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At least 163 records · Page 9

Crystal structure of intercalated four-stranded d(C3T) at 1.4 angstroms resolution

The crystal structure of d(C3T), solved at 1.4 angstroms resolution, reveals that the molecule forms a four-stranded intercalated complex. It consists of two parallel-stranded duplexes, each of which is held together by cytosine-protonated cytosine base pairs. The two duplexes are intercalated with each other and have opposite strand orientation. The molecule has a flat, lath-like appearance, and the covalently bonded cytosines have a slow right-handed twist of 17.1 degrees. However, there is considerable asymmetry. On one of the flat sides, the phosphate groups are rotated away from the center of the molecule. They are held in this orientation by bridging water molecules that bind the NH of cytosine and a phosphate group of an opposite chain. There is also considerable microheterogeneity in the structure. The cytosine hemiprotonation occurs even at pH 7 where stable crystals form.

Non-NASA Center↗

Stable loop in the crystal structure of the intercalated four-stranded cytosine-rich metazoan telomere

In most metazoans, the telomeric cytosine-rich strand repeating sequence is d(TAACCC). The crystal structure of this sequence was solved to 1.9-A resolution. Four strands associate via the cytosine-containing parts to form a four-stranded intercalated structure held together by C.C+ hydrogen bonds. The base-paired strands are parallel to each other, and the two duplexes are intercalated into each other in opposite orientations. One TAA end forms a highly stabilized loop with the 5' thymine Hoogsteen-base-paired to the third adenine. The 5' end of this loop is in close proximity to the 3' end of one of the other intercalated cytosine strands. Instead of being entirely in a DNA duplex, this structure suggests the possibility of an alternative conformation for the cytosine-rich telomere strands.

NASA Discipline Exobiology↗

Monolithic Microwave Integrated Circuit (MMIC) Phased Array Demonstrated With ACTS

Monolithic Microwave Integrated Circuit (MMIC) arrays developed by the NASA Lewis Research Center and the Air Force Rome Laboratory were demonstrated in aeronautical terminals and in mobile or fixed Earth terminals linked with NASA's Advanced Communications Technology Satellite (ACTS). Four K/Ka-band experimental arrays were demonstrated between May 1994 and May 1995. Each array had GaAs MMIC devices at each radiating element for electronic beam steering and distributed power amplification. The 30-GHz transmit array used in uplinks to ACTS was developed by Lewis and Texas Instruments. The three 20-GHz receive arrays used in downlinks from ACTS were developed in cooperation with the Air Force Rome Laboratory, taking advantage of existing Air Force integrated-circuit, active-phased-array development contracts with the Boeing Company and Lockheed Martin Corporation. Four demonstrations, each related to an application of high interest to both commercial and Department of Defense organizations, were conducted. The location, type of link, and the data rate achieved for each of the applications is shown. In one demonstration-- an aeronautical terminal experiment called AERO-X--a duplex voice link between an aeronautical terminal on the Lewis Learjet and ACTS was achieved. Two others demonstrated duplex voice links (and in one case, interactive video links as well) between ACTS and an Army high-mobility, multipurpose wheeled vehicle (HMMWV, or "humvee"). In the fourth demonstration, the array was on a fixed mount and was electronically steered toward ACTS. Lewis served as project manager for all demonstrations and as overall system integrator. Lewis engineers developed the array system including a controller for open-loop tracking of ACTS during flight and HMMWV motion, as well as a laptop data display and recording system used in all demonstrations. The Jet Propulsion Laboratory supported the AERO-X program, providing elements of the ACTS Mobile Terminal. The successful performance of experimental, proof-of-concept MMIC K/Ka-band arrays developed with U.S. industry in field demonstrations with ACTS indicates that high density MMIC integration at 20 and 30 GHz is indeed feasible. The successful development and demonstration of the MMIC array systems was possible only because of significant intergovernmental and Government/industry cooperation and the high level of teamwork within Lewis. The results provide a strong incentive for continuing the focused development of MMIC-array technology for satellite communications applications, with emphasis on packaging and cost issues, and for continuing the planning and conducting of other appropriate demonstrations or experiments of phased-array technology with ACTS. Given the present pressures on reducing funding for research and development in Government and industry, the extent to which this can be continued in a cooperative manner will determine whether MMIC array technology will make the transition from the proof-of-concept level to the operational system level.

Source record↗

Computational Study on Full-length Human Ku70 with Double Stranded DNA: Dynamics, Interactions and Functional Implications

The Ku70/80 heterodimer is the first repair protein in the initial binding of double-strand break (DSB) ends following DNA damage, and is a component of nonhomologous end joining repair, the primary pathway for DSB repair in mammalian cells. In this study we constructed a full-length human Ku70 structure based on its crystal structure, and performed 20 ns conventional molecular dynamic (CMD) simulations on this protein and several other complexes with short DNA duplexes of different sequences. The trajectories of these simulations indicated that, without the topological support of Ku80, the residues in the bridge and C-terminal arm of Ku70 are more flexible than other experimentally identified domains. We studied the two missing loops in the crystal structure and predicted that they are also very flexible. Simulations revealed that they make an important contribution to the Ku70 interaction with DNA. Dislocation of the previously studied SAP domain was observed in several systems, implying its role in DNA binding. Targeted molecular dynamic (TMD) simulation was also performed for one system with a far-away 14bp DNA duplex. The TMD trajectory and energetic analysis disclosed detailed interactions of the DNA-binding residues during the DNA dislocation, and revealed a possible conformational transition for a DSB end when encountering Ku70 in solution. Compared to experimentally based analysis, this study identified more detailed interactions between DNA and Ku70. Free energy analysis indicated Ku70 alone is able to bind DNA with relatively high affinity, with consistent contributions from various domains of Ku70 in different systems. The functional implications of these domains in the processes of Ku heterodimerization and DNA damage recognition and repair can be characterized in detail based upon this analysis.

Hu, Shaowen↗

Interactions of Ku70/80 with Double-Strand DNA: Energetic, Dynamics, and Functional Implications

Space radiation is a proficient inducer of DNA damage leading to mutation, aberrant cell signaling, and cancer formation. Ku is among the first responding proteins in nucleus to recognize and bind the DNA double strand breaks (DSBs) whenever they are introduced. Once loaded Ku works as a scaffold to recruit other repair factors of non-homologous end joining and facilitates the following repair processes. The crystallographic study of the Ku70/80 heterodimer indicate the core structure of this protein shows virtually no conformational change after binding with DNA. To investigate the dynamical features as well as the energetic characteristics of Ku-DNA binding, we conduct multi-nanosecond molecular dynamics simulations of a modeled Ku70/80 structure and several complexes with two 24-bp DNA duplexes. Free energy calculations show significant energy differences between the complexes with Ku bound at DSBs and those with Ku associated at an internal site of a chromosome. The results also reveal detailed interactions between different nucleotides and the amino acids along the DNA-binding cradle of Ku, indicating subtle binding preference of Ku at specific DNA sequences. The covariance matrix analyses along the trajectories demonstrate the protein is stimulated to undergo correlated motions of different domains once bound to DNA ends. Additionally, principle component analyses identify these low frequency collective motions suitable for binding with and translocation along duplex DNA. It is proposed that the modification of dynamical properties of Ku upon binding with DSBs may provide a signal for the further recruitment of other repair factors such as DNA-PKcs, XLF, and XRCC4.

Hu, Shaowen↗

The Influence of Silicon Additions on Friction and Wear of Nickel Alloys at Temperatures to 1000 Degrees Fahrenheit

Small additions of silicon have considerable beneficial effect on performance on slider alloys. This effect has most frequently been attributed to increased hardness. The research reported was conducted to consider a hypothesis that the primary role of silicon in slider alloys is one of supporting the formation of protective surface films. Friction and wear data were obtained at temperatures from 75 to 1000 degrees Fahrenheit with a series of binary silicon-nickel alloys containing up to 10 percent silicon. Pertinent hot hardness, metallurgical and surface-film analysis data are included. Atmospheres used were air, mixtures of oxygen and argon, a mixture of hydrogen and nitrogen, and a halogenated methane gas lubricant. The results show the role of silicon as a film former to be of great importance in success of silicon-containing alloys as slider materials for extreme temperatures. The range of variables studied gave friction coefficients from 0.05 to greater than 10.00 depending on film formation tendencies. Alloys with 5 percent or more silicon having a duplex structure showed the best results. Film formation resulted from surface reactions or the smearing of the softer phase from the alloys having duplex structure.

Buckley, Donald H.↗

Successful Validation of Sample Processing and Quantitative Real-Time PCR Capabilities on the International Space Station

The WetLab-2 system was developed by NASA Ames Research Center to offer new capabilities to researchers. The system can lyse cells and extract RNA (Ribonucleic Acid) on-orbit from different sample types ranging from microbial cultures to animal tissues. The purified RNA can then either be stabilized for return to Earth or can be used to conduct on-orbit quantitative Reverse Transcriptase PCR (Polymerase Chain Reaction) (qRT-PCR) analysis without the need for sample return. The qRT-PCR results can be downlinked to the ground a few hours after the completion of the run. The validation flight of the WetLab-2 system launched on SpaceX-8 on April 8, 2016. On orbit operations started on April 15th with system setup and was followed by three quantitative PCR runs using an E. coli genomic DNA template pre-loaded at three different concentrations. These runs were designed to discern if quantitative PCR functions correctly in microgravity and if the data is comparable to that from the ground control runs. The flight data showed no significant differences compared to the ground data though there was more variability in the values, this was likely due to the numerous small bubbles observed. The capability of the system to process samples and purify RNA was then validated using frozen samples prepared on the ground. The flight data for both E. coli and mouse liver clearly shows that RNA was successfully purified by our system. The E. coli qRT-PCR run showed successful singleplex, duplex and triplex capability. Data showed high variability in the resulting Cts (Cycle Thresholds [for the PCR]) likely due to bubble formation and insufficient mixing during the procedure run. The mouse liver qRT-PCR run had successful singleplex and duplex reactions and the variability was slightly better as the mixing operation was improved. The ability to purify and stabilize RNA and to conduct qRT-PCR on-orbit is an important step towards utilizing the ISS as a National Laboratory facility. The ability to get on-orbit data will provide investigators with the opportunity to adjust experimental parameters in real time without the need for sample return and re-flight. The WetLab-2 Project is supported by the Research Integration Office in the ISS Program.

gene expression↗

Successful Validation of Sample Processing and Quantitative Real-Time PCR Capabilities on the International Space Station

The WetLab-2 system was developed by NASA Ames Research Center to offer new capabilities to researchers. The system can lyse cells and extract RNA (Ribonucleic Acid) on-orbit from different sample types ranging from microbial cultures to animal tissues. The purified RNA can then either be stabilized for return to Earth or can be used to conduct on-orbit quantitative Reverse Transcriptase PCR (Polymerase Chain Reaction) (qRT-PCR) analysis without the need for sample return. The qRT-PCR results can be downlinked to the ground a few hours after the completion of the run. The validation flight of the WetLab-2 system launched on SpaceX-8 on April 8, 2016. On orbit operations started on April 15th with system setup and was followed by three quantitative PCR runs using an E. coli genomic DNA template pre-loaded at three different concentrations. These runs were designed to discern if quantitative PCR functions correctly in microgravity and if the data is comparable to that from the ground control runs. The flight data showed no significant differences compared to the ground data though there was more variability in the values, this was likely due to the numerous small bubbles observed. The capability of the system to process samples and purify RNA was then validated using frozen samples prepared on the ground. The flight data for both E. coli and mouse liver clearly shows that RNA was successfully purified by our system. The E. coli qRT-PCR run showed successful singleplex, duplex and triplex capability. Data showed high variability in the resulting Cts (Cycle Thresholds [for the PCR]) likely due to bubble formation and insufficient mixing during the procedure run. The mouse liver qRT-PCR run had successful singleplex and duplex reactions and the variability was slightly better as the mixing operation was improved. The ability to purify and stabilize RNA and to conduct qRT-PCR on-orbit is an important step towards utilizing the ISS as a National Laboratory facility. The ability to get on-orbit data will provide investigators with the opportunity to adjust experimental parameters in real time without the need for sample return and re-flight. The WetLab-2 Project is supported by the Research Integration Office in the ISS Program.

quantitative PCR↗

Pathfinder Technology Demonstrator: GlobalStar Testing and Results

The communications subsystem of a spacecraft is typically a SWaP (size, weight, and power) intensive subsystem in a SWaP constrained environment such as a CubeSat. Use of a satellite-based communication system, such as GlobalStars duplex GSP-1720 radio is a low SWaP potentially game-changing low-cost communication subsystem solution that was evaluated for feasibility for the NASA Pathfinder Technology Demonstrator (PTD) project. The PTD project is a series of 6U CubeSat missions to flight demonstrate and characterize novel small satellite payloads in low Earth orbit. GlobalStar is a low Earth orbit satellite constellation for satellite phone and low-speed data communications, and the GSP-1720 is their single board duplex radio most commonly used in satellite phones and shipment tracking devices. The PTD project tested the GSP-1720 to characterize its viability for flight using NASA GEVS (General Environmental Verification Standard) vibration and thermal vacuum levels, as well as testing the uplink-downlink connectivity, data throughput, and file transfer capabilities. This presentation will present the results of the environmental and capability testing of the GSP-1720 performed at NASA Ames Research Center, as well as the viability for CubeSat use in LEO.

satellite communication↗

Simulation and Verification System and Method

A simulation and verification system and method. An interoperability server provides a communications hub for communications between communicating nodes. Nodes connected to a first protocol data bus communicate in a first protocol, e.g., a half-duplex bus protocol. Nodes connected to a second protocol data bus communicate in a second protocol, e.g., a full-duplex bus protocol. A time synchronization bus provides time-frames for synchronizing operation of connected nodes. Interceptors optionally intercept communications between nodes.

Seeger, Steven↗

Advanced Lithium Ion Venus Explorer (ALIVE)

The COncurrent Multidisciplinary Preliminary Assessment of Space Systems (COMPASS) Team partnered with the Applied Research Laboratory to perform a NASA Innovative Advanced Concepts (NIAC) Program study to evaluate chemical based power systems for keeping a Venus lander alive (power and cooling) and functional for a period of days. The mission class targeted was either a Discovery ($500M) or New Frontiers ($750M to $780M) class mission. Historic Soviet Venus landers have only lasted on the order of 2 hours in the extreme Venus environment:temperatures of 460 degrees Centigrade and pressures of 93 bar. Longer duration missions have been studied using plutonium powered systems to operate and cool landers for up to a year. However, the plutonium load is very large. This NIAC study sought to still provide power and cooling but without the plutonium. Batteries are far too heavy but a system which uses the atmosphere (primarily carbon dioxide) and on on-board fuel to power a power generation and cooling system was sought. The resuling design was the Advanced Long-Life Lander Investigating the Venus Environment (ALIVE) Spacecraft (S/C) which burns lithium (Li) with the CO2 atmosphere to heat a Duplex Stirling to power and cool the lander for a 5-day duration (until the Li is exhausted). While it does not last years a chemical powered system surviving days eliminates the cost associated with utilizing a flyby relay S/C and allows a continuous low data rate direct to earth (DTE) link in this instance from the Ovda Regio of Venus. The five-day collection time provided by the chemical power systems also enables science personnel on earth to interact and retarget science - something not possible with an approximately 2-hour spacecraft lifetime. It also allows for contingency operations directed by the ground (reduced risk). The science package was based on that envisioned by the Venus Intrepid Tessera Lander (VITaL) Decadal Survey Study. The Li Burner within the long duration power system creates approximately 14000 W of heat. This 1300 degree Centigrade heat using Li in the bottom "ballast" tank is melted to liquid by the Venus temperature, drawn into a furnace by a wick and burned with atmospheric CO2. The Li carbonate exhaust is liquid at 1300 degrees Centigrade and being denser than Li drains into the the Li tank and solidifies. Since the exhaust product is a dense liquid no "chimney" is required which conserves the heat for the stirling power convertor. The Duplex Stirling provides about 300 W of power and removes about 300 W of heat from the avionics and heat that leaks into the 1-bar-insulated payload pressure vessel kept at 25 degrees Centigrade. The Na K radiator is run to the top of the drag flap.The ALIVE vehicle is carried to Venus via an Atlas 411 launch vehicle (LV) with a C3 of 7 km2/s2. An Aeroshell, derived from the Genesis mission, enables a direct entry into the atmosphere of Venus (-10 degrees Centigrade, 40 g max) and 6 m/s for landing (44 g) using a drag ring. For surface science and communication, a 100 WRF (WebEx Recording Format), X-Band 0.6-meter pointable DTE (Direct-to-Earth) antenna provides 2 kbps (kilobits per second) to DSN (Deep-Space Network) 34-meter antenna clusters.Table 1.1 summarizes the top-level details of each subsystem that was incorporated into the design. Cost estimates of the ALIVE mission show it at approximately $760M which puts it into the New Frontiers class.The ALIVE landed duration is only limited by the amount of Li which can be carried by the lander. Further studies are needed to investigate how additional mass can be carried, perhaps by a larger launcher and larger aeroshell.

Exploration↗

ESD: Ethernet Signal Differentiator [Poster]

Can Machine Learning Algorithms be trained to interpret and decode passively observed Automative Ethernet full-duplex signals without access to the original signals transmitted by either endpoint?

97 - MATHEMATICS AND COMPUTING↗

Up‐And‐Coming Advances in Optical and Microwave Nonreciprocity: From Classical to Quantum Realm

Reciprocity is a fundamental physical principle that roots in the time‐reversal symmetry of physical laws. It allows making predictions on any arbitrary complex system's response and operation and hence simplifies the analysis. However, there are many practical situations in which it is advantageous to break reciprocity, e.g., isolators preventing wave scattering back to lasers and generators, full‐duplex systems for multiplexing transmission and receiving in the same channel, nonreciprocal cavity excitation, and protection of fragile states of superconductor quantum computers from thermal noise. The most widespread approach to time‐reversal symmetry breaking and nonreciprocity based on magnetic field biasing suffers from bulkiness, cost ineffectiveness, and loss, motivating researchers and engineers to search for more practical approaches. Herein, the up‐and‐coming advances in optical nonreciprocity, including new materials (Weyl semimetals, topological insulators, metasurfaces), active structures, time‐modulation, parity‐time (PT)‐symmetry breaking, nonlinearity combined with a structural asymmetry, quantum nonlinearity, unidirectional gain and loss, chiral quantum states and valley polarization are overviewed. A general description of nonreciprocal systems is provided and the pros and cons of the mentioned approaches to nonreciprocity are discussed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Derivatization of Mirror-Image L -Nucleic Acids with 2'-OMe Modification for Thermal and Structural Stabilization

To further expand the functionality and enhance the stability of mirror-image nucleic acids as advanced agents for basic research and therapeutic design, we have synthesized 2'-deoxy-2'-methoxy- L -uridine phosphoramidite and incorporated it into L -DNA and L -RNA by solid-phase synthesis quantitatively. We found that the thermostability of L -nucleic acids is dramatically improved after introducing the modifications. Moreover, we successfully crystallized both L -DNA and L -RNA duplexes containing the 2'-OMe modifications and sharing identical sequences. Crystal structure determination and analysis revealed the overall structures of the mirror-image nucleic acids, and for the first time it was possible to interpret the structural deviations caused by 2'-OMe and 2'-OH groups in the oligonucleotides, which are very similar. In conclusion, this novel chemical nucleic acid modification has the potential to be used to design nucleic acid-based therapeutics and materials in the future.

2'-OMe-modifications↗

Synthesis and Structural Characterization of 2′‐Deoxy‐2′‐Methoxy‐ L ‐Cytidine Nucleic Acids

Abstract We report here for the first time the synthesis of a novel 2′‐methoxy‐modified L‐cytidine analog and its phosphoramidite, as well as its incorporation into oligonucleotides via solid‐phase synthesis. Our measure the thermostability of the modified L‐nucleic acids by UV‐melting studies, and find out the 2′‐methoxy‐derivatization enhances the thermostability of the L‐duplexes. Consistent with the thermostability result, our X‐ray crystal structure study reveals that the 2′‐methoxy‐L‐deoxycytidine forms the Watson‐Crick base pair with L‐guanosine virtually as the mirror‐image fashion of native pair. This novel chemically modified L‐cytidine provides a useful biochemical and structural strategy to create mirror‐image nucleic acid molecules with expanded functionalities.

2′-Methoxy↗

Synthesis of Pyrimidine Modified Seleno–DNA as a Novel Approach to Antisense Candidate

Chemically modified antisense oligonucleotides (ASO) currently in pre–clinical and clinical experiments mainly focus on the 2’–position derivatizations to enhance stability and targeting affinity. Considering the possible incompatibility of 2’–modifications with RNase H stimulation and activity, we have hypothesized that the atom specific modifications on nucleobases can retain the complex structure and RNase H activity, while enhancing ASO's binding affinity, specificity, and stability against nucleases. Herein we report a novel strategy to explore our hypothesis by synthesizing the deoxynucleoside phosphoramidite building block with the seleno–modification at 5–position of thymidine, as well as its Se–oligonucleotides. Via X–ray crystal structural study, we found that the Se–modification was located in the major groove of nucleic acid duplex and didn't cause the thermal and structural perturbations. Surprisingly, our nucleobase–modified Se–DNAs were exceptionally resistant to nuclease digestion, while compatible with RNase H activity. In conclusion, this affords a novel avenue for potential anti–sense modification in the form of Se–antisense oligonucleotides (Se–ASO).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Evaluating the mutagenicity of N-nitrosodimethylamine in 2D and 3D HepaRG cell cultures using error-corrected next generation sequencing

Human liver-derived metabolically competent HepaRG cells have been successfully employed in both two-dimensional (2D) and 3D spheroid formats for performing the comet assay and micronucleus (MN) assay. In the present study, we have investigated expanding the genotoxicity endpoints evaluated in HepaRG cells by detecting mutagenesis using two error-corrected next generation sequencing (ecNGS) technologies, Duplex Sequencing (DS) and High-Fidelity (HiFi) Sequencing. Both HepaRG 2D cells and 3D spheroids were exposed for 72 h to N-nitrosodimethylamine (NDMA), followed by an additional incubation for the fixation of induced mutations. NDMA-induced DNA damage, chromosomal damage, and mutagenesis were determined using the comet assay, MN assay, and ecNGS, respectively. The 72-h treatment with NDMA resulted in concentration-dependent increases in cytotoxicity, DNA damage, MN formation, and mutation frequency in both 2D and 3D cultures, with greater responses observed in the 3D spheroids compared to 2D cells. The mutational spectrum analysis showed that NDMA induced predominantly A:T → G:C transitions, along with a lower frequency of G:C → A:T transitions, and exhibited a different trinucleotide signature relative to the negative control. These results demonstrate that the HepaRG 2D cells and 3D spheroid models can be used for mutagenesis assessment using both DS and HiFi Sequencing, with the caveat that severe cytotoxic concentrations should be avoided when conducting DS. With further validation, the HepaRG 2D/3D system may become a powerful human-based metabolically competent platform for genotoxicity testing.

3D spheroids↗

Corrosion evaluation of Ti–6Al–4V manufactured by electron beam melting in Ringer’s physiological solution: an in vitro study of the passive film

We report that electrochemical characteristics and semiconducting behavior of additively manufactured electron beam melted (EBM) and wrought (WR) Ti–6Al–4V (Ti-G5) are compared in Ringer’s physiological solution. X-ray diffraction (XRD) and field emission scanning electron microscopy (FE-SEM) confirmed the α+β structure of the tested materials, with two different microstructure types of “bimodal” and “basket-weave” for WR and EBM, respectively. Potentiodynamic polarization (PDP) revealed that the corrosion current density for EBM (i corr =0.27±0.06 μA cm -2 ) is less than the WR (i corr =0.70±0.05 μA cm -2 ). Moreover, potentiostatic polarization (PS) that was employed to form the passive layers at three different potentials of 300, 500, and 700 mV Ag/AgCl , showed that the passive films on the EBM sample are thinner. This finding was confirmed by electrochemical impedance spectroscopy (EIS). Furthermore, through Mott–Schottky (M–S) analysis, donor densities on WR passive films were found to be ~1.5 times larger than EBM. Although PS and EIS confirmed that the passive layer on EBM is thinner, it provides higher corrosion resistance than WR. The passive layer on both samples were found to have n-type characteristics with a duplex structure.

36 MATERIALS SCIENCE↗