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At least 397 records · Page 22

Final Report - Hypergravity Effects on Chromatin Conformation and Nuclear Structure in Cultured Cells using High-throughput Sequencing

The conformation of the human genome is known to play an important role in transcriptional control of gene expression. Our aim is to assess whether exposure of cultured human cardiomyocytes to hypergravity can induce changes in chromatin organization as assayed by Hi-C proximity ligation technique. Hi-C is used to analyze chromatin interactions by using formaldehyde to crosslink regions of chromatin that are in close proximity. The DNA is then fragmented using a restriction enzyme and ligated under dilute conditions to favor intramolecular ligation of cross-linked fragments. Finally, the DNA is sequenced, allowing reconstruction of genomic structure. iCell cardiomyocyte cultures will be exposed to 40 g via an engineered device (incu-fuge) that allows for the chemical fixation of cells on a spinning centrifuge. Additionally, we plan on using fluorescence microscopy to analyze the nuclear and actin cytoskeletal conformation of cardiomyocytes post hypergravity exposure. We hypothesize that chromatin will rearrange in hypergravity conditions, both rapidly due to direct mechanical forces, as well as over longer time frames due to changes to structures necessary for transcriptional responses such as the de novo formation of promoter-enhancer loops. A negative result–no change between 1 g and hypergravity conditions–would nevertheless be an important data point in our understanding of the rheology of the nucleus, and how cells and cellular structures respond to different gravity fields. The cellular physiology of hypergravity has clinical relevance for spaceflight, and can further inform our understanding of microgravity physiology.

chromatin↗

Interacting fractons in 2+1-dimensional quantum field theory

We analyze, in perturbation theory, a theory of weakly interacting fractons and non-relativistic fermions in a 2+1 dimensional Quantum Field Theory. In particular we compute the 1-loop corrections to the self energies and interaction vertex, and calculate the associated 1-loop Renormalization Group flows of the coupling constants. Surprisingly, we find that the fracton-fermion coupling does not flow due to an emergent coordinate-dependent symmetry of the effective Lagrangian, making this model a well-defined quantum field theory. We provide additional discussions on the regularization and renormalization of interacting fractonic theories, as well as both qualitative and quantitative remarks regarding the theory at finite temperature and finite chemical potential.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Structural basis for ring-opening fluorescence by the RhoBAST RNA aptamer

Abstract Tagging RNAs with fluorogenic aptamers has enabled imaging of transcripts in living cells, revealing novel aspects of RNA metabolism and dynamics. While a diverse set of fluorogenic aptamers has been developed, a new generation of aptamers uses the ring-opening of spirocyclic rhodamine dyes to achieve robust performance in live mammalian cells. These fluorophores have two chemical states: a cell-permeable spirocyclic state and a fluorescent zwitterionic state. The SpyRho555 dye is mostly non-fluorescent in solution and becomes fluorescent in complex with the RhoBAST aptamer. To understand the basis for RhoBAST-SpyRho555 fluorogenicity, we have determined crystal structures of RhoBAST in complex with 5-carboxytetramethylrhodamine and a SpyRho555 analogue, MaP555. RhoBAST is organized by a perfect four-way junction that positions two loops to form the dye-binding pocket. The core of the ligand resides between a tri-adenine floor and a single guanine base, largely driven by π-stacking interactions. Importantly, the unpaired guanine interacts with the 3-position group of MaP555 to stabilize the open conformation, supported by mutagenesis data, and may play an active role in promoting the open conformation of the dye. This work has implications for the development of new fluorogenic aptamers with improved properties using structure-guided design approaches.

Biochemistry & Molecular Biology↗

Orion Emergency Mask Approach

Emergency mask approach on Orion poses a challenge to the traditional Shuttle or Station approaches. Currently, in the case of a fire or toxic spill event, the crew utilizes open loop oxygen masks that provide the crew with oxygen to breath, but also dumps the exhaled oxygen into the cabin. For Orion, with a small cabin volume, the extra oxygen will exceed the flammability limit within a short period of time, unless a nitrogen purge is also provided. Another approach to a fire or toxic spill event is the use of a filtering emergency masks. These masks utilize some form of chemical beds to scrub the air clean of toxic providing the crew safe breathing air for a period without elevating the oxygen level in the cabin. Using the masks and a form of smoke-eater filter, it may be possible to clean the cabin completely or to a level for safe transition to a space suit to perform a cabin purge. Issues with filters in the past have been the reaction temperature and high breathing resistance. Development in a new form of chemical filters has shown promise to make the filtering approach feasible.

Tuan, George C.↗

Orion Emergency Mask Approach

Emergency mask approach on Orion poses a challenge to the traditional Shuttle or Station approaches. Currently, in the case of a fire or toxic spill event, the crew utilizes open loop oxygen masks that provide the crew with oxygen to breath, but also dumps the exhaled oxygen into the cabin. For Orion, with a small cabin volume, the extra oxygen will exceed the flammability limit within a short period of time, unless a nitrogen purge is also provided. Another approach to a fire or toxic spill event is the use of a filtering emergency masks. These masks utilize some form of chemical beds to scrub the air clean of toxic providing the crew safe breathing air for a period without elevating the oxygen level in the cabin. Using the masks and a form of smoke-eater filter, it may be possible to clean the cabin completely or to a level for safe transition to a space suit to perform a cabin purge. Issues with filters in the past have been the reaction time, breakthroughs, and high breathing resistance. Development in a new form of chemical filters has shown promise to make the filtering approach feasible.

Tuan, George C.↗

A Comprehensive Investigation into the Effect of a Low Surface Energy Treatment on Gas Hydrate, Asphaltene, and Wax Formation, Deposition, and Adhesion

The formation/precipitation and deposition of pipeline solids, such as gas hydrates, asphaltenes, and waxes have long plagued production fields. Given the vast differences in chemistries of these solids, any current prevention or mitigation strategy, particularly for cases in which multiple issues are a concern, is likely to involve an extensive assortment of chemical additives that are both costly and add complexity to the system. Surface treatments (coatings), on the other hand, present a relatively viable option for management strategies. A chemically and physically robust surface treatment with the ability to address deposition issues for multiple pipeline solids could not only decrease the operating expenditures for a field through material cost savings and obviation of downstream separation, but could also simplify produced fluids by eliminating additional chemicals from the mixture. The purpose of this study was to explore the feasibility of a particular surface treatment as part of a solids management strategy. This work used an omniphobic surface treatment to probe its effects on gas hydrate, asphaltene, and wax deposition. Specifically, an interfacial tensiometer (IFT) collected contact angle measurements for wettability studies. High-pressure rocking cells studied gas hydrate nucleation and deposition. A bench-scale flow loop quantified the deposition of oil and asphaltenes after a set time period. Finally, a mechanical shear device measured the adhesion force of wax deposits on untreated/treated surfaces. Static contact angle results showed that the omniphobic surface treatment had reduced surface interaction with water droplets in air, altering from the complete wetting on corroded surfaces to slightly hydrophobic conditions of greater than 100°. In addition, rocking-cell tests indicated that these omniphobic surface treatments may prevent gas hydrate deposition for up to 72 hours. The gas hydrate rocking-cell tests also demonstrated possible increases in induction time and occasional elimination of hydrate nucleation with the surface treatment. Finally, the surface treatment application, which also decreased surface roughness, showed that crude oil and asphaltene particles deposition, as well as the shear required to remove solidified wax deposits, could be reduced by a large factor. Overall, promising results were recorded for all major flow-assurance solids in the presence of the surface treatment.

Engineering↗

Nutrient-substituted hydroxyapatites: synthesis and characterization

Incorporation of Mg, S, and plant-essential micronutrients into the structure of synthetic hydroxyapatite (HA) may be advantageous for closed-loop systems, such as will be required on Lunar and Martian outposts, because these apatites can be used as slow-release fertilizers. Our objective was to synthesize HA with Ca, P, Mg, S, Fe, Cu, Mn, Zn, Mo, B, and Cl incorporated into the structure, i.e., nutrient-substituted apatites. Hydroxyapatite, carbonate hydroxyapatite (CHA), nutrient-substituted hydroxyapatite (NHA), and nutrient-substituted carbonate hydroxyapatite (NCHA) were synthesized by precipitating from solution. Chemical and mineralogical analysis of precipitated samples indicated a considerable fraction of the added cations were incorporated into HA, without mineral impurities. Particle size of the HA was in the 1 to 40 nm range, and decreased with increased substitution of nutrient elements. The particle shape of HA was elongated in the c-direction in unsubstituted HA and NHA but more spherical in CHA and NCHA. The substitution of cations and anions in the HA structure was confirmed by the decrease of the d[002] spacing of HA with substitution of ions with an ionic radius less than that of Ca or P. The DTPA-extractable Cu ranged from 8 to 8429 mg kg-1, Zn ranged from 57 to 1279 mg kg-1, Fe from 211 to 2573 mg kg-1, and Mn from 190 to 1719 mg kg-1, depending on the substitution level of each element in HA. Nutrient-substituted HA has the potential to be used as a slow-release fertilizer to supply micronutrients, S, and Mg in addition to Ca and P.

NASA Discipline Life Support Systems↗

Structural Characterization of the Human Cytosolic Malate Dehydrogenase I

The first crystal structure of the human cytosolic malate dehydrogenase I (MDH1) is described. Structure determination at a high resolution (1.65 Å) followed production, isolation, and purification of human MDH1 using a bacterial expression system. The structure is a binary complex of MDH1 with only a bound malonate molecule in the substrate binding site. Comparisons of this structure with malate dehydrogenase enzymes from other species confirm that the human enzyme adopts similar secondary, tertiary, and quaternary structures and that the enzyme retains a similar conformation even when nicotinamide adenine dinucleotide (NAD + ) is not bound. A comparison to the highly homologous porcine (sus scrofa) MDH1 ternary structures leads to the conclusion that only small conformational differences are needed to accommodate binding by NAD + or other NAD + mimetics. Conformational differences observed in the second subunit show that the NAD + binding elements are nevertheless quite flexible. Comparison of hMDH1 to the human mitochondrial malate dehydrogenase (hMDH2) reveals some key differences in the α7–α8 loop, which lies directly beneath the substrate binding pocket. These differences might be exploited in the structure-assisted design of selective small molecule inhibitors of hMDH1, an emerging target for the development of anticancer therapeutics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Physical/chemical closed-loop water-recycling for long-duration missions

Water needs, water sources, and means for recycling water are examined in terms appropriate to the water quality requirements of a small crew and spacecraft intended for long duration exploration missions. Inorganic, organic, and biological hazards are estimated for waste water sources. Sensitivities to these hazards for human uses are estimated. The water recycling processes considered are humidity condensation, carbon dioxide reduction, waste oxidation, distillation, reverse osmosis, pervaporation, electrodialysis, ion exchange, carbon sorption, and electrochemical oxidation. Limitations and applications of these processes are evaluated in terms of water quality objectives. Computerized simulation of some of these chemical processes is examined. Recommendations are made for development of new water recycling technology and improvement of existing technology for near term application to life support systems for humans in space. The technological developments are equally applicable to water needs on earth, in regions where extensive water ecycling is needed or where advanced water treatment is essential to meet EPA health standards.

Herrmann, Cal C.↗

Scale-Up and Modeling Efforts Using an Omniphobic Surface Treatment for Mitigating Solids Deposition

Abstract Gas hydrates, waxes and asphaltenes represent some of the most significant flow assurance challenges, especially in subsea lines, where treatment options can be limited. Currently, complete avoidance is the primary strategy for hydrate management, while chemical or mechanical flushing/pigging may be utilized for other solids. Each system must also be treated with individualized solutions, as there have been no proved one-size-fits-all technologies demonstrated to date. As an alternative to constant chemical injection or thermodynamic controls such as insulation or heating, a robust omniphobic surface treatment material has been developed which has been shown in previous studies to significantly reduce the adhesion of flow assurance solids, resulting in lower risk for deposition and plugging of gas hydrates, waxes, and asphaltenes. As part of a Department of Energy study, laboratory scale tests were performed on a variety of apparatuses ranging from micromechanical force (micron scale) to laboratory flow loop testing (meter scale). While the results from these tests have been promising, there can be some disconnects between lab-scale observations and field-scale testing. Several factors can result in discrepancies between small-scale bench-top studies and deployment-scale efforts. These include flow conditions (Reynolds number, flow regime), chemistry (synthetic vs. crude oils, gas composition, and additives), physical differences (pipeline material, size, and geometry), etc. This work will describe the actions taken to better understand the deployment and performance of a material such as this omniphobic surface treatment in field scenarios, and to build confidence for deployment in a production scenario. These efforts include modeling field production scenarios using models developed from lab observations, application of the material to field-scale equipment to better understand application challenges, and expanded survivability and longevity testing. Understanding the bridge between laboratory testing and full-scale deployment allows for better technique and risk mitigation for field scale testing.

03 NATURAL GAS↗

Phytoplankton exudates and lysates support distinct microbial consortia with specialized metabolic and ecophysiological traits

Marine dissolved organic matter, which originates from phytoplankton, holds as much carbon as Earth’s atmosphere; yet, the biological processes governing its fate are primarily studied under idealized laboratory conditions or through indirect measures such as genome sequencing. In this work, we used isotope labeling to directly quantify uptake of complex carbon pools from the two primary sources of marine organic carbon (diatoms and cyanobacteria) by a natural microbial community. Furthermore, our data show that carbon pools are partitioned into distinct microbial lineages whose physiological properties and resource acquisition strategies match the chemical nature of their preferred substrates. Our results provide ecological and functional insights into the patterns of microbial community structure changes that occur during marine phytoplankton blooms.

59 BASIC BIOLOGICAL SCIENCES↗

Cryo neutron crystallography demonstrates influence of RNA 2'-OH orientation on conformation, sugar pucker and water structure

The ribose 2'-hydroxyl is the key chemical difference between RNA and DNA and primary source of their divergent structural and functional characteristics. Macromolecular X-ray diffraction experiments typically do not reveal the positions of hydrogen atoms. Thus, standard crystallography cannot determine 2'-OH orientation (H2'-C2'-O2'-HO2' torsion angle) and its potential roles in sculpting the RNA backbone and the expansive fold space. Here, we report the first neutron crystal structure of an RNA, the Escherichia coli rRNA Sarcin-Ricin Loop (SRL). 2'-OD orientations were established for all 27 residues and revealed O-D bonds pointing toward backbone (O3', 13 observations), nucleobase (11) or sugar (3). Most riboses in the SRL stem region show a 2'-OD backbone-orientation. GAGA-tetraloop riboses display a 2'-OD base-orientation. An atypical C2'-endo sugar pucker is strictly correlated with a 2'-OD sugar-orientation. Neutrons reveal the strong preference of the 2'-OH to donate in H-bonds and that 2'-OH orientation affects both backbone geometry and ribose pucker. We discuss 2'-OH and water molecule orientations in the SRL neutron structure and compare with results from a solution phase 10 μs MD simulation. We demonstrate that joint cryo-neutron/X-ray crystallography offers an all-in-one approach to determine the complete structural properties of RNA, i.e. geometry, conformation, protonation state and hydration structure.

59 BASIC BIOLOGICAL SCIENCES↗

Using Calibrated Water Data for Preliminary Validation of the SRT Code for Advanced Reactors

Recent interest and corresponding progress worldwide regarding advanced nuclear reactors has renewed focus on their performance and related safety assessments. Specifically, the U.S. Nuclear Regulatory Commission has emphasized the importance of mechanistic approaches to source term analysis for advanced reactor licensing applications, which attempt to realistically account radionuclide transport and retention phenomena. Further model development is required due to the numerous and complex physical and chemical phenomena associated with mechanistic source term analyses. Reflecting the need for modeling advancement, Argonne National Laboratory developed a mechanistic source term analysis tool for sodium fast reactors. The Simplified Radionuclide Transport (SRT) code describes fuel pin failure (for simulating the initial condition at the point of fuel pin breach), bubble scrubbing, deposition, leakage and following environmental impact. In the current work, a validation study of the SRT bubble scrubbing model is performed using a water-loop experiment performed at the University of Wisconsin-Madison. Through the analysis, the approach and fundamental bubble scrubbing models in SRT, which examine the removal of aerosols within the bubble as it is transported through a pool, have been widely evaluated. The results of the assessment demonstrate a high level of agreement in the regions of greater aerosol size. In the parameter range of minimal aerosol removal, the simulation slightly underpredicts the experiment results; however, considering the scale of plots and huge uncertainties inherently included, the deviation can be judged to be minor and would produce a conservative result. In addition, uncertainty analysis has been further refined to reflect the experimental distribution of parameters including aerosol sizes, which induces a span of performance for each representative aerosol size. Based upon the initial validation results along with uncertainty effects, SRT is expected to provide meaningful insights for the analysis of bubble scrubbing. Future sodium-loop tests will provide further validation basis.

Kam, Dong Hoon↗

Testing to Transition the J-2X from Paper to Hardware

The J-2X Upper Stage Engine (USE) will be the first new human-rated upper stage engine since the Apollo program of the 1960s. It is designed to carry the Ares I and Ares V into orbit and send the Ares V to the Moon as part of NASA's Constellation Program. This paper will provide an overview of progress on the design, testing, and manufacturing of this new engine in 2009 and 2010. The J-2X embodies the program goals of basing the design on proven technology and experience and seeking commonality between the Ares vehicles as a way to minimize risk, shorten development times, and live within current budget constraints. It is based on the proven J-2 engine used on the Saturn IB and Saturn V launch vehicles. The prime contractor for the J-2X is Pratt & Whitney Rocketdyne (PWR), which is under a design, development, test, and engineering (DDT&E) contract covering the period from June 2006 through September 2014. For Ares I, the J-2X will provide engine start at approximately 190,000 feet, operate roughly 500 seconds, and shut down. For Ares V, the J-2X will start at roughly 190,000 feet to place the Earth departure stage (EDS) in orbit, shut down and loiter for up to five days, re-start on command and operate for roughly 300 seconds at its secondary power level to perform trans lunar injection (TLI), followed by final engine shutdown. The J-2X development effort focuses on four key areas: early risk mitigation, design risk mitigation, component and subassembly testing, and engine system testing. Following that plan, the J-2X successfully completed its critical design review (CDR) in 2008, and it has made significant progress in 2009 and 2010 in moving from the drawing board to the machine shop and test stand. Post-CDR manufacturing is well under way, including PWR in-house and vendor hardware. In addition, a wide range of component and sub-component tests have been completed, and more component tests are planned. Testing includes heritage powerpack, turbopump inducer water flow, turbine air flow, turbopump seal testing, main injector and gas generator, injector testing, augmented spark igniter testing, nozzle side loads cold flow testing, nozzle extension film cooling flow testing, control system testing with hardware in the loop, and nozzle extension emissivity coating tests. In parallel with hardware manufacturing, work is progressing on the new A-3 test stand to support full duration altitude testing. The Stennis A-2 test stand is scheduled to be turned over to the Constellation Program in September 2010 to be modified for J-2X testing also. As the structural steel was rising on the A-3 stand, work was under way in the nearby E complex on the chemical steam generator and subscale diffuser concepts to be used to evacuate the A-3 test cell and simulate altitude conditions.

Byrd, Tom↗

Long Duration Life Test of Propylene Glycol Water Based Thermal Fluid Within Thermal Control Loop

Evaluations of thermal properties and resistance to microbial growth concluded that 50% Propylene Glycol (PG)-based fluid and 50% de-ionized water mixture was desirable for use as a fluid within a vehicle s thermal control loop. However, previous testing with a commercial mixture of PG and water containing phosphate corrosion inhibitors resulted in corrosion of aluminum within the test system and instability of the test fluid. This paper describes a follow-on long duration testing and analysis of 50% Propylene Glycol (PG)-based fluid and 50% de-ionized water mixture with inorganic corrosion inhibitors used in place of phosphates. The test evaluates the long-term fluid stability and resistance to microbial and chemical changes

Le, Hung↗

Compact Multi-Gas Monitor for Life Support Systems Control in Space: Evaluation Under Realistic Environmental Conditions

Advanced space life support systems require lightweight, low-power, durable sensors for monitoring critical gas components. A luminescence-based optical flow-through cell to monitor carbon dioxide, oxygen, and humidity has been developed and was demonstrated using bench top instrumentation under environmental conditions relevant to portable life support systems, including initially pure oxygen atmosphere, pressure range from 3.5 to 14.7 psi, temperature range from 50 F to 150 F, and humidity from dry to 100% RH and under liquid water saturation. This paper presents the first compact readout unit for these optical sensors, designed for the volume, power, and weight restrictions of a spacesuit portable Life support system and the analytical characterization of the optical sensors interrogated by the novel optoelectronic system. Trace gas contaminants in a space suit, originating from hardware and material off-gassing and crew member metabolism, are from many chemical families. The result is a gas mix much more complex than the pure oxygen fed into the spacesuit, which may interfere with gas sensor readings. The paper also presents an evaluation of optical sensor performance when exposed to the most significant trace gases reported to be found in spacesuits. The studies were conducted with the spacecraft maximum allowable concentrations for those trace gases and the calculated 8-hr. concentrations resulting from having no trace contaminant control system in the ventilation loop. Finally, a profile of temperature, pressure, humidity, and gas composition for a typical EVA mission has been defined, and the performance of sensors operated repeatedly under simulated EVA mission conditions has been studied.

Delgado, Jesus↗

Initial Engineering Framework for Species Tracking in MSRs Involving Fuel Salt and Structures

This report implements a high-fidelity multiphysics modeling framework using the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program tools to track leaching and plating of materials between the fuel salt and structures in Molten Salt Reactors (MSRs). Specifically, this framework is demonstrated in modeling various processes within MSRs including hot and cold leg corrosion, redox potential driven corrosion, colloid precipitation and deposition, and noble metal plating and decay heat modeling. The model integrates neutronics, thermal-hydraulics, depletion, and thermochemistry to simulate the evolving chemical behavior of the fuel salt in interactions with structural materials. Initial findings suggest that hot-cold leg corrosion in MSR systems may become significant if the redox potential of the fuel salt is not sufficiently controlled. Additionally, the impact of noble metal decay heat deposition in large power reactors is explored. The resulting engineering framework for species tracking will be applied in the future toward specific validation work with ongoing experimental efforts focusing on both chloride and fluoride salt loop experiments with in-situ corrosion and redox control instrumentation.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Design of A CVD Reactor for the Deposition of Diamond in A Microgravity Environment

There is a growing body of theoretical and experimental evidence suggesting that the uniformity, rate, adhesion, quality, and other key properties of Chemical Vapor Deposition (CVD) diamond coatings are influenced by the gas mixing kinetics in the thermal plasma environment of the reaction chamber. The implementation of, for example, Microwave Plasma Enhanced Chemical Vapor Deposition (MPECVD) process in microgravity has, thus, been suggested. Such a diamond deposition system, which overcomes the limitations of present systems and which is distiguishable from them by the use of high pressure MPECVD and recirculation of the would be effluent hydrogen and carbon, is described. Given the key fact that there is nothing in the effluent of the MPECVD process that is truly a byproduct or 'waste', the system can, at least in principle, lend itself to being closed loop yet dynamic. The exhaust contains hydrogen and carbon species which can be recirculated to the plasma reactor, that is, since there are no unusable reaction byproducts, the effluent can be fed back to the reaction chamber with no detriment, thus allowing deployment in a microgravity environment.

M L Languell↗