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At least 181 records · Page 10

The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases

Tracing the origin of CRISPR-Cas CRISPR-Cas systems have transformed genome editing and other biotechnologies; however, the broader origins and diversity of RNA-guided nucleases have largely remained unexplored. Altae-Tran et al . show that three distinct transposon-encoded proteins, IscB, IsrB, and TnpB, are naturally occurring, reprogrammable RNA-guided DNA nucleases (see the Perspective by Rousset and Sorek). In addition to identifying diverse guide-encoding mechanisms, the authors elucidate the evolutionary relationship between IsrB, IscB, and CRISPR-Cas9. Overall, these newly characterized systems, called OMEGA (for obligate mobile element–guided activity) systems, are found in all domains of life and may be harnessed for biotechnology development. —DJ

Science & Technology - Other Topics↗

CRISPR Tools for Engineering Prokaryotic Systems: Recent Advances and New Applications

In the past decades, the broad selection of CRISPR-Cas systems has revolutionized biotechnology by enabling multimodal genetic manipulation in diverse organisms. Rooted in a molecular engineering perspective, we recapitulate the different CRISPR components and how they can be designed for specific genetic engineering applications. We first introduce the repertoire of Cas proteins and tethered effectors used to program new biological functions through gene editing and gene regulation. We review current guide RNA (gRNA) design strategies and computational tools and how CRISPR-based genetic circuits can be constructed through regulated gRNA expression. Then, we present recent advances in CRISPR-based biosensing, bioproduction, and biotherapeutics across in vitro and in vivo prokaryotic systems. Finally, we discuss forthcoming applications in prokaryotic CRISPR technology that will transform synthetic biology principles in the near future.

59 BASIC BIOLOGICAL SCIENCES↗

Data for "Discovery, Characterization, and Application of Chromosomal Integration Sites in the Hyperthermophilic Archaeon Sulfolobus islandicus"

Sulfolobus islandicus , an emerging archaeal model organism, offers unique advantages for metabolic engineering and synthetic biology applications owing to its ability to thrive in extreme environments. Although several genetic tools have been established for this organism, the lack of well-characterized chromosomal integration sites has limited its potential as a cellular factory. Here, we systematically identified and characterized 13 artificial CRISPR RNAs targeting eight integration sites in S. islandicus using the CRISPR-COPIES pipeline and a multi-omics-informed computational workflow. We leveraged the endogenous CRISPR-Cas system to integrate the reporter gene lacS and validated heterologous expression through a β-galactosidase assay, revealing significant positional effects. As a proof of concept, we utilized these sites to genetically manipulate lipid ether composition by overexpressing glycerol dibiphytanyl glycerol tetraether (GDGT) ring synthase B (GrsB). This study expands the genetic toolbox for S. islandicus and advances its potential as a robust platform for archaeal synthetic biology and industrial biotechnology.

AI/ML↗

RISE: robust iterative surface extension for sub-nanometer X-ray mirror fabrication

Precision optics have been widely required in many advanced technological applications. X-ray mirrors, as an example, serve as the key optical components at synchrotron radiation and free electron laser facilities. They are rectangular silicon or glass substrates where a rectangular Clear Aperture (CA) needs to be polished to sub-nanometer Root Mean Squared (RMS) to keep the imaging capability of the incoming X-ray wavefront at the diffraction limit. The convolutional polishing model requires a CA to be extended with extra data, from which the dwell time is calculated via deconvolution. However, since deconvolution is very sensitive to boundary errors and noise, the existing surface extension methods can hardly fulfill the sub-nanometer requirement. On one hand, the figure errors in a CA were improperly modeled during the extension, leading to continuity issues along the boundary. On the other hand, uncorrectable high-frequency errors and noise were also extended. In this study, we propose a novel Robust Iterative Surface Extension (RISE) method that resolves these problems with a data fitting strategy. RISE models the figure errors in a CA with orthogonal polynomials and ensures that only correctable errors are fit and extended. Combined with boundary conditions, an iterative refinement of dwell time is then proposed to compensate the errors brought by the extension and deconvolution, which drastically reduces the estimated figure error residuals in a CA while the increase of total dwell time is negligible. To our best knowledge, RISE is the first data fitting-based surface extension method and is the first to optimize dwell time based on iterative extension. An experimental verification of RISE is given by fabricating two elliptic cylinders (10 mm × 80 mm CAs) starting from a sphere with a radius of curvature around 173 m using ion beam figuring. The figure errors in the two CAs greatly improved from 204.96 nm RMS and 190.28 nm RMS to 0.62 nm RMS and 0.71 nm RMS, respectively, which proves that RISE is an effective method for sub-nanometer level X-ray mirror fabrication.

36 MATERIALS SCIENCE↗

XANES spectroscopy of sulfides stable under reducing conditions

X-ray absorption near-edge structure (XANES) spectroscopy is a powerful technique to quantitatively investigate sulfur speciation in geologically complex materials such as minerals, glasses, soils, organic compounds, industrial slags, and extraterrestrial materials. This technique allows non-destructive investigation of the coordination chemistry and oxidation state of sulfur species ranging from sulfide (2–oxidation state) to sulfate (6+ oxidation state). Each sulfur species has a unique spectral shape with a characteristic K-edge representing the s → p and d hybridization photoelectron transitions. As such, sulfur speciation is used to measure the oxidation state of samples by comparing the overall XANES spectra to that of reference compounds. Although many S XANES spectral standards exist for terrestrial applications under oxidized conditions, new sulfide standards are needed to investigate reduced (oxygen fugacity, f O 2 , below IW) silicate systems relevant for studies of extraterrestrial materials and systems. Sulfides found in certain meteorites (e.g., enstatite chondrites and aubrites) and predicted to exist on Mercury, such as CaS (oldhamite), MgS (niningerite), and FeCr 2 S 4 (daubréelite), are stable at f O 2 below IW-3 but rapidly oxidize to sulfate and/or produce sulfurous gases under terrestrial surface conditions. XANES spectra of these compounds collected to date have been of variable quality, possibly due to the unstable nature of certain sulfides under typical (e.g., oxidizing) laboratory conditions. A new set of compounds was prepared for this study and their XANES spectra are analyzed for comparison with potential extraterrestrial analogs. S K -edge XANES spectra were collected at Argonne National Lab for FeS (troilite), MnS (alabandite), CaS (oldhamite), MgS (niningerite), Ni 1–x S, NiS 2 , CaSO 4 (anhydrite), MgSO 4 , FeSO 4 , Fe 2 (SO 4 ) 3 , FeCr 2 S 4 (daubréelite), Na 2 S, Al 2 S 3 , Ni 7 S 6 , and Ni 3 S 2 ; the latter five were analyzed for the first time using XANES. These standards expand upon the existing S XANES end-member libraries at a higher spectral resolution (0.25 eV steps) near the S K -edge. Processed spectra, those that have been normalized and “flattened,” are compared to quantify uncertainties due to data processing methods. Future investigations that require well-characterized sulfide standards, such as the ones presented here, may have important implications for understanding sulfur speciation in reduced silicate glasses and minerals with applications for the early Earth, Moon, Mercury, and enstatite chondrites.

Anzures, Brendan A.↗

Project 57 Air Monitoring Report: January 1 through September 30, 2020, with a Review of the Period of Record Radionuclide Analyses

The DOE Environmental Management Nevada Program (EM NV) identified the Project 57 contaminated area as Corrective Action Unit (CAU) 415, Project 57 No. 1 Plutonium Dispersion Site, which consisted of one Corrective Action Site (CAS): NAFR-23- 02, Pu Contaminated Soil (U.S. DOE, 2014). The CAS included several Project 57 operational facilities in addition to the plutonium-contaminated soil. With approval of the State of Nevada Division of Environmental Protection, the DOE closed the Project 57 surface soil contamination site in October 2020. Closure was accomplished by installing a clean soil cap constructed over ground zero and the surrounding areas of the CA that may be entrained with wind-transported soil particles. After completion of the ground zero cap in October 2020, DRI discontinued monitoring of meteorological and associated environmental conditions at the Project 57 site as directed by DOE EM NV. Navarro dismantled air monitoring stations P57-3 and P57-4 and removed the equipment on October 20, 2020. This report presents the meteorological and dust observations and radiological analyses accomplished during the approximately 10 months when the air monitoring data collection equipment was operational during CY2020.

54 ENVIRONMENTAL SCIENCES↗

Calendar Year 2020 Post-Closure Monitoring Report for Corrective Action Unit 99: Rainier Mesa/Shoshone Mountain, Underground Test Area, Nevada National Security Site, Nevada (Rev. 1)

This report presents the results of monitoring conducted for water quality, water levels, and institutional controls in calendar year (CY) 2020 by the U.S. Department of Energy (DOE), Environmental Management (EM) Nevada Program’s Underground Test Area (UGTA) Activity at Corrective Action Unit (CAU) 99, Rainier Mesa/Shoshone Mountain (RM/SM), at the Nevada National Security Site (NNSS), Nevada. This report also presents analytical laboratory results (including results of quality assurance/quality control samples, such as field duplicates [FDs]), and verification of use restrictions (URs), institutional controls, and water usage. Groundwater samples were collected; water levels were measured; and well site surveillance was conducted in support of the Underground Test Area Closure Report (CR) for Corrective Action Unit 99: Rainier Mesa/Shoshone Mountain, Nevada National Security Site, Nevada (DOE/EMNV, 2020). Rainier Mesa (RM) was the site of 61 underground nuclear tests, and Shoshone Mountain (SM) was the site of 6 underground nuclear tests. As a result of these activities, which took place from 1957 to 1992, radionuclides (RNs) were released in the subsurface in the vicinity of the detonations. These 67 underground nuclear tests are associated with 66 specific corrective action site (CAS) numbers, as listed in the Federal Facility Agreement and Consent Order (FFACO) (1996, as amended). Two tests, HURON LANDING and DIAMOND ACE (conducted simultaneously), are included within one CAS. The CR (DOE/EMNV, 2020) establishes the regulatory boundaries and regulatory boundary objectives, monitoring program, UR boundaries and URs, and other institutional controls agreed to by EM Nevada Program and the Nevada Division of Environmental Protection (NDEP) for closure of CAU 99. Regulatory boundaries for the RM/SM CAU were established to protect receptors of groundwater from RN contamination within the three downgradient groundwater basins that receive recharge from RM. The SM regulatory boundary was established to verify that RN contamination does not reach the lower carbonate aquifer below SM. The UR boundaries were established based on contaminant simulation forecasts from the flow and transport simulations with consideration of site-specific topographical controls. The URs associated with the UR boundaries were identified to protect onsite workers and the public from inadvertent exposure to contaminated groundwater as forecasted to occur assuming current conditions. The UR is intended to restrict activities that might expose workers to contaminated groundwater within the UR area. In addition to the URs, other institutional controls are established to monitor and limit access to groundwater. These include federal ownership and management in perpetuity, controlled access of the NNSS and surrounding areas, and reporting water use on the NNSS and surrounding hydrographic basins.

54 ENVIRONMENTAL SCIENCES↗

Streamlined Approach for Environmental Restoration (SAFER) Plan for Corrective Action Unit 578: Miscellaneous Inactive Sites Nevada National Security Site, Nevada, (Rev. 0)

This Streamlined Approach for Environmental Restoration (SAFER) Plan addresses the actions needed to achieve closure for Corrective Action Unit (CAU) 578, Miscellaneous Inactive Sites, identified in the Federal Facility Agreement and Consent Order (FFACO). CAU 578 comprises the following 11 corrective action sites (CASs) located in Areas 2, 3, 4, 6, 7, 12, and 23 of the Nevada National Security Site: • 02-26-01, Lead (Concrete Box w/Lining) • 02-26-07, Gun Turret w/Lead in Barrel • 03-16-01, U-3auS Disposal Site • 04-26-02, Lead on Instrument Bunker • 06-99-07, Sump • 07-99-01, Miscellaneous Debris • 12-02-11, UST-P-2 • 12-06-01, Muckpile • 12-06-04, Muckpile • 23-12-01, Boiler (2) • 23-99-04, Salvage Yard This plan provides the methodology for field activities needed to gather the necessary information for closing each CAS. There is sufficient information and process knowledge from historical documentation and investigations of similar sites regarding the expected nature and extent of potential contaminants to recommend closure of CAU 578 using the SAFER process. Additional information will be obtained by conducting a field investigation before selecting the appropriate corrective action for each CAS. The results of the field investigation will support a defensible recommendation that no further corrective action is necessary. This will be presented in a closure report that will be prepared and submitted to the Nevada Division of Environmental Protection (NDEP) for review and approval.

54 ENVIRONMENTAL SCIENCES↗

DECOVALEX-2023: Task D Final Report

Task D of DECOVALEX-2023 is focused on the simulation of the coupled thermal hydraulic-mechanical (THM) behaviour in the full-scale engineered barrier system (EBS). The Horonobe EBS experiment is the demonstration of the full-scale EBS in the underground research laboratory (URL) (performed by JAEA in the Horonobe URL in Japan). Task D consisted of the three steps, a preliminary step (Step 0), simulation of the laboratory tests (Step 1) and simulation of the in-situ full-scale EBS experiment (Step 2). Since the Horonobe EBS experiment demonstrates the vertical emplacement option of the EBS, the experiment gallery is also backfilled with the backfill material. Therefore, interaction between the EBS and the backfill material can also be demonstrated, such as deformation (change of density) of the buffer material. The underground water in the Horonobe URL is saline. This fact adds chemical processes to THM behaviour. For example, mechanical properties (such as swelling pressure of the buffer material and backfill material) and hydraulic properties (such as permeability of the buffer material and backfill material) change depending on the water chemistry. Task D was therefore a challenging Task focused on not only the relatively simple THM behaviour but also complex THM behaviour including chemical processes. Six research teams (BGR, CAS, JAEA, KAERI, SNL and Taipower) participated the Task D. BGR, CAS, JAEA, KAERI and Taipower research teams selected a THM approach, while the SNL research team selected a TH approach. Step 1 involved the simulation of laboratory test results and was important to check the numerical codes developed by the research teams. Step 1 was divided into four sub steps. The simulation results through the Step 1 identified the parameters for simulation of the Step 2. Basic parameters of the materials (buffer material, backfill material, rock mass, concrete, sand) were provided by JAEA. Special parameters which research team needed were identified by back analysis of Step 1. Most notably the mechanical behaviour of swelling and displacement depended on the applied model (elastic model or elastoplastic model). Parameters such as Young’s modulus were found to need smaller values than characterised in the fundamental laboratory test results (Step 1-1, 1-2) for the elastic model. Although laboratory experiments are usually simple, test results contained some error. For example, if the saturation level is 100 % or higher, it should be considered an error. This situation was presented in the Step 1-3. A possible reason is that the buffer material is a mixture of bentonite and silica sand. When a specimen is cut to measure volume or weight, sand grains will affect the measurement data. In Step 2, boundary conditions such as temperature on the surface of the simulated overpack, heater power of the electrical heaters installed in the simulated overpack, injection pressure and inflow rate of the test water, were applied. The outer boundary conditions can be selected using measured data (injection pressure and inflow rate of the test water that is controlled by the injection systems installed in the sand layer around the buffer material and in the boundary between backfill material and concrete support). Since such measured data has some noise, research teams developed their own simplified boundary conditions. Inner boundary conditions can be selected using measured data as heater power and temperature on the surface of the simulated overpack. These data also contain some noise, so research teams developed their own simplified developed boundary conditions. Task D validated various approaches thorough the simulation of the in-situ full scale EBS system including backfill of the gallery: variations in the coupling processes (THM or THC), analysis codes, and boundary conditions. Temperature distribution in the buffer material was simulated well by all research teams. This means thermal behaviour is not sensitive to the simulation approaches. Although the water content distribution on the outside of the buffer material was well simulated by all research teams, the simulation results differ from the measured values inside the buffer material (at the centre and inside, near the simulated overpack). The buffer material is made from tap water, but in the in-situ experiment, saline groundwater infiltrates the buffer material. Therefore, the selection of the hydraulic parameters of the buffer material greatly affects the simulation results of the re saturation behaviour of the buffer material. In the Horonobe EBS experiment, measured values suitable for validating the simulation results were not obtained near the simulated overpack. When simulating the pressure and deformation of the buffer material, the measurement data is easily affected by the installation conditions of the measurement sensors, so verifying the measurement data itself remains an issue. Mechanical simulation results differ depending on whether they are considered as elastic or elastoplastic phenomena. The accuracy of measured in-situ data can be assessed by detailed analysis comparing sampling specimen analysis and measured data. The Horonobe EBS experiment is scheduled to be dismantled in the future (FY2026 and 2027). This detailed dismantling investigation will finally confirm the measured data.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

A JWST Survey of the Supernova Remnant Cassiopeia A

We present initial results from a James Webb Space Telescope (JWST) survey of the youngest Galactic core-collapse supernova remnant, Cassiopeia A (Cas A), made up of NIRCam and MIRI imaging mosaics that map emission from the main shell, interior, and surrounding circumstellar/interstellar material (CSM/ISM). We also present four exploratory positions of MIRI Medium Resolution Spectrograph integral field unit spectroscopy that sample ejecta, CSM, and associated dust from representative shocked and unshocked regions. Surprising discoveries include (1) a weblike network of unshocked ejecta filaments resolved to ~0.01 pc scales exhibiting an overall morphology consistent with turbulent mixing of cool, low-entropy matter from the progenitor's oxygen layer with hot, high-entropy matter heated by neutrino interactions and radioactivity; (2) a thick sheet of dust-dominated emission from shocked CSM seen in projection toward the remnant's interior pockmarked with small (~1'') round holes formed by ≲0$^"_•$1 knots of high-velocity ejecta that have pierced through the CSM and driven expanding tangential shocks; and (3) dozens of light echoes with angular sizes between ~0$^"_•$1 and 1' reflecting previously unseen fine-scale structure in the ISM. NIRCam observations place new upper limits on infrared emission (≲20 nJy at 3 μm) from the neutron star in Cas A's center and tightly constrain scenarios involving a possible fallback disk. These JWST survey data and initial findings help address unresolved questions about massive star explosions that have broad implications for the formation and evolution of stellar populations, the metal and dust enrichment of galaxies, and the origin of compact remnant objects.

79 ASTRONOMY AND ASTROPHYSICS↗

Molecular mechanism of active Cas7-11 in processing CRISPR RNA and interfering target RNA

Cas7-11 is a Type III-E CRISPR Cas effector that confers programmable RNA cleavage and has potential applications in RNA interference. Cas7-11 encodes a single polypeptide containing four Cas7- and one Cas11-like segments that obscures the distinction between the multi-subunit Class 1 and the single-subunit Class-2 CRISPR Cas systems. We report a cryo-EM (cryo-electron microscopy) structure of the active Cas7-11 from Desulfonema ishimotonii (DiCas7-11) that reveals the molecular basis for RNA processing and interference activities. DiCas7-11 arranges its Cas7- and Cas11-like domains in an extended form that resembles the backbone made up by four Cas7 and one Cas11 subunits in the multi-subunit enzymes. Unlike the multi-subunit enzymes, however, the backbone of DiCas7-11 contains evolutionarily different Cas7 and Cas11 domains, giving rise to their unique functionality. The first Cas7-like domain nearly engulfs the last 15 direct repeat nucleotides in processing and recognition of the CRISPR RNA, and its free-standing fragment retains most of the activity. Both the second and the third Cas7-like domains mediate target RNA cleavage in a metal-dependent manner. The structure and mutational data indicate that the long variable insertion to the fourth Cas7 domain has little impact on RNA processing or targeting, suggesting the possibility for engineering a compact and programmable RNA interference tool.

59 BASIC BIOLOGICAL SCIENCES↗

Upper limits of hard gamma-ray emission from six X-ray sources

The Cornell 100-inch gamma-ray telescope has been used to set upper limits for the gamma-ray flux above 400 MeV from the X-ray sources Cyg X-1, Cyg X-2, Cyg X-3, Cas A, Cas B, and Per X-1. An upper limit for the diffuse flux of the galactic disk was set which is consistent with OSO-3 and SAS-2 data. A new measurement of the atmospheric gamma-ray generation rate is presented.

Campbell, M.↗

The ratio of deuterium to hydrogen in interstellar space. III - The lines of sight to Zeta Puppis and Gamma Cassiopeiae

An extensive set of measurements of the ratio of deuterium to hydrogen in the interstellar medium has been undertaken. The general observing program is described along with the data reduction techniques used to separate the complex deuterium and hydrogen profiles, and the results of the measurements for two stars, Zeta Pup and Gamma Cas. For Gamma Cas, log N(D)/N(H) is found to be approximately -4.8, in agreement with previous measurements. For Zeta Pup, a complicated structure of absorbing clouds in the interstellar medium is inferred. The best value of log N(D)/N(H) is about -4.6 for each of two components. One component is probably more complex than can be demonstrated directly at the resolution employed, and log N(D)N(H) could be -4.0 or larger in this component.

Vidal-Madjar, A.↗

Search for X-ray line emission from Cassiopeia A

The large area graphite crystal spectrometer aboard OSO 8 has been used to search for X-ray line emission from Cas A from ions of Si, S, and Fe over the energy band 1.865 to 8 keV. No evidence was obtained for line emission. The upper limits for the Si and S line fluxes are used to establish upper limits on the abundances of these elements. The limit on the Fe line flux is consistent with the strength of the emission feature reported in proportional counter experiments. Questions of nonequilibrium in ionization in Cas A and the effects on X-ray line emission are considered.

Kestenbaum, H. L.↗

Ultraviolet and optical spectral variability in the Be star Gamma Cassiopeiae - A coronal model for the emission

This paper reports the presence of Mg II emission, the probable presence of Si IV emission, and the possible presence of N V absorption in the UV spectrum of the B0.5 IVe star Gamma Cas. Changes in these features on time scales of several months are described. The detached-ring and mass-exchange binary models are briefly discussed and shown to be inadequate for Gamma Cas. An ad hoc generalization of the detailed stellar-wind model of Poeckert and Marlborough (1978) is presented and suggested as being qualitatively compatible with the UV data as well as with photoelectric H-alpha observations and the X-ray outburst observed in 1976. The presence of a 1-solar-mass neutron star companion with an orbital period of about 4 yr is hypothesized.

Marlborough, J. M.↗

Detection of a weak maser emission pedestal associated with the SiO maser

Results are reported for high-spectral-resolution observations of the v = 1, J = 1-0 SiO maser sources at 43,122.027 MHz (6.95 mm wavelength) associated with the variable stars Omega Cet, NML Tau, VY CMa, R Leo, W Hya, VX Sgr, NML Cyg, and R Cas. A weak underlying maser emission pedestal is clearly observed in the spectra of all but NML Cyg and R Cas. The data indicate that the underlying pedestal of SiO emission appears to originate in a shell-like region around the star, has a thermal appearance even though it must be due to weak maser emission, and appears to be part of the spectral signature of SiO maser emission from late-type stars. It is found that the center velocities of the pedestals may be used to determine stellar radial velocities. Observations of large-scale time variations in the intensity of the Ori A SiO maser and the detection of weak maser pedestals associated with each of the two strong emission-feature groups in Orion are also discussed. It is suggested that the Orion molecular cloud might contain two late-type long-period variable stars that may be semiregular variables.

Snyder, L. E.↗

Spectrophotometric variability in the Be star Gamma Cassiopeiae - Simultaneous ultraviolet and H-alpha observations

Simultaneous scans of the ultraviolet Si IV and Mg II resonance doublets in the spectrum of Gamma Cas with the Copernicus satellite during 64 continuous hours of observation, and H-alpha scans from a ground station, are described. No evidence is found for a rotation period of Gamma Cas, but narrow emission components in both ultraviolet doublets are reported along with a sudden emission increase on January 29.1, 1977 UT which appeared to be present in both H-alpha and the ultraviolet lines.

Slettebak, A.↗

X-ray evidence for electron-ion equilibrium and ionization nonequilibrium in young supernova remnants

The A-2 spectroscopy experiment on HEAO 1 detected X-ray emission up to 25 keV from the supernova remnants Cas A and Tycho. The spectra must include continuum components with effective temperature equivalent or 10 to the 8th power K which could arise from optically thin plasmas in the collisionless shock fronts. This is the first indication of electron-ion temperature equilibrium in the expanding shell of young remnants. Measurements of the equivalent widths of the K alpha and K beta iron line blends in Cas A, show that their ratio is not compatible with the measured X-ray temperature in the collisional ionization equilibrium model. The search for hard X-ray pulsars in both remnants was unsuccessful.

Pravdo, S. H.↗