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At least 1,729 records · Page 96

Atomic Force Microscopy and Infrared Nanospectroscopy of COVID-19 Spike Protein for the Quantification of Adhesion to Common Surfaces

The COVID-19 pandemic has claimed millions of lives worldwide, sickened many more, and has resulted in severe socio-economic consequences. As society returns to normal, understanding the spread and persistence of SARS CoV-2 on commonplace surfaces can help to mitigate future outbreaks of coronaviruses and other pathogens. We hypothesize that such an understanding can be aided from studying the binding and interaction of viral proteins with non-biological surfaces. Here, we propose a methodology for investigating the adhesion of the SARS CoV-2 spike glycoprotein on common inorganic surfaces such as aluminum-, copper-, iron-, silica-, and ceria-oxides as well as metallic gold. Quantitative adhesion was obtained from the analysis of measured forces at the nanoscale using an atomic force microscope operated under ambient conditions. Without imposing further constraints on the measurement conditions, our preliminary findings suggest that spike glycoproteins interact with similar adhesion forces across the majority of the metal oxides tested with the exception to gold, for which attraction forces ~10 times stronger than all other materials studied were observed. Ferritin, which was used as a reference protein, was found to exhibit similar adhesion forces as SARS CoV-2 spike protein. Further, this study results show that glycoprotein adhesion forces for similar ambient humidity, tip shape, and contact surface are non-specific to the properties of metal oxide surfaces, which are expected to be covered by a thin water film. The findings suggest that at ambient conditions glycoprotein adhesion to metal oxides is primarily controlled by the water capillary forces and they depend on the surface tension of the liquid (water). We discuss further strategies warranted to decipher the intricate nanoscale forces for improved quantification of the adhesion.

59 BASIC BIOLOGICAL SCIENCES↗

Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles

Broad immune responses are needed to mitigate viral evolution and escape. To induce antibodies against conserved receptor-binding domain (RBD) regions of SARS-like betacoronavirus (sarbecovirus) spike proteins that recognize SARS-CoV-2 variants of concern and zoonotic sarbecoviruses, we developed mosaic-8b RBD nanoparticles presenting eight sarbecovirus RBDs arranged randomly on a 60-mer nanoparticle. Mosaic-8b immunizations protected animals from challenges from viruses whose RBDs were matched or mismatched to those on nanoparticles. Here, we describe neutralizing mAbs isolated from mosaic-8b-immunized rabbits, some on par with Pemgarda, the only currently FDA-approved therapeutic mAb. Deep mutational scanning, in vitro selection of spike resistance mutations, and single-particle cryo-electron microscopy structures of spike–antibody complexes demonstrated targeting of conserved RBD epitopes. Rabbit mAbs included critical D-gene segment RBD-recognizing features in common with human anti-RBD mAbs, despite rabbit genomes lacking an equivalent human D-gene segment, thus demonstrating that the immune systems of humans and other mammals can utilize different antibody gene segments to arrive at similar modes of antigen recognition. These results suggest that animal models can be used to elicit anti-RBD mAbs with similar properties to those raised in humans, which can then be humanized for therapeutic use, and that mosaic RBD nanoparticle immunization coupled with multiplexed screening represents an efficient way to generate and select broadly cross-reactive therapeutic pan-sarbecovirus and pan-SARS-CoV-2 variant mAbs.

Science & Technology - Other Topics↗

Novel fisheries investigations by Harald Dannevig: some parallels with Johan Hjort on the other side of the world

Abstract Harald Dannevig was Australia’s first Director of fisheries research and Director of Australia’s first ocean-going research vessel. Dannevig’s initial contributions concerned hatchery technology, freshwater fisheries, and impacts of estuarine prawn trawling. Later, he revealed the growth and migration of sea mullet, the spawning of pelagic eggs in the coastal ocean, and he was the first to demonstrate the effect of onshore winds on recruitment to estuarine fisheries. Using plans of the first Norwegian research trawler Michael Sars, he advised on the construction and commissioning of Endeavour. He organized 99 research voyages over 6 years to determine suitable trawling grounds over ∼7000 km, discovering 263 new species, including 96 new fish species and ∼5000 catalogued specimens. Harald Dannevig’s significant achievements in Australia were soon forgotten after his death with the loss of Endeavour in the Southern Ocean at the beginning of World War I. Both Johan Hjort and Dannevig were numerate, loved natural history, and were keenly observant on the deck. As these two scientists did not correspond, their innovative and parallel thinking stems from the shared university environment with G.O. Sars, and the rapport between Sars and Harald’s father Gunder Dannevig, concerning the fish hatchery and stocking of larval cod.

Suthers, Iain M.↗

Bioinformatics and 3D Structural Analysis of the Coronavirus Main Protease Active Site Diversity

Coronaviruses (Coronaviridae) such as SARS‐CoV‐2 (severe acute respiratory syndrome coronavirus) and MERS‐CoV (Middle East respiratory syndrome coronavirus) have been the source of recent outbreaks and global health concerns. While vaccines have been essential for controlling the SARS‐CoV‐2 (COVID‐19) pandemic, it is uncertain whether they will be effective against future coronavirus strains. Therefore, identification or design of a broad‐spectrum drug that targets highly conserved regions of the main protease of multiple coronavirus strains is essential in the long term. As part of a virtual summer research experience with the RCSB PDB, bioinformatics tools were employed to predict and construct 3D models of the coronavirus main protease (MPro) using SARS‐CoV‐2 as the template, with a focus on mutational trends and active sites. This study focused on the active sites of MPro, a cysteine protease essential for viral assembly and replication. Sequence alignments and structure modeling of MPro structures has identified conserved regions across multiple coronavirus strains. Inhibition of MPro halts coronavirus replication, making it an ideal drug target, and studies of MPro may foster and accelerate the discovery of high affinity broad‐spectrum drugs.

Wu Wu, Amy↗

Practical Three-Dimensional Curvilinear Aperture Monopulse Synthetic Aperture Radar

When collected over a curved path, Synthetic Aperture Radar (SAR) contains information about the three-dimensional content of a scene that can aid interpretation of this difficult imaging modality. In a point scatterer simulation with amplitudes and heights derived from a real SAR image pair, we supplement confocal processing with a monopulse-based algorithm to compute heights of certain bright points, which we find automatically. In SAR, bright points often reflect man-made infrastructure central to scene interpretation.

Story, Mark [ORNL] (ORCID:0000000289148911)↗

An antibody class with a common CDRH3 motif broadly neutralizes sarbecoviruses

The devastation caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made clear the importance of pandemic preparedness. To address future zoonotic outbreaks due to related viruses in the sarbecovirus subgenus, we identified a human monoclonal antibody, 10-40, that neutralized or bound all sarbecoviruses tested in vitro and protected against SARS-CoV-2 and SARS-CoV in vivo. Comparative studies with other receptor-binding domain (RBD)–directed antibodies showed 10-40 to have the greatest breadth against sarbecoviruses, suggesting that 10-40 is a promising agent for pandemic preparedness. Moreover, structural analyses on 10-40 and similar antibodies not only defined an epitope cluster in the inner face of the RBD that is well conserved among sarbecoviruses but also uncovered a distinct antibody class with a common CDRH3 motif. Our analyses also suggested that elicitation of this class of antibodies may not be overly difficult, an observation that bodes well for the development of a pan-sarbecovirus vaccine.

59 BASIC BIOLOGICAL SCIENCES↗

Thermal Evaluation of the SAVY-4000 1 Quart Container at High Heat Loads

The SAVY-4000 Safety Analysis Report (SAR) was published in 2013 which established the design life of the container series through physical testing that meets applicable requirements from DOE M 441.1-1, Nuclear Material Packaging Manual. One critical requirement in DOE M 441.1-1 is to set a maximum heat load for the entire series to ensure that throughout the lifetime of the container, each of the components still performs within manufacture specifications. The original maximum decay heat limit has been defined within the SAVY-4000 SAR, which was accomplished by completing a series of tests that heat loaded the SAVY-4000 series and measured the steady state temperature and graded it against manufacture specifications. The container series is comprised of a corrosion resistant 316L stainless steel containment boundary, ceramic composite filter for the prevention of radiological particulate release and a chemically stable O-ring made of Viton ® . Currently, the SAVY 4000 maximum decay heat load is set at 25 Watts and the heat load expected during normal handling and storage is considered sufficient that the SAVY 4000 container requirements will not be the limiting factor for storage of most common material in use at TA-55, e.g. weapons grade oxide, americium, Pu-238 oxide and encapsulated heat sources. The SAVY 4000 lifetime was originally set as 5 years within the SAVY-4000 SAR, but in July 2019 the lifetime was extended to 15 years through a technical basis justification approved by the Department of Energy (DOE) Los Alamos Field Office. The 25 Watt limit applies to all SAVY 4000 container sizes; 1-quart, 2-quart, 3-quart, 5-quart, 8-quart, 12-quart, 5-gallon, and 10-gallon.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

National Technology & Engineering Solutions of Sandia, LLC Technical Assistance With Energy Cloud (Final CTAP Report)

Sandia provided technical assistance to Energy Cloud to support the assessment of Energy Cloud’s technology for air filtration of the SARS-CoV-2 virus. The Energy Cloud system was developed to filter the SARS-CoV-2 virus from commercial HVAC systems, ducts, and enclosed rooms without generating ozone. The project included a 3-week experimental series with aerosolized SARS-CoV-2 virus at the University of Southern California’s biosafety level 3 (BSL-3) laboratory. USC provided the facility as well as experimentally derived measurements and assessment of the Energy Cloud system efficacy for SARSCoV-2 filtration from air handling systems.

42 ENGINEERING↗

Decontamination and Sterilization of Surfaces using Low Cost Ionic Liquids (CRADA Final Report)

The current study made a comprehensive literature review of the structure activity relationship (SAR) for microcidal and virucidal influence of ionic liquids. It summarized the key structure parameters that have close correlation to the antimicrobial and antiviral properties of the ILs. It proposed an experimental plan on developing and testing an effective ionic liquid from renewable lignocellulosic biomass. The goal is to understand the structure activity relationship (SAR) for virucidal influence of ionic liquids through comprehensive literature search and data analysis. A full experimental plan will be drafted based on the literature summary. Perform a comprehensive literature search to aid the development of an effective and easily deployable method to inactivate SARS-CoV-2 and decontaminate surfaces based on low-cost functional ionic liquids. These designer solvents have the potential to be a compelling and environmentally friendly alternative to common chemical disinfectants. Literature summary report including reported ionic liquid structures, synthesis and testing methods, and the structure activity relationship. Experimental plan on developing a low cost effective antiviral ionic liquid.

59 BASIC BIOLOGICAL SCIENCES↗

Bayesian Inference of State-Level COVID-19 Basic Reproduction Numbers across the United States

Although many persons in the United States have acquired immunity to COVID-19, either through vaccination or infection with SARS-CoV-2, COVID-19 will pose an ongoing threat to non-immune persons so long as disease transmission continues. We can estimate when sustained disease transmission will end in a population by calculating the population-specific basic reproduction number ℛ0, the expected number of secondary cases generated by an infected person in the absence of any interventions. The value of ℛ0 relates to a herd immunity threshold (HIT), which is given by 1−1/ℛ0. When the immune fraction of a population exceeds this threshold, sustained disease transmission becomes exponentially unlikely (barring mutations allowing SARS-CoV-2 to escape immunity). Here, we report state-level ℛ0 estimates obtained using Bayesian inference. Maximum a posteriori estimates range from 7.1 for New Jersey to 2.3 for Wyoming, indicating that disease transmission varies considerably across states and that reaching herd immunity will be more difficult in some states than others. ℛ0 estimates were obtained from compartmental models via the next-generation matrix approach after each model was parameterized using regional daily confirmed case reports of COVID-19 from 21 January 2020 to 21 June 2020. Our ℛ0 estimates characterize the infectiousness of ancestral strains, but they can be used to determine HITs for a distinct, currently dominant circulating strain, such as SARS-CoV-2 variant Delta (lineage B.1.617.2), if the relative infectiousness of the strain can be ascertained. On the basis of Delta-adjusted HITs, vaccination data, and seroprevalence survey data, we found that no state had achieved herd immunity as of 20 September 2021.

60 APPLIED LIFE SCIENCES↗

Antenna dimensions of synthetic aperture radar systems on satellites

Design of a synthetic aperture radar (SAR) for a satellite must take into account the limitation in weight and dimensions of the antenna. The lower limits of the antenna area are derived from the conditions of unambiguity of the SAR system. This result is applied to estimate the antenna requirements for SARs on satellites in circular orbits of various altitudes around Earth and Venus.

Richter, K. R.↗

Vibrationally excited nitrogen in stable auroral red arcs and its effect on ionospheric recombination

The time-dependent continuity equations, including diffusion, were solved for the first six energy levels of molecular nitrogen for conditions in the thermosphere corresponding to stable auroral red (SAR) arcs. The results show that molecular nitrogen is excited vibrationally to the degree that the rate constant for the ionospheric loss process, O(+) + N2 yields NO(+) + N, is increased by as much as a factor of 7.6 at F2 region altitudes. It was found that deviations from the energetically equivalent Boltzmann distribution were large, causing the rate constant to be as much as 1.6 times the rate constant calculated for the Boltzmann distribution. These results indicate that SAR arc intensities as small as 58 R can produce noticeable increases in the ionosphere ion-atom interchange reaction rate and hence in the rate of loss of ionospheric electrons. It is suggested that the observed decrease of electron density in the F2 region in SAR arcs can probably be explained by enhanced reaction rates for ion-atom interchange between O(+) and N2 caused by vibrational excitation of molecular nitrogen by electron impact.

Newton, G. P.↗

Simultaneous observations of the proton ring current and stable auroral red arcs

Explorer 45 observed the equatorial proton ring current in the plasmapause region and Fritz Peak Observatory observed stable auroral red (SAR) arcs on Dec. 17, 1971 during a geomagnetic storm. An estimate of energy lost from the ring current was obtained by using Explorer 45 observations of pitch angle distribution transitions which are probably due to pitch angle diffusion-driven resonant interactions with ion cyclotron waves. Estimates of the equatorial loss rate yield values greater than the required SAR arc energy input rate, and the location of the peaks in these loss rates agrees with the observed location of the arcs. It is thus concluded that this energy loss is sufficient to sustain the SAR arcs.

Williams, D. J.↗

A synthetic aperture processor using CCD signal processing techniques

Synthetic aperture radar (SAR) imaging was the most suitable technique for achieving high resolution imagery through atmospheric cloud cover. This feature was important for planetary as well as earth orbiting satellite systems, and for military aircraft applications. Such applications require onboard data processing or wide-band data transmission systems in order to handle the large amounts of raw data produced by such systems. A number of techniques were utilized in implementing SAR processors. Frequency filtering and Fourier transform operations using both optical and digital techniques were utilized in SAR processing.

Bailey, W. H.↗

Precipitation mapping with an airborne synthetic aperture imaging radar

Use of an airborne synthetic-aperture radar (SAR) of 3.1-cm wavelength for the detection and mapping of precipitation echoes is described. Difficulties in mapping related to the incoherence of the echoes are discussed; methods of increasing resolution by Doppler filtering are suggested. Observations made with a vertical side-looking SAR system flying above a stratiform storm were found to resemble vertical cross sections obtained with conventional radar showing snow streamers, the bright band and rain. However, the actual section sampled by the SAR after filtering for zero Doppler is shown to depend upon both the relative motion of the particles and the relative winds below the aircraft. Knowledge of the relative winds, deduced from Doppler spectrum variations, and of the particle fall speeds permits the generation of horizontal and vertical cross sections displaced from the aircraft's position.

Atlas, D.↗

Optimal sampling and quantization of synthetic aperture radar signals

Some theoretical and experimental results on optimal sampling and quantization of synthetic aperture radar (SAR) signals are presented. It includes a description of a derived theoretical relationship between the pixel signal to noise ratio of processed SAR images and the number of quantization bits per sampled signal, assuming homogeneous extended targets. With this relationship known, a solution may be realized for the problem of optimal allocation of a fixed data bit-volume (for specified surface area and resolution criterion) between the number of samples and the number of bits per sample. The results indicate that to achieve the best possible image quality for a fixed bit rate and a given resolution criterion, one should quantize individual samples coarsely and thereby maximize the number of multiple looks. The theoretical results are then compared with simulation results obtained by processing aircraft SAR data.

Wu, C.↗

Measurement of hurricane winds and waves with a synthetic aperture radar

An analysis of data collected in a hurricane research program is presented. The data were collected with a Synthetic Aperture Radar (SAR) during five aircraft flights in the Atlantic in August and September, 1976. Work was conducted in two areas. The first is an analysis of the L-band SAR data in a scatterometer mode to determine the surface windspeeds in hurricanes, in a similar manner to that done by an X-band scatterometer. The second area was to use the SAR to examine the wave patterns in hurricanes. The wave patterns in all of the storms are similar and show a marked radial asymmetry.

Shemdin, O. H.↗

Combined synthetic aperture radar/Landsat imagery

This paper presents the results of investigations into merging synthetic aperture radar (SAR) and Landsat multispectral scanner (MSS) images using optical and digital merging techniques. The unique characteristics of airborne and orbital SAR and Landsat MSS imagery are discussed. The case for merging the imagery is presented and tradeoffs between optical and digital merging techniques explored. Examples of Landsat and airborne SAR imagery are used to illustrate optical and digital merging. Analysis of the merged digital imagery illustrates the improved interpretability resulting from combining the outputs from the two sensor systems.

Marque, R. E.↗