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NASA NTRS2014

Cofactors in the RNA World

RNA world theories figure prominently in many scenarios for the origin and early evolution of life. These theories posit that RNA molecules played a much larger role in ancient biology than they do now, acting both as the dominant biocatalysts and as the repository of genetic information. Many features of modern RNA biology are potential examples of molecular fossils from an RNA world, such as the pervasive involvement of nucleotides in coenzymes, the existence of natural aptamers that bind these coenzymes, the existence of natural ribozymes, a biosynthetic pathway in which deoxynucleotides are produced from ribonucleotides, and the central role of ribosomal RNA in protein synthesis in the peptidyl transferase center of the ribosome. Here, we uses both a top-down approach that evaluates RNA function in modern biology and a bottom-up approach that examines the capacities of RNA independent of modern biology. These complementary approaches exploit multiple in vitro evolution techniques coupled with high-throughput sequencing and bioinformatics analysis. Together these complementary approaches advance our understanding of the most primitive organisms, their early evolution, and their eventual transition to modern biochemistry.

RNA↗

NASA NTRS2011

Automated Miniaturized Instrument for Space Biology Applications and the Monitoring of the Astronauts Health Onboard the ISS

Human space travelers experience a unique environment that affects homeostasis and physiologic adaptation. The spacecraft environment subjects the traveler to noise, chemical and microbiological contaminants, increased radiation, and variable gravity forces. As humans prepare for long-duration missions to the International Space Station (ISS) and beyond, effective measures must be developed, verified and implemented to ensure mission success. Limited biomedical quantitative capabilities are currently available onboard the ISS. Therefore, the development of versatile instruments to perform space biological analysis and to monitor astronauts' health is needed. We are developing a fully automated, miniaturized system for measuring gene expression on small spacecraft in order to better understand the influence of the space environment on biological systems. This low-cost, low-power, multi-purpose instrument represents a major scientific and technological advancement by providing data on cellular metabolism and regulation. The current system will support growth of microorganisms, extract and purify the RNA, hybridize it to the array, read the expression levels of a large number of genes by microarray analysis, and transmit the measurements to Earth. The system will help discover how bacteria develop resistance to antibiotics and how pathogenic bacteria sometimes increase their virulence in space, facilitating the development of adequate countermeasures to decrease risks associated with human spaceflight. The current stand-alone technology could be used as an integrated platform onboard the ISS to perform similar genetic analyses on any biological systems from the tree of life. Additionally, with some modification the system could be implemented to perform real-time in-situ microbial monitoring of the ISS environment (air, surface and water samples) and the astronaut's microbiome using 16SrRNA microarray technology. Furthermore, the current system can be enhanced substantially by combining it with other technologies for automated, miniaturized, high-throughput biological measurements, such as fast sequencing, protein identification (proteomics) and metabolite profiling (metabolomics). Thus, the system can be integrated with other biomedical instruments in order to support and enhance telemedicine capability onboard ISS. NASA's mission includes sustained investment in critical research leading to effective countermeasures to minimize the risks associated with human spaceflight, and the use of appropriate technology to sustain space exploration at reasonable cost. Our integrated microarray technology is expected to fulfill these two critical requirements and to enable the scientific community to better understand and monitor the effects of the space environment on microorganisms and on the astronaut, in the process leveraging current capabilities and overcoming present limitations.

Human space travelers↗

NASA NTRS2014

A Multiple Parameters Biodosimetry Tool with Various Blood Cell Counts - the Hemodose Approach

There continue to be important concerns about the possibility of the occurrence of acute radiation syndromes following nuclear and radiological terrorism or accidents that may result in mass casualties in densely populated areas. To guide medical personnel in their clinical decisions for effective medical management and treatment of the exposed individuals, biological markers are usually applied to examine radiation induced biological changes to assess the severity of radiation injury to sensitive organ systems. Among these the peripheral blood cell counts are widely used to assess the extent of radiation induced bone marrow injury. This is due to the fact that the hematopoietic system is the most vulnerable part of the human body to radiation damage. Particularly, the lymphocyte, granulocyte, and platelet cells are the most radiosensitive of the blood elements, and monitoring their changes after exposure is regarded as a practical and recommended laboratory test to estimate radiation dose and injury. Based upon years of physiological and pathophysiological investigation of mammalian hematopoietic systems, and rigorous coarse-grained bio-mathematical modeling and validation on species from mouse, to dog, monkey, and human, we have developed a set of software tools Hemodose, which can use single or serial granulocyte, lymphocyte, leukocyte, or platelet counts after exposure to estimate absorbed doses of adult victims very rapidly and accurately. Some patient data from historical accidents are utilized as examples to demonstrate the capabilities of these tools as a rapid point-of-care diagnostic or centralized high-throughput assay system in a large-scale radiological disaster scenario. Most significant to the improvement of national and local preparedness of a potential nuclear/radiological disaster, this HemoDose approach establishes robust correlations between the absorbed doses and victim's various types of blood cell counts not only in the early time window (1 or 2 days), but also in the very late phase (up to 4 weeks) after exposure.

Hu, Shaowen↗

NASA NTRS2009

Delta-Doped Back-Illuminated CMOS Imaging Arrays: Progress and Prospects

In this paper, we report the latest results on our development of delta-doped, thinned, back-illuminated CMOS imaging arrays. As with charge-coupled devices, thinning and back-illumination are essential to the development of high performance CMOS imaging arrays. Problems with back surface passivation have emerged as critical to the prospects for incorporating CMOS imaging arrays into high performance scientific instruments, just as they did for CCDs over twenty years ago. In the early 1990's, JPL developed delta-doped CCDs, in which low temperature molecular beam epitaxy was used to form an ideal passivation layer on the silicon back surface. Comprising only a few nanometers of highly-doped epitaxial silicon, delta-doping achieves the stability and uniformity that are essential for high performance imaging and spectroscopy. Delta-doped CCDs were shown to have high, stable, and uniform quantum efficiency across the entire spectral range from the extreme ultraviolet through the near infrared. JPL has recently bump-bonded thinned, delta-doped CMOS imaging arrays to a CMOS readout, and demonstrated imaging. Delta-doped CMOS devices exhibit the high quantum efficiency that has become the standard for scientific-grade CCDs. Together with new circuit designs for low-noise readout currently under development, delta-doping expands the potential scientific applications of CMOS imaging arrays, and brings within reach important new capabilities, such as fast, high-sensitivity imaging with parallel readout and real-time signal processing. It remains to demonstrate manufacturability of delta-doped CMOS imaging arrays. To that end, JPL has acquired a new silicon MBE and ancillary equipment for delta-doping wafers up to 200mm in diameter, and is now developing processes for high-throughput, high yield delta-doping of fully-processed wafers with CCD and CMOS imaging devices.

imagers↗

NASA NTRS2016

A Simple and Sensitive LC-MS/MS Method for the Determination of Free 8-Hydroxy-2'-Deoxyguanosine in Human Urine

Urinary free 8-hydroxy-2'-deoxyguanosine (8OHdG), an oxidized product of DNA, and is frequently chosen as a biomarker of oxidative stress in humans, including studies of oxidative DNA damage during space flight. It is challenging to accurately and efficiently quantify urinary free 8OHdG in large scale human studies. LC-MS/MS is emerging as a preferable analytical technique owing its high sensitivity, selectivity and efficiency, compared to some traditional methods such as ELISA and HPLC. A simple and sensitive LC-MS/MS method has been developed for the determination of free 8OHdG in human urine. Sample preparation was done by solid phase extraction with a Waters Oasis HLB 96 well plate. A Waters Alliance 2795 HT Separation Module combined with a Quattro Micro tandem mass spectrometer was used as the LC-MS/MS system. The runtime of one injection can be less than 5 minutes using a reversed phase C18 column and an isocratic flow of methanol/water. ESI positive ions were quantified in the multiple reaction modes (MRM) using m/z 284 yields 168 for 8OHdG and m/z 289 yields173 for stable isotope labeled internal standard [(15)N5] 8OHdG. With this method for 8OHdG, a lower limit of quantitation of 1.0 nM (0.28 ng/mL) has been achieved using 100 microliter urine sample. The analytical range is between 1.0 and 100 nM with a correlation coefficient greater than or equal to 0.99. Good reproducibility can be obtained with intra-assay and inter-assay CVs less than or equal to 10% for 8OHdG spiked urine QC samples. This method can be used in high-throughput routine analysis of free 8OHdG in human urine.

Wang, Zuwei↗

NASA NTRS2015

Fabrication of Feedhorn-Coupled Transition Edge Sensor Arrays for Measurement of the Cosmic Microwave Background Polarization

Characterization of the minute cosmic microwave background (CMB) polarization signature requires multi-frequency high-throughput precision instrument systems. We have previously described the detector fabrication of a 40 gigahertz focal plane and now describe the fabrication of a 37-element dual-polarization detector module for measurement of the CMB at 90 gigahertz. The 72-TES (Transition Edge Sensor)-based bolometers in each module are coupled to a niobium-based planar orthomode transducer with integrated band defining filters implemented in microstrip transmission line. A single crystal silicon dielectric substrate serves as microstrip dielectric and as a thermal link between the membrane isolated MoAu TES operating at 150 millikelvins and the heat bath. A short silicon leg between the heat bath and the TES bolometer is designed for ballistic phonon transport and provides improved process control and uniformity of thermal conductance in the presence of phonon scattering on roughened surfaces. Micro-machined structures are used to realize the orthomode transducer backshort, provide out of band signal rejection, and a silicon photonic choke for feedhorn coupling are described. The backshort, choke wafer, and detector wafer are indium bump-bonded to create a single 37-element dual-polarization detector module. Fourteen such hexagonally shaped modules each 80 millimeters in size comprise two focal planes. These, along with the recently delivered 40 gigahertz focal plane, will survey a large fraction of the sky as part of the Johns Hopkins University-led ground-based CLASS (Cosmology Large Angular Scale Surveyor) telescope.

Detectors↗

NASA NTRS2015

Fabrication of Feedhorn-Coupled Transition Edge Sensor Arrays for Measurement of the Cosmic Microwave Background Polarization

Characterization of the minute cosmic microwave background polarization signature requires multi-frequency high-throughput precision instrument systems. We have previously described the detector fabrication of a 40 GHz focal plane and now describe the fabrication of the detector modules for measurement of the CMB at 90GHz. The 74-TES based bolometers in each module are coupled to a niobium based planar orthomode transducer with integrated band defining filters implemented in microstrip transmission line. A single crystal silicon dielectric substrate serves as microstrip dielectric and as a thermal link between the membrane isolated MoAu TES operating at 150mK and the heat bath. A short silicon leg between the heat bath and the TES bolometer is designed for ballistic phonon transport and provides improved process control and uniformity of thermal conductance in the presence of phonon scattering on roughened surfaces. Micro-machined structures are used to realize the orthomode transducer backshort, provide out of band signal rejection, and a silicon photonic choke for feedhorn coupling are described. The backshort, choke wafer, and detector wafer are indium bump bonded to create a single 37-element dual-polarization detector module. Fourteen such hexagonally shaped modules each 90 mm in size comprise two focal planes. These, along with the recently delivered 40GHz focal plane, will survey a large fraction of the sky as part of the Johns Hopkins University led ground based CLASS (Cosmology Large Angular Scale Surveyor) telescope.

Characterization↗

NASA NTRS2015

GeneLab: NASA's Open Access, Collaborative Platform for Systems Biology and Space Medicine

NASA is investing in GeneLab1 (http:genelab.nasa.gov), a multi-year effort to maximize utilization of the limited resources to conduct biological and medical research in space, principally aboard the International Space Station (ISS). High-throughput genomic, transcriptomic, proteomic or other omics analyses from experiments conducted on the ISS will be stored in the GeneLab Data Systems (GLDS), an open-science information system that will also include a biocomputation platform with collaborative science capabilities, to enable the discovery and validation of molecular networks.

Berrios, Daniel C.↗

NASA NTRS2015

GeneLab: NASA's Open Access, Collaborative Platform for Systems Biology and Space Medicine

Berrios, Daniel C.↗

NASA NTRS2015

Near-Surface Plasma Characterization of the 12.5-kW NASA TDU1 Hall Thruster

To advance the state-of-the-art in Hall thruster technology, NASA is developing a 12.5-kW, high-specific-impulse, high-throughput thruster for the Solar Electric Propulsion Technology Demonstration Mission. In order to meet the demanding lifetime requirements of potential missions such as the Asteroid Redirect Robotic Mission, magnetic shielding was incorporated into the thruster design. Two units of the resulting thruster, called the Hall Effect Rocket with Magnetic Shielding (HERMeS), were fabricated and are presently being characterized. The first of these units, designated the Technology Development Unit 1 (TDU1), has undergone extensive performance and thermal characterization at NASA Glenn Research Center. A preliminary lifetime assessment was conducted by characterizing the degree of magnetic shielding within the thruster. This characterization was accomplished by placing eight flush-mounted Langmuir probes within each discharge channel wall and measuring the local plasma potential and electron temperature at various axial locations. Measured properties indicate a high degree of magnetic shielding across the throttle table, with plasma potential variations along each channel wall being less than or equal to 5 eV and electron temperatures being maintained at less than or equal to 5 eV, even at 800 V discharge voltage near the thruster exit plane. These properties indicate that ion impact energies within the HERMeS will not exceed 26 eV, which is below the expected sputtering threshold energy for boron nitride. Parametric studies that varied the facility backpressure and magnetic field strength at 300 V, 9.4 kW, illustrate that the plasma potential and electron temperature are insensitive to these parameters, with shielding being maintained at facility pressures 3X higher and magnetic field strengths 2.5X higher than nominal conditions. Overall, the preliminary lifetime assessment indicates a high degree of shielding within the HERMeS TDU1, effectively mitigating discharge channel erosion as a life-limiting mechanism.

Lifetime↗

NASA NTRS2015

GeneLab: A Systems Biology Platform for Spaceflight Omics Data

NASA's mission includes expanding our understanding of biological systems to improve life on Earth and to enable long-duration human exploration of space. Resources to support large numbers of spaceflight investigations are limited. NASA's GeneLab project is maximizing the science output from these experiments by: (1) developing a unique public bioinformatics database that includes space bioscience relevant "omics" data (genomics, transcriptomics, proteomics, and metabolomics) and experimental metadata; (2) partnering with NASA-funded flight experiments through bio-sample sharing or sample augmentation to expedite omics data input to the GeneLab database; and (3) developing community-driven reference flight experiments. The first database, GeneLab Data System Version 1.0, went online in April 2015. V1.0 contains numerous flight datasets and has search and download capabilities. Version 2.0 will be released in 2016 and will link to analytic tools. In 2015 Genelab partnered with two Biological Research in Canisters experiments (BBRIC-19 and BRIC-20) which examine responses of Arabidopsis thaliana to spaceflight. GeneLab also partnered with Rodent Research-1 (RR1), the maiden flight to test the newly developed rodent habitat. GeneLab developed protocols for maxiumum yield of RNA, DNA and protein from precious RR-1 tissues harvested and preserved during the SpaceX-4 mission, as well as from tissues from mice that were frozen intact during spaceflight and later dissected. GeneLab is establishing partnerships with at least three planned flights for 2016. Organism-specific nationwide Science Definition Teams (SDTs) will define future GeneLab dedicated missions and ensure the broader scientific impact of the GeneLab missions. GeneLab ensures prompt release and open access to all high-throughput omics data from spaceflight and ground-based simulations of microgravity and radiation. Overall, GeneLab will facilitate the generation and query of parallel multi-omics data, and deep curation of metadata for integrative analysis, allowing researchers to uncover cellular networks as observed in systems biology platforms. Consequently, the scientific community will have access to a more complete picture of functional and regulatory networks responsive to the spaceflight environment.. Analysis of GeneLab data will contribute fundamental knowledge of how the space environment affects biological systems, and enable emerging terrestrial benefits resulting from mitigation strategies to prevent effects observed during exposure to space. As a result, open access to the data will foster new hypothesis-driven research for future spaceflight studies spanning basic science to translational science.

proteomics↗

NASA NTRS2015

Remotely Controlled Mixers for Light Microscopy Module (LMM) Colloid Samples

Developed by NASA Glenn Research Center, the LMM aboard the International Space Station (ISS) is enabling multiple biomedical science experiments. Techshot, Inc., has developed a series of colloid specialty cell systems (C-SPECS) for use in the colloid science experiment module on the LMM. These low-volume mixing devices will enable uniform particle density and remotely controlled repetition of LMM colloid experiments. By automating the experiment process, C-SPECS allow colloid samples to be processed more quickly. In addition, C-SPECS will minimize the time the crew will need to spend on colloid experiments as well as eliminate the need for multiple and costly colloid samples, which are expended after a single examination. This high-throughput capability will lead to more efficient and productive use of the LMM. As commercial launch vehicles begin routine visits to the ISS, C-SPECS could become a significant means to process larger quantities of high-value materials for commercial customers.

Kurk, Michael A. (Andy)↗

NASA NTRS2016

Visible-Light-Responsive Photocatalysis: Ag-Doped TiO2 Catalyst Development and Reactor Design Testing

In recent years, the alteration of titanium dioxide to become visible-light-responsive (VLR) has been a major focus in the field of photocatalysis. Currently, bare titanium dioxide requires ultraviolet light for activation due to its band gap energy of 3.2 eV. Hg-vapor fluorescent light sources are used in photocatalytic oxidation (PCO) reactors to provide adequate levels of ultraviolet light for catalyst activation; these mercury-containing lamps, however, hinder the use of this PCO technology in a spaceflight environment due to concerns over crew Hg exposure. VLR-TiO2 would allow for use of ambient visible solar radiation or highly efficient visible wavelength LEDs, both of which would make PCO approaches more efficient, flexible, economical, and safe. Over the past three years, Kennedy Space Center has developed a VLR Ag-doped TiO2 catalyst with a band gap of 2.72 eV and promising photocatalytic activity. Catalyst immobilization techniques, including incorporation of the catalyst into a sorbent material, were examined. Extensive modeling of a reactor test bed mimicking air duct work with throughput similar to that seen on the International Space Station was completed to determine optimal reactor design. A bench-scale reactor with the novel catalyst and high-efficiency blue LEDs was challenged with several common volatile organic compounds (VOCs) found in ISS cabin air to evaluate the system's ability to perform high-throughput trace contaminant removal. The ultimate goal for this testing was to determine if the unit would be useful in pre-heat exchanger operations to lessen condensed VOCs in recovered water thus lowering the burden of VOC removal for water purification systems.

Photocatalysis↗

NASA NTRS2016

GeneLab for High Schools: Data Mining for the Next Generation

Modern biological sciences have become increasingly based on molecular biology and high-throughput molecular techniques, such as genomics, transcriptomics, and proteomics. NASA Scientists and the NASA Space Biology Program have aimed to examine the fundamental building blocks of life (RNA, DNA and protein) in order to understand the response of living organisms to space and aid in fundamental research discoveries on Earth. In an effort to enable NASA funded science to be available to everyone, NASA has collected the data from omics studies and curated them in a data system called GeneLab. Whilst most college-level interns, academics and other scientists have had some interaction with omics data sets and analysis tools, high school students often have not. Therefore, the Space Biology Program is implementing a new Summer Program for high-school students that aims to inspire the next generation of scientists to learn about and get involved in space research using GeneLabs Data System. The program consists of three main components core learning modules, focused on developing students knowledge on the Space Biology Program and Space Biology research, Genelab and the data system, and previous research conducted on model organisms in space; networking and team work, enabling students to interact with guest lecturers from local universities and their fellow peers, and also enabling them to visit local universities and genomics centers around the Bay area; and finally an independent learning project, whereby students will be required to form small groups, analyze a dataset on the Genelab platform, generate a hypothesis and develop a research plan to test their hypothesis. This program will not only help inspire high-school students to become involved in space-based research but will also help them develop key critical thinking and bioinformatics skills required for most college degrees and furthermore, will enable them to establish networks with their peers and connections with university Professors that may help them achieve their educational goals.

genelab↗

NASA NTRS2016

Genomic and Phenotypic Characterization of Yeast Biosensor for Deep-space Radiation

The BioSentinel mission was selected to launch as a secondary payload onboard NASA Exploration Mission 1 (EM-1) in 2018. In BioSentinel, the budding yeast Saccharomyces cerevisiae will be used as a biosensor to measure the long-term impact of deep-space radiation to living organisms. In the 4U-payload, desiccated yeast cells from different strains will be stored inside microfluidic cards equipped with 3-color LED optical detection system to monitor cell growth and metabolic activity. At different times throughout the 12-month mission, these cards will be filled with liquid yeast growth media to rehydrate and grow the desiccated cells. The growth and metabolic rates of wild-type and radiation-sensitive strains in deep-space radiation environment will be compared to the rates measured in the ground- and microgravity-control units. These rates will also be correlated with measurements obtained from onboard physical dosimeters. In our preliminary long-term desiccation study, we found that air-drying yeast cells in 10% trehalose is the best method of cell preservation in order to survive the entire 18-month mission duration (6-month pre-launch plus 12-month full-mission periods). However, our study also revealed that desiccated yeast cells have decreasing viability over time when stored in payload-like environment. This suggests that the yeast biosensor will have different population of cells at different time points during the long-term mission. In this study, we are characterizing genomic and phenotypic changes in our yeast biosensor due to long-term storage and desiccation. For each yeast strain that will be part of the biosensor, several clones were reisolated after long-term storage by desiccation. These clones were compared to their respective original isolate in terms of genomic composition, desiccation tolerance and radiation sensitivity. Interestingly, clones from a radiation-sensitive mutant have better desiccation tolerance compared to their original isolate without losing radiation sensitivity. We employed Next-Generation Sequencing technology to better understand this phenotypic variation. Current effort is focusing on the analysis of high-throughput sequencing data to look for genomic changes in these reisolated clones compared to their original isolate.

yeast↗

NASA NTRS2016

Multi-Objective Reinforcement Learning for Cognitive Radio-Based Satellite Communications

Previous research on cognitive radios has addressed the performance of various machine-learning and optimization techniques for decision making of terrestrial link properties. In this paper, we present our recent investigations with respect to reinforcement learning that potentially can be employed by future cognitive radios installed onboard satellite communications systems specifically tasked with radio resource management. This work analyzes the performance of learning, reasoning, and decision making while considering multiple objectives for time-varying communications channels, as well as different cross-layer requirements. Based on the urgent demand for increased bandwidth, which is being addressed by the next generation of high-throughput satellites, the performance of cognitive radio is assessed considering links between a geostationary satellite and a fixed ground station operating at Ka-band (26 GHz). Simulation results show multiple objective performance improvements of more than 3.5 times for clear sky conditions and 6.8 times for rain conditions.

software defined radio↗

NASA NTRS2016

Ground Calibration of the Astro-H (Hitomi) Soft X-Ray Spectrometer

The Astro-H (Hitomi) Soft X-ray Spectrometer (SXS) was a pioneering imaging x-ray spectrometer with 5 eV energy resolution at 6 keV. The instrument used a microcalorimeter array at the focus of a high-throughput soft x-ray telescope to enable high-resolution non-dispersive spectroscopy in the soft x-ray waveband (0.3-12 keV). We present the suite of ground calibration measurements acquired from 2012-2015, including characterization of the detector system, anti-coincidence detector, optical blocking filters, and filter-wheel filters. The calibration of the 36-pixel silicon thermistor microcalorimeter array includes parameterizations of the energy gain scale and line spread function for each event grade over a range of instrument operating conditions, as well as quantum efficiency measurements. The x-ray transmission of the set of five Al/polyimide thin-film optical blocking filters mounted inside the SXS dewar has been modeled based on measurements at synchrotron beamlines, including with high spectral resolution at the C, N, O, and Al K-edges. In addition, we present the x-ray transmission of the dewar gate valve and of the filters mounted on the SXS filter wheel (external to the dewar), including beryllium, polyimide, and neutral density filters.

detectors↗

NASA NTRS2016

Calibration of the Microcalorimeter Spectrometer On-Board the Hitomi (Astro-H) Observatory (invited)

The Hitomi Soft X-ray Spectrometer (SXS) was a pioneering non-dispersive imaging x-ray spectrometer with 5 eV FWHM energy resolution, consisting of an array of 36 silicon-thermistor microcalorimeters at the focus of a high-throughput soft x-ray telescope. The instrument enabled astrophysical plasma diagnostics in the 0.3-12 keV band. We introduce the SXS calibration strategy and corresponding ground calibration measurements that took place from 2012-2015, including both the characterization of the microcalorimeter array and measurements of the x-ray transmission of optical blocking filters.

ASTRO H↗