Overcoming GNA/RNA base-pairing limitations using isonucleotides improves the pharmacodynamic activi
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Schlegel, Mark K.↗
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Results for “Active target”
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DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation
DNA methylation maintenance by DNMT1 is an essential process in mammals but molecular mechanisms connecting DNA methylation patterns and enzyme activity remain elusive. Here, we systematically analyzed the specificity of DNMT1, revealing a pronounced influence of the DNA sequences flanking the target CpG site on DNMT1 activity. We determined DNMT1 structures in complex with preferred DNA substrates revealing that DNMT1 employs flanking sequence-dependent base flipping mechanisms, with large structural rearrangements of the DNA correlating with low catalytic activity. Moreover, flanking sequences influence the conformational dynamics of the active site and cofactor binding pocket. Importantly, we show that the flanking sequence preferences of DNMT1 highly correlate with genomic methylation in human and mouse cells, and 5-azacytidine triggered DNA demethylation is more pronounced at CpG sites with flanks disfavored by DNMT1. Overall, our findings uncover the intricate interplay between CpG-flanking sequence, DNMT1-mediated base flipping and the dynamic landscape of DNA methylation.
59 BASIC BIOLOGICAL SCIENCES↗
Kinetic analysis of Cas12a and Cas13a RNA-Guided nucleases for development of improved CRISPR-Based diagnostics
Bacterial CRISPR systems provide acquired immunity against invading nucleic acids by activating RNA-programmable RNases and DNases. Cas13a and Cas12a enzymes bound to CRISPR RNA (crRNA) recognize specific nucleic acid targets, initiating cleavage of the targets as well as non-target (trans) nucleic acids. Here, we examine the kinetics of single-turnover target and multi-turnover trans-nuclease activities of both enzymes. High-turnover, non-specific Cas13a trans-RNase activity is coupled to rapid binding of target RNA. By contrast, low-turnover Cas12a trans-nuclease activity is coupled to relatively slow cleavage of target DNA, selective for DNA over RNA, indifferent to base identity, and preferential for single-stranded substrates. Combining multiple crRNA increases detection sensitivity of targets, an approach we use to quantify pathogen DNA in samples from patients suspected of Buruli ulcer disease. Results reveal that these enzymes are kinetically adapted to play distinct roles in bacterial adaptive immunity and show how kinetic analysis can be applied to CRISPR-based diagnostics.
59 BASIC BIOLOGICAL SCIENCES↗
Detection of active and latent infections with microfluidic devices and systems thereof
The present invention relates to methods of detecting one or more targets of interest in a sample. In one instance, the target can be correlated to an active infection (e.g., by a virus and/or a bacterium). Methods can include treating the sample with a dissociation agent, thereby releasing the target of interest for more accurate detection (e.g., by use of a sedimentation-based centrifugal microfluidic devices). Also described herein are microfluidic devices and systems for use with a dissociation agent.
59 BASIC BIOLOGICAL SCIENCES↗
Resurfacing promotes antibacterial activity of a lipid A–binding nanobody
Nanobodies have been pursued as candidates for antimicrobial design due to their small size and versatile binding capacities, but direct antibacterial activity of a nanobody has yet to be described. Here, we employed a bacterial surface display platform to screen a synthetic library of nanobody variants for antimicrobial potential. We identified a candidate that binds the essential lipid A component of gram-negative lipopolysaccharide. Nonetheless, this nanobody required a weakened outer membrane to access its target and elicit its toxic activity. Borrowing from observations of innate immune proteins, we found that resurfacing nanobodies with positively charged residues enabled them to bind and perturb the gram-negative outer membrane, but this alone was not sufficient for toxic activity. However, when we resurface our lipid A-targeting nanobody, it gained the ability to disrupt the outer membrane and enact its antibacterial function against wild-type bacteria. This development of a dual-function nanobody that can reach and bind previously inaccessible gram-negative targets introduces a route for antimicrobial biologic advancement.
antibacterial↗
Charged particle activation studies on the surface of LDEF spacecraft
High energy proton induced nuclear reaction products are examined using seven elements, namely, Aluminum, Silicon, Nickel, Copper, Zirconium, Tantalum, and Tungsten. The samples were in the form of plates, 2 x 2 x 1/8 inches. Activities due to Na-22 from Al, Co-56 and Co-57 from Ni, Co-58 from Cu, and Y-88 from Zr targets were detected. No induced activity was observed in Si, Ta, and W, most probably due to the long cooling times. Only the Zr sample contained a weak Be-7 peak, although Ta and W were also located at the leading edge of the spacecraft. Gamma-rays of individual isotopes were measured using high-resolution Ge(Li) solid state detector coupled to 4096-multichannel analyzer. Activities were calculated for Co-56 (846 keV) and Co-57 (122 and 136 keV's) at the time of the entry of the spacecraft and found to be 0.014 plus or minus 0.005 c/sec. g, 0.018 plus or minus 0.002 c/sec. g, and 0.0024 plus or minus 0.0007 c/sec. g, respectively.
Olmez, Ilhan↗
CATLAC - Calibration and Validation Analysis Tool of Local Area Coverage for the SeaWiFS Mission
Calibration and validation Analysis Tool of Local Area Coverage (CATLAC) is an analysis package for selecting and graphically displaying Earth and space targets for calibration and validation activities on a polar orbiting satellite. The package is written in the Interactive Data Language (IDL) and includes a graphical user interface. Although it is designed specifically for the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) mission, the package can be used for analysis on other Earth-viewing missions. An individual can use text or graphical methods in CATLAC to select Earth targets to be scanned by a satellite. Additional onboard calibration activities (such as observations of the moon, or solar irradiance from a solar diffuser), which use data recorder time, can also be specified. All information pertinent to the creation of a command schedule can be written to a file which is read by a command scheduler. The scheduler can be invoked and the Local Area Coverage (LAC) recording periods can be visually verified using CATLAC. The schedule can also be verified by examining record and error files written by the scheduler.
Woodward, Robert H.↗
Linear Covariance Techniques to Analyze a Multi-Vehicle, Multi-GN&C System with Applications to Rendezvous in a Near Rectilinear Halo Orbit
Typically for a rendezvous and docking scenario, only a single vehicle is considered the active vehicle. As a result, the target vehicle’s GN&C system is typically not a factor in the integrated performance analysis as it assumes a passive role. However, for upcoming NASA Artemis missions the active vehicle is both the chaser and target spacecraft. In addition, both vehicles are cooperating with one another, sharing telemetry data, and relying on data extracted from the GN&C system of the other. The process also includes a team of ground support personnel in mission control are tracking and monitoring each spacecraft uplinking state estimates and targeting solutions to support mission operations and enhance the onboard flight system performance. Being able to quickly analyze the impact of both vehicles with two different GN&C systems that also interact with the ground that does its own navigation and targeting uploads is critical. This paper outlines how to perform this rapid analysis using linear covariance techniques and applies them to a rendezvous scenario initiated in low lunar orbit and completed in a Near Rectilinear Halo Orbit (NRHO) representative of the NASA Artemis III mission.
Linear Covariance Analysis↗
HyspIRI High-Temperature Saturation Study
As part of the precursor activities for the HyspIRI mission, a small team was assembled to determine the optimum saturation level for the mid-infrared (4-?m) channel, which is dedicated to the measurement of hot targets. Examples of hot targets include wildland fires and active lava flows. This determination took into account both the temperature expected for the natural phenomena and the expected performance of the mid-infrared channel as well as its overlap with the other channels in the thermal infrared (7.5-12 ?m) designed to measure the temperature of lower temperature targets. Based on this work, the hot target saturation group recommends a saturation temperature of 1200 K for the mid-infrared channel. The saturation temperature of 1200 K represents a good compromise between the prevention of saturation and sensitivity to ambient temperature.
saturation↗
A modERN resource: identification of Drosophila transcription factor candidate target genes using RNAi
Transcription factors (TFs) play a key role in development and in cellular responses to the environment by activating or repressing the transcription of target genes in precise spatial and temporal patterns. In order to develop a catalog of target genes of Drosophila melanogaster TFs, the modERN consortium systematically knocked down the expression of TFs using RNAi in whole embryos followed by RNA-seq. We generated data for 45 TFs which have 18 different DNA-binding domains and are expressed in 15 of the 16 organ systems. The range of inactivation of the targeted TFs by RNAi ranged from log2fold change -3.52 to +0.49. The TFs also showed remarkable heterogeneity in the numbers of candidate target genes identified, with some generating thousands of candidates and others only tens. We present detailed analysis from five experiments, including those for three TFs that have been the focus of previous functional studies (ERR, sens, and zfh2) and two previously uncharacterized TFs (sens-2 and CG32006), as well as short vignettes for selected additional experiments to illustrate the utility of this resource. The RNA-seq datasets are available through the ENCODE DCC (http://encodeproject.org) and the Sequence Read Archive (SRA). TF and target gene expression patterns can be found here: https://insitu.fruitfly.org. These studies provide data that facilitate scientific inquiries into the functions of individual TFs in key developmental, metabolic, defensive, and homeostatic regulatory pathways, as well as provide a broader perspective on how individual TFs work together in local networks during embryogenesis.
59 BASIC BIOLOGICAL SCIENCES↗
Deciphering Microbial Metal Toxicity Responses using RB-TnSeq and Activity-Based Metabolomics
To uncover metal toxicity targets and defense mechanisms of the facultative anaerobe Pantoea sp. strain MT58 (MT58), we used a multiomic strategy combining two global techniques, random bar code transposon site sequencing (RB-TnSeq) and activity-based metabolomics. MT58 is a metal-tolerant Oak Ridge Reservation (ORR) environmental isolate that was enriched in the presence of metals at concentrations measured in contaminated groundwater at an ORR nuclear waste site. The effects of three chemically different metals found at elevated concentrations in the ORR contaminated environment were investigated: the cation Al 3+ , the oxyanion CrO 4 2- , and the oxycation UO 2 2+ . Both global techniques were applied using all three metals under both aerobic and anaerobic conditions to elucidate metal interactions mediated through the activity of metabolites and key genes/proteins. These revealed that Al 3+ binds intracellular arginine, CrO 4 2- enters the cell through sulfate transporters and oxidizes intracellular reduced thiols, and membrane-bound lipopolysaccharides protect the cell from UO 2 2+ toxicity. In addition, the Tol outer membrane system contributed to the protection of cellular integrity from the toxic effects of all three metals. Likewise, we found evidence of regulation of lipid content in membranes under metal stress. Individually, RB-TnSeq and metabolomics are powerful tools to explore the impact various stresses have on biological systems. In this work, we show that together they can be used synergistically to identify the molecular actors and mechanisms of these pertubations to an organism, furthering our understanding of how living systems interact with their environment.
59 BASIC BIOLOGICAL SCIENCES↗
Mycorrhiza Better Predict Soil Fungal Community Composition and Function than Aboveground Traits in Temperate Forest Ecosystems
Forests in the northeastern US are experiencing shifts in community composition due to the northward migration of warm-adapted tree species and certain species’ declines (for example, white ash and eastern hemlock) due to invasive insects. Changes in belowground fungal communities and associated functions will inevitably follow. Therefore, we sought to investigate the relative importance of two important tree characteristics—mycorrhizal type [ectomycorrhizal (EcM) or arbuscular mycorrhizal (AM)] and leaf habit (deciduous or evergreen) on soil fungal community composition and organic matter cycling. We sampled soil in the organic and mineral horizons beneath two AM-associated (Fraxinus americana and Thuja occidentalis) and two ECM-associated tree species (Betula alleghaniensis and Tsuga canadensis), with an evergreen and deciduous species in each mycorrhizal group. To characterize fungal communities and organic matter decomposition beneath each tree species, we sequenced the ITS1 region of fungal DNA and measured the potential activity of carbon- and nitrogen-targeting extracellular enzymes. Each tree species harbored distinct fungal communities, supporting the need to consider both mycorrhizal type and leaf habit. However, between tree characteristics, mycorrhizal type better predicted fungal communities. Across fungal guilds, saprotrophic fungi were the most important group in shaping fungal community differences in soils beneath all tree species. The effect of leaf habit on carbon- and nitrogen-targeting hydrolytic enzymes depended on tree mycorrhizal association in the organic horizon, while oxidative enzyme activities were higher beneath EcM-associated trees across both soil horizons and leaf habits.
54 ENVIRONMENTAL SCIENCES↗
Mycorrhiza better predict soil fungal community composition and function than aboveground traits in temperate forest ecosystems
We sampled soil in the organic and mineral horizons beneath two AM-associated (Fraxinus americana, Thuja occidentalis) and two ECM-associated tree species (Betula alleghaniensis, and Tsuga canadensis), with an evergreen and deciduous species in each mycorrhizal group. To characterize fungal communities and organic matter decomposition beneath each tree species, we sequenced the ITS1 region of fungal DNA and measured the potential activity of carbon and nitrogen-targeting extracellular enzymes. Each tree species harbored distinct fungal communities, supporting the need to consider both mycorrhizal type and leaf habit. However, between tree characteristics, mycorrhizal type better predicted fungal communities. Across fungal guilds, saprotrophic fungi were the most important group in shaping fungal community differences in soils beneath all tree species. The effect of leaf habit on carbon and nitrogen-targeting hydrolytic enzymes depended on tree mycorrhizal association in the organic horizon, while oxidative enzyme activities were higher beneath EcM-associated trees across both soil horizons and leaf habits. These data include extracellular hydrolytic and oxidative enzyme activities, ITS sequencing fungal community data, soil carbon to nitrogen, and soil pH. Site level data include climate (mean annual temperature, precipitation), elevation, and soil series and order information.
54 ENVIRONMENTAL SCIENCES↗
Decay Dose Shielding Analysis with Hybrid Unstructured Mesh/Constructive Solid Geometry Monte Carlo Calculation and ADVANTG Acceleration
The Oak Ridge National Laboratory (ORNL) Second Target Station (STS) neutron production facility is an accelerator driven pulsed neutron source that is currently being actively developed at ORNL. The neutrons are produced by proton-induced spallation reactions. A proton beam of 700 kW power is delivered to a spallation target in short, less than 1 µs long pulses, with 15 Hz repetition rate. The spallation target of ORNL STS is a rotating water-cooled tungsten target with tantalum cladding housed in a stainless-steel shroud. It is divided into 21 segments. These segments become highly activated due to spallation reactions or nuclei transmutation by the emitted neutrons. The radioactive nuclides continue to decay after ceasing operation. The decay dose rates generated from the target segments once they are removed from their operational location within the core vessel must be accurately quantified to determine the shielding configurations of remote handling tools and transport casks and to aid in planning maintenance events. To determine the shielding configurations needed for an activated target segment after ceasing operation, both the hybrid unstructured mesh (UM)/constructive solid geometry (CSG) approach that was previously utilized for STS analyses [1] and the ADVANTG code [2] were used. Even though the ADVANTG code does not include UM capability, the utilization of its advanced variance reduction technique was crucial to accelerate the extremely difficult final photon transport calculation in this analysis. This paper also describes the procedures taken to mitigate the convergence issues that occur when ADVANTG uses a source definition that does not match the source of the final Monte Carlo (MC) calculation. These convergence issues often occur because of inconsistencies between source and transport biasing parameters.
Ibrahim, Ahmad↗
Functional Imaging of Human Vestibular Cortex Activity Elicited by Skull Tap and Auditory Tone Burst
The aim of the current study was to characterize the brain activation in response to two modes of vestibular stimulation: skull tap and auditory tone burst. The auditory tone burst has been used in previous studies to elicit saccular Vestibular Evoked Myogenic Potentials (VEMP) (Colebatch & Halmagyi 1992; Colebatch et al. 1994). Some researchers have reported that airconducted skull tap elicits both saccular and utricle VEMPs, while being faster and less irritating for the subjects (Curthoys et al. 2009, Wackym et al., 2012). However, it is not clear whether the skull tap and auditory tone burst elicit the same pattern of cortical activity. Both forms of stimulation target the otolith response, which provides a measurement of vestibular function independent from semicircular canals. This is of high importance for studying the vestibular disorders related to otolith deficits. Previous imaging studies have documented activity in the anterior and posterior insula, superior temporal gyrus, inferior parietal lobule, pre and post central gyri, inferior frontal gyrus, and the anterior cingulate cortex in response to different modes of vestibular stimulation (Bottini et al., 1994; Dieterich et al., 2003; Emri et al., 2003; Schlindwein et al., 2008; Janzen et al., 2008). Here we hypothesized that the skull tap elicits the similar pattern of cortical activity as the auditory tone burst. Subjects put on a set of MR compatible skull tappers and headphones inside the 3T GE scanner, while lying in supine position, with eyes closed. All subjects received both forms of the stimulation, however, the order of stimulation with auditory tone burst and air-conducted skull tap was counterbalanced across subjects. Pneumatically powered skull tappers were placed bilaterally on the cheekbones. The vibration of the cheekbone was transmitted to the vestibular cortex, resulting in vestibular response (Halmagyi et al., 1995). Auditory tone bursts were also delivered for comparison. To validate our stimulation method, we measured the ocular VEMP outside of the scanner. This measurement showed that both skull tap and auditory tone burst elicited vestibular evoked activation, indicated by eye muscle response. Our preliminary analyses showed that the skull tap elicited activation in medial frontal gyrus, superior temporal gyrus, postcentral gyrus, transverse temporal gyrus, anterior cingulate, and putamen. The auditory tone bursts elicited activation in medial frontal gyrus, superior temporal gyrus, superior frontal gyrus, precentral gyrus, inferior and superior parietal lobules. In line with our hypothesis, skull taps elicited a pattern of cortical activity closely similar to one elicited by auditory tone bursts. Further analysis will determine the extent to which the skull taps can replace the auditory tone stimulation in clinical and basic science vestibular assessments.
Noohi, Fatemeh↗
Glove-Enabled Computer Operations (GECO): Design and Testing of an Extravehicular Activity Glove Adapted for Human-Computer Interface
The Glove-Enabled Computer Operations (GECO) system enables an extravehicular activity (EVA) glove to be dual-purposed as a human-computer interface device. This paper describes the design and human participant testing of a right-handed GECO glove in a pressurized glove box. As part of an investigation into the usability of the GECO system for EVA data entry, twenty participants were asked to complete activities including (1) a Simon Says Games in which they attempted to duplicate random sequences of targeted finger strikes and (2) a Text Entry activity in which they used the GECO glove to enter target phrases in two different virtual keyboard modes. In a within-subjects design, both activities were performed both with and without vibrotactile feedback. Participants mean accuracies in correctly generating finger strikes with the pressurized glove were surprisingly high, both with and without the benefit of tactile feedback. Five of the subjects achieved mean accuracies exceeding 99 in both conditions. In Text Entry, tactile feedback provided a statistically significant performance benefit, quantified by characters entered per minute, as well as reduction in error rate. Secondary analyses of responses to a NASA Task Loader Index (TLX) subjective workload assessments reveal a benefit for tactile feedback in GECO glove use for data entry. This first-ever investigation of employment of a pressurized EVA glove for human-computer interface opens up a wide range of future applications, including text chat communications, manipulation of procedureschecklists, cataloguingannotating images, scientific note taking, human-robot interaction, and control of suit andor other EVA systems.
Adams, Richard J.↗
Glove-Enabled Computer Operations (GECO): Design and Testing of an Extravehicular Activity Glove Adapted for Human-Computer Interface
The Glove-Enabled Computer Operations (GECO) system enables an extravehicular activity (EVA) glove to be dual-purposed as a human-computer interface device. This paper describes the design and human participant testing of a right-handed GECO glove in a pressurized glove box. As part of an investigation into the usability of the GECO system for EVA data entry, twenty participants were asked to complete activities including (1) a Simon Says Games in which they attempted to duplicate random sequences of targeted finger strikes and (2) a Text Entry activity in which they used the GECO glove to enter target phrases in two different virtual keyboard modes. In a within-subjects design, both activities were performed both with and without vibrotactile feedback. Participants' mean accuracies in correctly generating finger strikes with the pressurized glove were surprisingly high, both with and without the benefit of tactile feedback. Five of the subjects achieved mean accuracies exceeding 99% in both conditions. In Text Entry, tactile feedback provided a statistically significant performance benefit, quantified by characters entered per minute, as well as reduction in error rate. Secondary analyses of responses to a NASA Task Loader Index (TLX) subjective workload assessments reveal a benefit for tactile feedback in GECO glove use for data entry. This first-ever investigation of employment of a pressurized EVA glove for human-computer interface opens up a wide range of future applications, including text "chat" communications, manipulation of procedures/checklists, cataloguing/annotating images, scientific note taking, human-robot interaction, and control of suit and/or other EVA systems.
Adams, Richard J.↗
OVERVIEW OF RECENT PU-238 PRODUCTION ACTIVITIES AT IDAHO NATIONAL LABORATORY
The Plutonium Fuel Services (PFS) program at Idaho National Laboratory (INL) is active in the qualification of irradiation targets containing Np-237 for irradiation in the Advanced Test Reactor (ATR) to produce Pu-238 for future NASA missions. INL qualified and loaded 7 targets in ATR’s South Flux Trap (SFT) for cycle 169A, which occurred in Spring 2021. This program was reinitiated after two baseline production targets in three positions validated significant production of Pu-238 [ref.1]. The validation model was followed by the PFS-1 experimental test in the ATRC (Critical) facility [ref.2]. This paper outlines the progress and status of the PFS program. The qualification effort, safety analysis, hardware status, and future activities for qualification of an updated target design for use in the ATR will be discussed.
36 MATERIALS SCIENCE↗