation. The habitable area of any lunar landing vehicle or outpost would inevitably become contaminated with lunar dust. To assess the health risks of exposure of humans to airborne lunar dust, we evaluated the toxicity of Apollo 14 moon dust in animal lungs. Studies of the pulmonary toxicity of a dust are generally first done by intratracheal instillation (ITI) of aqueous suspensions of the test dust into the lungs of rodents. If a test dust is irritating or cytotoxic to the lungs, the alveolar macrophages, after phagocytizing the dust particles, will release cellular messengers to recruit white blood cells (WBCs) and to induce dilation of blood capillary walls to make them porous, allowing the WBCs to gain access to the alveolar space. The dilation of capillary walls also allows serum proteins and water entering the lung. Besides altering capillary integrity, a toxic dust can also directly kill the cells that come into contact with it or ingest it, after which the dead cells would release their contents, including lactate dehydrogenase (a common enzyme marker of cell death or tissue damage). In the treated animals, we lavaged the lungs 1 and 4 weeks after the dust instillation and measured the concentrations of these biomarkers of toxicity in the bronchioalveolar lavage fluids to determine the toxicity of the dust. To assess whether the inflammation and cellular injury observed in the biomarker study would lead to persistent or progressive histopathological changes, a similar study was conducted to microscopically examine rat lung tissue and the associated lymph nodes for lesions, including fibrosis, 1 or 3 months after the instillation. The results from this ITI study led us to select two concentrations (20 and 60 mg/cu m) for an inhalation study, in which rats were exposed to lunar dust 6 h daily for 4 weeks (5d/wk). Similar biochemical and histopathological assessments were carried out in these rats 1 day or 1, 4, or 13 weeks after the dust exposure. Rats exposed to lunar dust by ITI or inhalation showed effects indicating that the dust is moderately toxic. The data will be useful to establish safe exposure limits for astronauts working in a lunar habitat and also help engineers designing dust mitigation systems for lunar vehicles and habitats.

Lam, Chiu-Wing↗

Analysis of Exercise Loads to Inform Vibration Isolation System Design

BACKGROUND: This study was conducted with the primary interest of providing data that would inform Vibration Isolation and Stabilization (VIS) system design and performance for the European Enhanced Exploration Exercise Device (E4D). In preparation for the International Space Station (ISS) in-flight demonstration, a list of critical Human Health Countermeasures (HHC) exercises was compiled [1]. The goal of this study was to assess the ground reaction forces and moments imposed by an exercising subject in each of the six VIS Degrees of Freedom (DOFs) during a comprehensive set of these critical exercises performed on the E4D. METHODS AND RESULTS: The ISS in-flight demonstration list of critical exercises included seated aerobic rowing, bent-over rowing, cycling, front squats, back squats, conventional deadlifts, Romanian deadlifts, heel raises, overhead presses, reverse chops, and power clean presses. At the NASA Johnson Space Center (JSC) Prototype Immersive Technology (PIT) laboratory, motion capture data were collected on critical E4D exercises for six subjects. At the NASA JSC Active Response Gravity Offload System (ARGOS) facility, additional motion capture and load cell data were collected on offloaded trials for four subjects. Select data were extrapolated to represent a 5th percentile female subject and a 95th percentile male subject. A previous investigation comparing the forces obtained from the load cell and from motion capture based data found a satisfactory level of agreement between the two measurements [2]. The motion capture based data were analyzed for this study since it is driven by the subject’s trajectory alone, automatically excluding any forces exerted on the subject by the ARGOS offloading harness. The OpenSim [3, 4] biomechanical simulation inverse kinematics tool was used to calculate the joint angles based on the locations of motion capture markers placed at key positions on the subject’s body. An OpenSim plugin was then used to obtain the forces and moments generated by the subject during each trial, with the moments computed relative to the equilibrium location of the subject’s feet [5]. The force of gravity was also removed to simulate the loads generated by the exercise when performed in microgravity. The load plots for each trial were generated and visually analyzed to obtain the magnitudes of the peak loads for each exercise in each DOF. The typical period of exercise for each trial was also estimated and used to calculate the frequency for each trial. The exercise loads data was then organized in multiple ways to capture different aspects of the data. As a result of this study, we present a summary of the load magnitudes observed during these critical exercises utilizing the E4D.

C A Bell↗

Flow properties along field lines in a 3-D tilted-dipole geometry

A 3-D MHD simulation of a global, tilted-dipole solar wind flow pattern is analyzed to determine flow properties along individual magnetic field lines. In the model, flow conditions near the Sun are chosen to provide a reasonable match to the interplanetary configuration prevailing during the recent south polar passage by Ulysses, i.e., a streamer belt inclined approximately 30 deg to the solar equator and speeds ranging from 325-800 km/s. Field lines all across the stream pattern are traced from 1 to 10 AU by following the motion of marker particles embedded in the flow. It is found that those field lines threading the core of the interaction region are subject to significant latitudinal and relative longitudinal displacement over this range of heliocentric distance. Thus, observations taken at a fixed latitude in the inner solar system sample, over the course of a solar rotation, field lines which connect to a range of latitudes in the outer heliosphere. Maps of the field line displacements are presented to help visualize these connections. In addition, it is found that depending upon the location relative to the CIR structure, the radial evolution of fluid elements frozen to different field lines can deviate considerably from that of the canonical solar wind. That is, for selected subsets of field lines, large speed changes (not just at shocks) can be experienced; the density variation can be far from 1/r(exp 2), and the magnetic field intensity need not decay monotonically with distance.

Pizzo, V. J.↗

Prediction of Cognitive States During Flight Simulation Using Multimodal Psychophysiological Sensing

The Commercial Aviation Safety Team found the majority of recent international commercial aviation accidents attributable to loss of control inflight involved flight crew loss of airplane state awareness (ASA), and distraction was involved in all of them. Research on attention-related human performance limiting states (AHPLS) such as channelized attention, diverted attention, startle/surprise, and confirmation bias, has been recommended in a Safety Enhancement (SE) entitled "Training for Attention Management." To accomplish the detection of such cognitive and psychophysiological states, a broad suite of sensors was implemented to simultaneously measure their physiological markers during a high fidelity flight simulation human subject study. Twenty-four pilot participants were asked to wear the sensors while they performed benchmark tasks and motion-based flight scenarios designed to induce AHPLS. Pattern classification was employed to predict the occurrence of AHPLS during flight simulation also designed to induce those states. Classifier training data were collected during performance of the benchmark tasks. Multimodal classification was performed, using pre-processed electroencephalography, galvanic skin response, electrocardiogram, and respiration signals as input features. A combination of one, some or all modalities were used. Extreme gradient boosting, random forest and two support vector machine classifiers were implemented. The best accuracy for each modality-classifier combination is reported. Results using a select set of features and using the full set of available features are presented. Further, results are presented for training one classifier with the combined features and for training multiple classifiers with features from each modality separately. Using the select set of features and combined training, multistate prediction accuracy averaged 0.64 +/- 0.14 across thirteen participants and was significantly higher than that for the separate training case. These results support the goal of demonstrating simultaneous real-time classification of multiple states using multiple sensing modalities in high fidelity flight simulators. This detection is intended to support and inform training methods under development to mitigate the loss of ASA and thus reduce accidents and incidents.

Harrivel, Angela R.↗

Development, optimization, and application of an episomal plasmid system for Rhodotorula toruloides

Rhodotorula toruloides is an emerging oleaginous yeast with strong potential as a microbial cell factory for the production of acetyl-CoA-derived bioproducts. However, engineering of this organism has been limited by the absence of a functional episomal plasmid system, a foundational genetic tool for rapid gene expression, pathway testing, and CRISPR-based genome engineering. Here, we report the first episomal plasmid system for R. toruloides . Through systematic screening of candidate autonomously replicating sequences (ARSs) from diverse sources, we identified multiple functional ARS elements and selected C63F4, a fragment derived from Contig 63 of R. toruloides CBS14, because of its stable performance. The resulting pC63F4 plasmid was maintained episomally, supported GFP reporter expression, exhibited a copy number of 2.39 ± 0.13, and showed good stability during long term cultivation. To overcome poor transformation efficiency, we developed a Cre- loxP -mediated in vivo re-circularization strategy that enabled reliable delivery of the episomal plasmid. Using this improved system, we demonstrated functional episomal expression of metabolic engineering genes and multi-gene pathways for the production of triacetic acid lactone, fatty alcohols, and limonene. Finally, we leveraged this platform to establish a redesigned CRISPR system that enables seamless genome editing in R. toruloides for the first time, while also simplifying marker recycling. Together, this work establishes a long-needed episomal plasmid platform and associated CRISPR toolkit that will accelerate metabolic engineering, synthetic biology, and fundamental studies in R. toruloides .

CRISPR-Cas9↗

Data for Development, Optimization, and Application of an Episomal Plasmid System for Rhodotorula toruloides

Rhodotorula toruloides is an emerging oleaginous yeast with strong potential as a microbial cell factory for the production of acetyl-CoA-derived bioproducts. However, engineering of this organism has been limited by the absence of a functional episomal plasmid system, a foundational genetic tool for rapid gene expression, pathway testing, and CRISPR-based genome engineering. Here, we report the first episomal plasmid system for R. toruloides . Through systematic screening of candidate autonomously replicating sequences (ARSs) from diverse sources, we identified multiple functional ARS elements and selected C63F4, a fragment derived from Contig 63 of R. toruloides CBS14, because of its stable performance. The resulting pC63F4 plasmid was maintained episomally, supported GFP reporter expression, exhibited a copy number of 2.39 ± 0.13, and showed good stability during long term cultivation. To overcome poor transformation efficiency, we developed a Cre-loxP-mediated in vivo re-circularization strategy that enabled reliable delivery of the episomal plasmid. Using this improved system, we demonstrated functional episomal expression of metabolic engineering genes and multi-gene pathways for the production of triacetic acid lactone, fatty alcohols, and limonene. Finally, we leveraged this platform to establish a redesigned CRISPR system that enables seamless genome editing in R. toruloides for the first time, while also simplifying marker recycling. Together, this work establishes a long-needed episomal plasmid platform and associated CRISPR toolkit that will accelerate metabolic engineering, synthetic biology, and fundamental studies in R. toruloides .

Gene Editing↗

Cleanroom Microbes Survive Drying, Vacuum, and Proton Irradiation

Introduction : The goal of planetary protection at NASA is to mitigate the risk of contaminating sensitive target bodies with biological life. While many cleaning procedures have been put in place to reduce bioburden on spacecraft, microbes are experts at evolving to survive harsh conditions. Specifically, the dry, low-nutrient environment of a cleanroom (commonly used for assembly of spacecraft) can represent an environment where extremophiles can survive. Methods : Scientists at NASA MSFC wished to gather a snapshot of the microbial population within a variety of cleanrooms on site. A study was undertaken to collect air, surface, and floor samples from clean-rooms and isolate unique morphologies. From this study, 95 isolates were collected and saved in a microbial library. About 86% of these were identified at least to a genus level. Following identification, 24 microbes were selected, based on a literature review, as potential extremophiles. These were grown in liquid cultures, diluted to a set optical density, washed with water, and then applied to a sterilized Kapton coupon. Droplets were allowed to dry overnight in a biosafety cabinet. Coupons were then installed in a pelletron and pumped down to high vacuum (~1E-6 Torr). Samples were then subjected 100 keV protons at a fluence of 2x10 15 p+/cm 2 up to 4x10 15 p+/cm 2 . Following exposure, samples were returned to the microbiology lab where they were pro-cessed by submerging in water, vortexing, and then plating either droplets or spread plates. Recovery data collected was qualitative with a ranking or +, minor, or – for growth. Some selected radiotolerant strains were sequenced using the Illumina sequencing platform. The resulting genomes were annotated with the Rapid Annotations using Subsystems Technology (RAST) server and analyzed for conserved and unique stress response relevant genomic signatures to identify clues related to specific tolerances. Results and Discussion : After five rounds of proton radiation, we narrowed our isolates to five, non-spore forming bacteria that demonstrated survival: Arthrobacter koreensis, Paenarthrobacter nitroguajacolicus, Mycetocola manganoxydans , and an Erwinia sp. Furthermore, we exposed these four microbes to 254 nm wavelength light at an intensity of 80 W/m 2 at a distance of ~18 cm for 10 minutes. Only A. koreensis demonstrated survival following UV exposure. Finally, we performed whole genome sequencing on the four strains to look for genetic markers of stress resistance. When we compared the genomes of the four strains, we found that genes coding for GGDEF and EAL domains with PAS/PAC sensors were only found in A. koreensis . These domains, modulated by PAS/PAC sensors, are hypothesized to facilitate survival under drying, desiccation, and proton irradiation. Drying and Desiccation : PAS domains sense hydration changes and modulate GGDEF and EAL domain activity to adjust c-di-GMP levels, enhancing resistance to desiccation. For instance, in Pseudomonas aeruginosa , the PAS domain of RbdA modulates activity under varying hydration conditions, affecting stress responses [1]. Proton Irradiation : Proton irradiation causes oxidative stress, leading to ROS generation. PAS domains detect this stress and modulate GGDEF and EAL domains to manage oxidative stress responses. In Shewanella , EAL domain proteins modulated by PAS sensors help bacteria adapt to extreme conditions [2]. These genes upregulate other stress response genes, protecting membrane function, protein stability, DNA repair, and antioxidant defenses. The modulation of c-di-GMP by PAS domains is crucial for bacterial adaptation to stress conditions, enabling dynamic physio-logical adjustments [3]. Understanding these mechanisms provides insights into bacterial stress responses and strategies for controlling bacterial growth [4]. Conclusions : These findings indicate that clean-rooms harbor extremophile microbes that may be able to survive conditions in deep space. Furthermore, while we identified certain stress-response genes that may be at least partly responsible for the phenotypes observed in this study, there are likely unidentified genes or characteristics about A. koreensis , and other bacteria, that may allow them to survive in harsh environments. Future studies will focus on identifying these unknown genes and characteristics, further elucidating the mechanisms of extremophile survival and potentially informing the development of new biotechnologies for space exploration and other extreme environments.

Chelsi Cassilly↗

The Role of Calcium in the Response of Osteoblasts to Mechanical Stimulation

A major biomedical concern in the exploration and development of space is the rapid loss of bone associated with extended periods of spaceflight. Mineral content, bone formation, matrix protein production and total body calcium are all reduced during long-term periods of weightlessness. These effects of weightlessness appears to be due to decreases in the anabolic function of osteoblasts and osteocytes rather than changes in the resorptive activity of osteoclasts. Conversely, subjecting the skeleton to exogenous mechanical loading increases matrix protein synthesis and bone formation rate, a process which also appears mediated through osteogenic cells. Osteoblasts have been shown to respond to a number of types of mechanical stimulation. However recently we have demonstrated that osteoblasts respond to fluid shear, but not physiologic levels of mechanical strain, with increases in expression of the matrix protein, osteopontin. We have also shown similar responses in other markers for the anabolic response in bone. The expression of the early response gene, c-fos, and the inducible-isoform of the prostaglandin synthetic enzyme, cyclooygenase-2 (COX-2), both increase rapidly in response to fluid shear, but not strain. How osteoblasts and osteocytes perceive mechanical stimuli and convert this stimulus into a biochemical event within the cell is still unknown. However, examination of the cellular events following mechanical stimulation indicate that two of the earliest responses are a rapid increase in intracellular calcium ([Ca(2+)](sub i)) and a reorganization of the actin cytoskeleton. The increase in [Ca(2+)](sub i) is dependent on the presence of extracellular Ca(2+), suggesting the activation of membrane Ca(2+) channel. We have previously characterized a mechanosensitive, cation-selective channel (MSCC) in osteoblast-like clonal cells, which we postulate is important in this early response to mechanical loading. Using an antisense oligodeoxynucleotide strategy, we have tentatively identified this channel as an isoform of the alc subunit of the dihydropyridine-sensitive, voltage sensitive Ca(2+) channel (VSCC). However, a major component in this mechanically induced rise in [Ca(2+)](sub i) is the release of Ca(2+) from intracellular stores. The actin cytoskeleton also rapidly responds to fluid shear with an increase in stress fiber formation and a realignment of the cell parallel to the direction of flow. To ascertain whether these two observations are related and how they effect shear-induced gene expression, we examined the role of Ca(2+) channels and intracellular Ca(2+) release on cytoskeletal reorganization and the resultant increases in the expression and production of c-fos and COX-2 in response to fluid shear.

Duncan, R. L.↗