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At least 19 records

A red algal polysaccharide influences the multicellular development of the choanoflagellate Salpingoeca rosetta

The choanoflagellate Salpingoeca rosetta exemplifies the capacity of marine microeukaryotes to integrate environmental cues into their life histories. Some of the cues that S. rosetta detects are lipids from their bacterial prey that induce the development of multicellular colonies called rosettes. In the aquatic environments where S. rosetta would encounter bacterial cues, microbial communities gain refuge and food from algae. For example, microbes in coastal environments benefit from macroalgae that annually release ∼10 14 g of carbon, primarily in the form of polysaccharides that comprise ∼80% of dissolved organic carbon in surface waters. Despite the ecological impact of algae and historical descriptions of choanoflagellates attached to algae, the influence of algae on choanoflagellate life history transitions has remained unexplored. Here, we report that porphyran, a polysaccharide produced by the red macroalga Porphyra umbilicalis, induces multicellular development in S. rosetta. We first noticed this response when S. rosetta formed multicellular rosette colonies while growing in media prepared from P. umbilicalis, even though rosette-inducing bacteria were absent. By biochemically purifying extracts of P. umbilicalis, we identified porphyran as the rosette-inducing factor. This response provides a biochemical insight that indicates algal polysaccharides may serve as cues to mediate associations between choanoflagellates and algae. Moreover, this observation complements evidence from environmental and geochemical studies that show the impact that algae have exerted on the ecology and evolution of eukaryotes, including a rise in algal productivity during the origin of animals, the closest living relatives of choanoflagellates.

59 BASIC BIOLOGICAL SCIENCES↗

De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV -2 spike receptor binding domain ( RBD )

The continued emergence of new SARS-CoV-2 variants has accentuated the growing need for fast and reliable methods for the design of potentially neutralizing antibodies (Abs) to counter immune evasion by the virus. Here, we report on the de novo computational design of high-affinity Ab variable regions (Fv) through the recombination of VDJ genes targeting the most solvent-exposed hACE2-binding residues of the SARS-CoV-2 spike receptor binding domain (RBD) protein using the software tool OptMAVEn-2.0. Subsequently, we carried out computational affinity maturation of the designed variable regions through amino acid substitutions for improved binding with the target epitope. Immunogenicity of designs was restricted by preferring designs that match sequences from a 9-mer library of “human Abs” based on a human string content score. We generated 106 different antibody designs and reported in detail on the top five that trade-off the greatest computational binding affinity for the RBD with human string content scores. We further describe computational evaluation of the top five designs produced by OptMAVEn-2.0 using a Rosetta-based approach. We used Rosetta SnugDock for local docking of the designs to evaluate their potential to bind the spike RBD and performed “forward folding” with DeepAb to assess their potential to fold into the designed structures. Ultimately, our results identified one designed Ab variable region, P1.D1, as a particularly promising candidate for experimental testing. This effort puts forth a computational workflow for the de novo design and evaluation of Abs that can quickly be adapted to target spike epitopes of emerging SARS-CoV-2 variants or other antigenic targets.

59 BASIC BIOLOGICAL SCIENCES↗

Feature Design for Protein Interface Hotspots Using KFC2 and Rosetta

Protein–protein interactions regulate many essential biological processes and play an important role in health and disease. The process of experimentally characterizing protein residues that contribute the most to protein–protein interaction affinity and specificity is laborious. Thus, developing models that accurately characterize hotspots at protein–protein interfaces provides important information about how to inhibit therapeutically relevant protein–protein interactions. During the course of the ICERM WiSDM workshop 2017, we combined the KFC2a protein–protein interaction hotspot prediction features with Rosetta scoring function terms and interface filter metrics. A two-way and three-way forward selection strategy was employed to train support vector machine classifiers, as was a reverse feature elimination strategy. From these results, we identified subsets of KFC2a and Rosetta combined features that show improved performance over KFC2a features alone.

Seeger, Franziska↗

Formaldehyde chemistry in cometary ices: on the prospective detection of NH{sub 2}CH{sub 2}OH, HOCH{sub 2}OH, and POM by the on-board ROSINA instrument of the Rosetta mission

The thermal reactivity of a water-dominated cometary ice analog containing H{sub 2}CO and NH{sub 3} is investigated by means of Fourier transform infrared spectroscopy, mass spectrometry, and B3LYP calculations. Three products are characterized by these techniques: aminomethanol (NH{sub 2}CH{sub 2}OH), methyleneglycol (HOCH{sub 2}OH), and polyoxymethylene (POM, HO-(CH{sub 2}-O) {sub n}-H). Their formation strongly depends on the initial NH{sub 3}/H{sub 2}CO ratio. In addition, the influence of the initial ice composition on the thermal stability of POM has also been investigated. It is shown that POM formed during warming of the ices consists of short-chain polymers (i.e., oligomers of formaldehyde HO-(CH{sub 2}-O) {sub n}-H, n < 5), which are volatile at temperatures higher than 200 K. This suggests that gas-phase detection by the ROSINA instrument on board the Rosetta mission would be the most appropriate method to detect POM. Moreover, the mass spectra presented in this work might help in the interpretation of data that will be recorded by this instrument. Finally, a new scenario to explain the distributed source of formaldehyde observed in comets is discussed.

79 ASTRONOMY AND ASTROPHYSICS↗

PLASMA ENVIRONMENT AROUND COMET 67P/CHURYUMOV–GERASIMENKO AT PERIHELION: MODEL COMPARISON WITH ROSETTA DATA

The plasma environment near comet 67P/Churyumov–Gerasimenko (67P/CG) is dynamically affected by various factors, including the incident solar wind and outgassing from the nucleus. The Rosetta spacecraft MAGnetometer (MAG) instrument observations near perihelion showed crossing events into a magnetic field-free region at about 170 km from the nucleus in 2015 July at 1.26 au from the Sun. At each crossing, the magnitude of the magnetic field dropped by more than 20 nT to near zero. We compared the Ion and Electron Sensor (IES) electron differential flux energy spectrum inside and outside the crossing boundaries. The IES observations show a modest but consistent drop in electron flux for energies between 40 eV and a few hundred eV at each cavity crossing event. This drop in the electron spectra might be due to the absence or attenuation of solar wind electrons inside the observed diamagnetic regions, which might or might not be a diamagnetic cavity. There is no apparent simple linear correlation between the electron count rate measured by the IES at different energies and the magnitude of the magnetic field, however; at all energies, the highest electron count rates are recorded at the highest magnetic field magnitudes. From model-data comparisons it seems that inside diamagnetic regions, pure coma photoelectrons are not sufficient to explain the observations and that a trapping mechanism and/or infused solar wind electrons are necessary to explain the observed electron fluxes.

79 ASTRONOMY AND ASTROPHYSICS↗

Stellar Occultation by Comet 67P/Churyumov–Gerasimenko Observed with Rosetta's Alice Far-ultraviolet Spectrograph

Following our previous detection of ubiquitous H{sub 2}O and O{sub 2} absorption against the far-ultraviolet continuum of stars located near the nucleus of Comet 67P/Churyumov–Gerasimenko, we present a serendipitously observed stellar occultation that occurred on 2015 September 13, approximately one month after the comet’s perihelion passage. The occultation appears in two consecutive 10-minute spectral images obtained by Alice, Rosetta’s ultraviolet (700–2100 Å) spectrograph, both of which show H{sub 2}O absorption with column density >10{sup 17.5} cm{sup −2} and significant O{sub 2} absorption (O{sub 2}/H{sub 2}O ≈ 5%–10%). Because the projected distance from the star to the nucleus changes between exposures, our ability to study the H{sub 2}O column density profile near the nucleus (impact parameters <1 km) is unmatched by our previous observations. We find that the H{sub 2}O and O{sub 2} column densities decrease with increasing impact parameter, in accordance with expectations, but the O{sub 2} column decreases ∼3 times more quickly than H{sub 2}O. When combined with previously published results from stellar appulses, we conclude that the O{sub 2} and H{sub 2}O column densities are highly correlated, and O{sub 2}/H{sub 2}O decreases with the increasing H{sub 2}O column.

79 ASTRONOMY AND ASTROPHYSICS↗

The TW Hya Rosetta Stone Project. I. Radial and Vertical Distributions of DCN and DCO{sup +}

Molecular D/H ratios are frequently used to probe the chemical past of solar system volatiles. Yet it is unclear which parts of the solar nebula hosted an active deuterium fractionation chemistry. To address this question, we present 0."2–0."4 Atacama Large Millimeter/submillimeter Array (ALMA) observations of DCO{sup +} and DCN 2–1, 3–2, and 4–3 toward the nearby protoplanetary disk around TW Hya, taken as part of the TW Hya Rosetta Stone project, augmented with archival data. DCO{sup +} is characterized by an excitation temperature of ~40 K across the 70 au radius pebble disk, indicative of emission from a warm, elevated molecular layer. Tentatively, DCN is present at even higher temperatures. Both DCO{sup +} and DCN present substantial emission cavities in the inner disk, while in the outer disk the DCO{sup +} and DCN morphologies diverge: most DCN emission originates from a narrow ring peaking around 30 au, with some additional diffuse DCN emission present at larger radii, while DCO{sup +} is present in a broad structured ring that extends past the pebble disk. Based on a set of simple parametric disk abundance models, these emission patterns can be explained by a near-constant DCN abundance exterior to the cavity, and an increasing DCO{sup +} abundance with radius. In conclusion, the ALMA observations reveal an active deuterium fractionation chemistry in multiple disk regions around TW Hya, but not in the cold planetesimal-forming midplane and in the inner disk. More observations are needed to explore whether deuterium fractionation is actually absent in these latter regions, and if its absence is a common feature or something peculiar to the old TW Hya disk.

36 MATERIALS SCIENCE↗

ON THE ORIGIN OF INNER COMA STRUCTURES OBSERVED BY ROSETTA DURING A DIURNAL ROTATION OF COMET 67P/CHURYUMOV–GERASIMENKO

The Rosetta probe around comet 67P/Churyumov–Gerasimenko (67P) reveals an anisotropic dust distribution of the inner coma with jet-like structures. The physical processes leading to jet formation are under debate, with most models for cometary activity focusing on localized emission sources, such as cliffs or terraced regions. Here we suggest, by correlating high-resolution simulations of the dust environment around 67P with observations, that the anisotropy and the background dust density of 67P originate from dust released across the entire sunlit surface of the nucleus rather than from few isolated sources. We trace back trajectories from coma regions with high local dust density in space to the non-spherical nucleus and identify two mechanisms of jet formation: areas with local concavity in either two dimensions or only one. Pits and craters are examples of the first case; the neck region of the bi-lobed nucleus of 67P is an example of the latter case. The conjunction of multiple sources, in addition to dust released from all other sunlit areas, results in a high correlation coefficient (∼0.8) of the predictions with observations during a complete diurnal rotation period of 67P.

79 ASTRONOMY AND ASTROPHYSICS↗

THE NATURE AND FREQUENCY OF THE GAS OUTBURSTS IN COMET 67P/CHURYUMOV–GERASIMENKO OBSERVED BY THE ALICE FAR-ULTRAVIOLET SPECTROGRAPH ON ROSETTA

ALICE is a far-ultraviolet imaging spectrograph on board Rosetta that, among multiple objectives, is designed to observe emissions from various atomic and molecular species from within the coma of comet 67P/Churyumov–Gerasimenko. The initial observations, made following orbit insertion in 2014 August, showed emissions of atomic hydrogen and oxygen spatially localized close to the nucleus and attributed to photoelectron impact dissociation of H{sub 2}O vapor. Weaker emissions from atomic carbon were subsequently detected and also attributed to electron impact dissociation, of CO{sub 2}, the relative H i and C i line intensities reflecting the variation of CO{sub 2} to H{sub 2}O column abundance along the line of sight through the coma. Beginning in 2015 mid-April, Alice sporadically observed a number of outbursts above the sunward limb characterized by sudden increases in the atomic emissions, particularly the semi-forbidden O i λ 1356 multiplet, over a period of 10–30 minutes, without a corresponding enhancement in long-wavelength solar reflected light characteristic of dust production. A large increase in the brightness ratio O i λ 1356/O i λ 1304 suggests O{sub 2} as the principal source of the additional gas. These outbursts do not correlate with any of the visible images of outbursts taken with either OSIRIS or the navigation camera. Beginning in 2015 June the nature of the Alice spectrum changed considerably with CO Fourth Positive band emission observed continuously, varying with pointing but otherwise fairly constant in time. However, CO does not appear to be a major driver of any of the observed outbursts.

79 ASTRONOMY AND ASTROPHYSICS↗

Studies on Thorium Adsorption Characteristics upon Activated Titanium Hydroxide Prepared from Rosetta Ilmenite Concentrate

The titanium hydroxide prepared from Rosetta ilmenite concentrate has been applied for Th (IV) adsorption from its acid aqueous solutions. The prepared hydroxide is first characterized by both Fourier transform infrared (FT-IR) spectrum and thermogravimetric analysis. The relevant factors affecting the adsorption process have been studied. The obtained equilibrium data fits well with the Langmuir isotherm rather than Freundlich isotherm, while the adsorption kinetic data follow the pseudo-second order model. The different thermodynamic parameters have also been calculated and indicate that the adsorption process is spontaneous.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Rapid Phase Transitions of Thermotropic Glycolipid Quasicrystal and Frank‐Kasper Mesophases: A Mechanistic Rosetta Stone

Abstract Experimental results are presented that serve to lower the barrier for developing the science and technology of non‐classical thermotropic glycolipid mesophases, which now include dodecagonal quasicrystal (DDQC) and Frank–Kasper (FK) A15 and σ mesophases that can be produced under mild conditions from a versatile class of sugar‐polyolefin conjugates. By employing “alloys” comprised of mono‐ and disaccharide‐polyolefin conjugates, and optionally with vitamin E as a small molecule phase modulator, we report the spontaneous formation of stable A15 mesophases at ambient temperature. We further document a rich thermotropic phase map that includes DDQC, A15, and σ mesophases of tunable periodicity that are connected through rapid thermotropic phase transitions as a function of increasing temperature in the order: liquid‐like packing (LLP)→DDQC → A15→σ→ disorder. This first direct observation of a rapid thermotropic A15→σ phase transition provides support for a diffusionless martensitic process proceeding through strain‐induced introduction of planar defects into the A15 lattice.

36 MATERIALS SCIENCE↗

Rapid Phase Transitions of Thermotropic Glycolipid Quasicrystal and Frank‐Kasper Mesophases: A Mechanistic Rosetta Stone

Abstract Experimental results are presented that serve to lower the barrier for developing the science and technology of non‐classical thermotropic glycolipid mesophases, which now include dodecagonal quasicrystal (DDQC) and Frank–Kasper (FK) A15 and σ mesophases that can be produced under mild conditions from a versatile class of sugar‐polyolefin conjugates. By employing “alloys” comprised of mono‐ and disaccharide‐polyolefin conjugates, and optionally with vitamin E as a small molecule phase modulator, we report the spontaneous formation of stable A15 mesophases at ambient temperature. We further document a rich thermotropic phase map that includes DDQC, A15, and σ mesophases of tunable periodicity that are connected through rapid thermotropic phase transitions as a function of increasing temperature in the order: liquid‐like packing (LLP)→DDQC → A15→σ→ disorder. This first direct observation of a rapid thermotropic A15→σ phase transition provides support for a diffusionless martensitic process proceeding through strain‐induced introduction of planar defects into the A15 lattice.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

La$_{2-x}$Ba$_x$CuO$_4$ as a superconducting Rosetta Stone

The high-temperature superconductivity in layered cuprates discovered by Bednorz and Müller arrived as a shock. Gradually, the presence of competing orders, such as antiferromagnetism and charge order, were discovered; however, the relationship to the superconductivity has been confusing. Importantly, it so happens that the original cuprate superconductor family La$_{2-x}$Ba$_x$CuO$_4$ contains all of the relevant phases, with extreme competition among them, and analysis of these phases provides strong clues to the nature of the superconductivity in cuprates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

The Open Science Cyber Risk Profile: The Rosetta Stone for Open Science and Cybersecurity

The Open Science Cyber Risk Profile (OSCRP) working group has created a document that motivates scientists by demonstrating how improving their security posture reduces the risks to their science. This effort aims to both bridge the communication gap between scientists and IT security professionals and allows for the effective management of risks to open science caused by IT security threats.

97 MATHEMATICS AND COMPUTING↗