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"Spherules"
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A unifying structural and functional model of the coronavirus replication organelle: Tracking down RNA synthesis
by
de Wilde, Adriaan H.
,
Bárcena, Montserrat
,
Snijder, Eric J.
in
Animals
,
Autoradiography
,
Betacoronavirus - genetics
2020
Zoonotic coronavirus (CoV) infections, such as those responsible for the current severe acute respiratory syndrome-CoV 2 (SARS-CoV-2) pandemic, cause grave international public health concern. In infected cells, the CoV RNA-synthesizing machinery associates with modified endoplasmic reticulum membranes that are transformed into the viral replication organelle (RO). Although double-membrane vesicles (DMVs) appear to be a pan-CoV RO element, studies to date describe an assortment of additional CoV-induced membrane structures. Despite much speculation, it remains unclear which RO element(s) accommodate viral RNA synthesis. Here we provide detailed 2D and 3D analyses of CoV ROs and show that diverse CoVs essentially induce the same membrane modifications, including the small open double-membrane spherules (DMSs) previously thought to be restricted to gamma- and delta-CoV infections and proposed as sites of replication. Metabolic labeling of newly synthesized viral RNA followed by quantitative electron microscopy (EM) autoradiography revealed abundant viral RNA synthesis associated with DMVs in cells infected with the beta-CoVs Middle East respiratory syndrome-CoV (MERS-CoV) and SARS-CoV and the gamma-CoV infectious bronchitis virus. RNA synthesis could not be linked to DMSs or any other cellular or virus-induced structure. Our results provide a unifying model of the CoV RO and clearly establish DMVs as the central hub for viral RNA synthesis and a potential drug target in CoV infection.
Journal Article
Osteopontin stabilization and collagen containment slows amorphous calcium phosphate transformation during human aortic valve leaflet calcification
by
Ajijola, Olujimi A.
,
Bhargava, Rohit
,
Shivkumar, Kalyanam
in
631/443/592/2193
,
631/443/592/75/591
,
Amorphous calcium phosphate (ACP)
2024
Calcification of aortic valve leaflets is a growing mortality threat for the 18 million human lives claimed globally each year by heart disease. Extensive research has focused on the cellular and molecular pathophysiology associated with calcification, yet the detailed composition, structure, distribution and etiological history of mineral deposition remains unknown. Here transdisciplinary geology, biology and medicine (GeoBioMed) approaches prove that leaflet calcification is driven by amorphous calcium phosphate (ACP), ACP at the threshold of transformation toward hydroxyapatite (HAP) and cholesterol biomineralization. A paragenetic sequence of events is observed that includes: (1) original formation of unaltered leaflet tissues: (2) individual and coalescing 100’s nm- to 1 μm-scale ACP spherules and cholesterol crystals biomineralizing collagen fibers and smooth muscle cell myofilaments; (3) osteopontin coatings that stabilize ACP and collagen containment of nodules preventing exposure to the solution chemistry and water content of pumping blood, which combine to slow transformation to HAP; (4) mm-scale nodule growth via ACP spherule coalescence, diagenetic incorporation of altered collagen and aggregation with other ACP nodules; and (5) leaflet diastole and systole flexure causing nodules to twist, fold their encasing collagen fibers and increase stiffness. These in vivo mechanisms combine to slow leaflet calcification and establish previously unexplored hypotheses for testing novel drug therapies and clinical interventions as viable alternatives to current reliance on surgical/percutaneous valve implants.
Journal Article
A seismically induced onshore surge deposit at the KPg boundary, North Dakota
2019
The most immediate effects of the terminal-Cretaceous Chicxulub impact, essential to understanding the global-scale environmental and biotic collapses that mark the Cretaceous–Paleogene extinction, are poorly resolved despite extensive previous work. Here, we help to resolve this by describing a rapidly emplaced, high-energy onshore surge deposit from the terrestrial Hell Creek Formation in Montana. Associated ejecta and a cap of iridium-rich impactite reveal that its emplacement coincided with the Chicxulub event. Acipenseriform fish, densely packed in the deposit, contain ejecta spherules in their gills and were buried by an inland-directed surge that inundated a deeply incised river channel before accretion of the fine-grained impactite. Although this deposit displays all of the physical characteristics of a tsunami runup, the timing (< 1 hour postimpact) is instead consistent with the arrival of strong seismic waves from the magnitude Mw ∼10 to 11 earthquake generated by the Chicxulub impact, identifying a seismically coupled seiche inundation as the likely cause. Our findings present high-resolution chronology of the immediate aftereffects of the Chicxulub impact event in the Western Interior, and report an impact-triggered onshore mix of marine and terrestrial sedimentation—potentially a significant advancement for eventually resolving both the complex dynamics of debris ejection and the full nature and extent of biotic disruptions that took place in the first moments postimpact.
Journal Article
A Raman Spectroscopic Study of Lightning‐Induced Glass Produced From Five Mineral Phases
by
Genareau, K.
,
Park, C.
,
Woods, T. W.
in
Atmospheric aerosols
,
Chemical properties
,
dendritic magnetite
2024
Lightning‐induced volcanic spherules (LIVS) are glasses produced by the rapid melting and solidification of molten volcanic ash grains. High temperatures generated by lightning will alter the physical and chemical properties of minerals exposed to the discharge. Laboratory experiments reveal that LIVS glass composition varies depending on the starting material, exhibiting heterogeneous compositional features common in other glasses created by cloud‐to‐ground lightning, nuclear explosions, and high velocity impact events. This study uses scanning electron microscopy, energy dispersive spectroscopy, and Raman spectroscopy to investigate the structure and Raman signatures of lightning‐induced glass spherules manufactured from five igneous minerals (<32 μm powders of albite, labradorite, augite, hornblende, and magnetite). LIVS were created through high‐current impulse experiments using peak currents of 25 and 40 kA. Analysis of the post‐experimental albite, labradorite, augite, and hornblende LIVS reveal primarily homogeneous silicate or aluminosilicate glasses with limited heterogeneity. Their amorphous Raman spectra are comparable to rhyolitic and mafic natural glasses along with Na2O‐K2O‐Al2O3‐SiO2, CaCO3‐Al2O3‐SiO2, and CaO‐MgO‐SiO2 synthetic glass networks. A few of the augite and hornblende LIVS spectra exhibit premelting effects, which occur below the melting point and represent the onset of cation disordering in phases that remain crystalline. Magnetite samples produced crystal‐rich, glass‐poor LIVS characterized by the growth of dendritic microcrystals and crystalline spectra that also contain a few bands alluding to the composition of their silicate–phosphate glass matrix. By understanding these chemical changes induced by lightning, we can extract information from other types of glasses produced during high temperature, short duration events. Plain Language Summary High temperatures generated by volcanic lightning melt and fuse airborne volcanic ash grains consisting of mineral crystals and glassy fragments. Molten grains will rapidly quench into solid or hollow glass spheres termed lightning‐induced volcanic spherules, thereby altering the chemical and structural properties of the ash grains. This study utilizes Raman spectroscopy to characterize the structural properties of glass spherules produced from five common minerals (albite, labradorite, augite, hornblende, and magnetite) through lightning simulation experiments. Results reveal that lightning can alter these mineral samples irrevocably by transforming them into glass with complex compositions and Raman signatures corresponding to mineral and glass phases. The four minerals with a higher abundance of silica, a glass‐forming element, primarily produced chemically complex glass spheres with compositions representing a mixture of different melted minerals, and Raman signals similar to synthetic and naturally occurring glasses. In contrast, the post‐experimental spheres created from the silica‐poor, iron‐rich mineral magnetite are composed of newly formed iron micrometer‐sized crystals, limited amounts of glass, and Raman signals indicative of crystalline material. Although specific to volcanic ash, the impact of lightning on mineral fragments has broader implications for a wide range of geoscientists and planetary scientists. Key Points Lightning simulation experiments conducted on powdered minerals produce particles containing both glass and crystalline phases Raman spectroscopy of lightning‐induced spherules reveal spectra comparable to naturally occurring and synthetic multicomponent glasses Crystalline spectra derive from surviving mineral fragments and lightning‐induced crystallization of iron oxide dendrites
Journal Article
Contamination Fingerprints in an Inactive W (Sn) Mine: The Regoufe Mine Study Case (Northern Portugal)
by
Flores, Deolinda
,
Guedes, Alexandra
,
Santos, Patrícia
in
Anthropogenic factors
,
Arsenic
,
Bioaccumulation
2023
The target of this study was the tungsten Regoufe mine, whose exploitation stopped in the 1970s. When the mine closed, an unacceptable legacy constituted of mining waste tailings and the ruins of infrastructure was left behind. This work assessed the soil, plants, and water contamination in the mining area; namely their content in potentially toxic elements (PTEs). The global impact of PTEs in the Regoufe mine surface soil points to a very high to ultrahigh degree of contamination of the area having a serious ecological risk level, mainly related to As and Cd contributions. However, establishing the direct relation between As contamination and the anthropogenic effects caused by the mining process cannot be carried out in a straightforward manner, since the soils were already enriched in metals and metalloids as a result of the geological processes that gave origin to the mineral deposits. The studies performed on the plants revealed that the PTE levels in the plants were lower than in the soil, but site-specific soil concentrations in As and Pb positively influence bioaccumulation in plants. The magnetic studies showed the presence of magnetic technogenic particles concentrated in the magnetic fraction, in the form of magnetic spherules. The magnetic technogenic particles probably result from temperature increases induced by some technological process related to ore processing/mining activity. The PTEs in the surface and groundwater samples were similar and relatively low, being unlikely to pose potential health and environmental risks. Arsenic (As) constituted the exception, with levels above reference for drinking water purposes.
Journal Article
The Porcine Deltacoronavirus Replication Organelle Comprises Double-Membrane Vesicles and Zippered Endoplasmic Reticulum with Double-Membrane Spherules
2019
Porcine deltacoronavirus (PDCoV) was first identified in Hong Kong in 2012 from samples taken from pigs in 2009. PDCoV was subsequently identified in the USA in 2014 in pigs with a history of severe diarrhea. The virus has now been detected in pigs in several countries around the world. Following the development of tissue culture adapted strains of PDCoV, it is now possible to address questions regarding virus–host cell interactions for this genera of coronavirus. Here, we presented a detailed study of PDCoV-induced replication organelles. All positive-strand RNA viruses induce the rearrangement of cellular membranes during virus replication to support viral RNA synthesis, forming the replication organelle. Replication organelles for the Alpha-, Beta-, and Gammacoronavirus genera have been characterized. All coronavirus genera induced the formation of double-membrane vesicles (DMVs). In addition, Alpha- and Betacoronaviruses induce the formation of convoluted membranes, while Gammacoronaviruses induce the formation of zippered endoplasmic reticulum (ER) with tethered double-membrane spherules. However, the structures induced by Deltacoronaviruses, particularly the presence of convoluted membranes or double-membrane spherules, are unknown. Initially, the dynamics of PDCoV strain OH-FD22 replication were assessed with the onset of viral RNA synthesis, protein synthesis, and progeny particle release determined. Subsequently, virus-induced membrane rearrangements were identified in infected cells by electron microscopy. As has been observed for all other coronaviruses studied to date, PDCoV replication was found to induce the formation of double-membrane vesicles. Significantly, however, PDCoV replication was also found to induce the formation of regions of zippered endoplasmic reticulum, small associated tethered vesicles, and double-membrane spherules. These structures strongly resemble the replication organelle induced by avian Gammacoronavirus infectious bronchitis virus.
Journal Article
DID 'ALIEN' DEBRIS HIT EARTH? RESEARCHERS CLASH AT MEETING
2024
During his presentation, Fu described tiny metallic blobs that Loeb's expedition dredged from the sea floor near Papua New Guinea last year, and said that the spherules have a chemical composition of unknown origin1. Interstellar' objects remained in the realm of theory until 2017, when astronomers spotted the first known celestial object to be on a trajectory that meant it could only have come from outside the Solar System. 'Oumuamua passed through the Solar System far from Earth, but Loeb hoped to find another interstellar object that had hit the planet.
Journal Article
Magnetic enhancement of road dusts in Shanghai and its implications for the urban environment
by
Hu, Xue-Feng
,
Zhang, Yan-Shuo
,
Wang, Xin-Dong
in
Anthropogenic factors
,
Atmospheric particulates
,
Cadmium
2024
PurposeRoad dust samples in Baoshan District, Shanghai, were collected to explore magnetic and chemical properties of atmospheric dustfall in urban areas, intensively impacted by anthropogenic activities. Magnetic particles in road dusts were separated and analyzed to track their sources and then to discuss the influences of industrial and traffic emissions on the urban environment.Materials and methodsOne hundred twenty-two road dust samples in the industrial, traffic, residential, and agricultural areas of Baoshan District, Shanghai, were collected. Magnetic susceptibility (χlf) and heavy metal content of the samples were determined. Micromorphological and microchemical features of magnetic particles separated from the road dusts were analyzed by a scanning electron microscope (SEM) equipped with energy spectrum.Results and discussionThe road dusts are usually alkaline and strong in magnetic signal, of which, magnetic susceptibility (χlf), 838.7 × 10−8 m3 kg−1 on average, is much higher than the nearby topsoils. Moreover, χlf of the industrial and traffic road dusts, 1363.0 × 10−8 m3 kg−1 and 775.9 × 10−8 m3 kg−1 on average, respectively, is significantly higher than that of the others. Magnetic spherules, mainly composed of Fe oxides, were commonly observed in the road dusts, which are mostly formed during industrial high-temperature processes. A high number of flake-like, rod-like, and other irregular-shaped magnetic particles were also found in the road dusts, which may come from metal processing or vehicular wearing. The road dusts in the study areas are heavily polluted by Cu, Zn, Pb, Cd, and Cr. The principal component analyses (PCA) indicate that χlf and Zn, Mn, and Fe contents in the road dusts belong to the same principal component.ConclusionsMagnetic dustfall commonly occurs in urban areas due to industrial or vehicular emissions, which leads to the enhancement of magnetic signal and heavy metal content in urban road dusts simultaneously. χlf can indicate the accumulation of toxic heavy metals in the road dusts effectively. This also highlights a fact that the urban environment is continuously and significantly affected by the deposition of artificial atmospheric magnetic particles.
Journal Article
A New Contaminant Superhighway? A Review of Sources, Measurement Techniques and Fate of Atmospheric Microplastics
by
Jenkins, Graham
,
Pratt, Chris
,
Mbachu Oluchi
in
Addition polymerization
,
Analytical methods
,
Anthropogenic factors
2020
Microplastic pollution is a significant and growing environmental issue. Recent studies have evaluated the atmosphere as an important pathway of microplastic contamination. Airborne microplastics can be transported long distances and accumulate in various terrestrial and aquatic environmental matrices, where they represent a threat to the biosphere. This review systematically summarizes the existing knowledge on airborne microplastics, including the different sampling and analytical techniques, occurrence and sources. We investigate the different sample collection techniques from street dust to indoor and outdoor air and examined sample preparation, pre-treatment and characterization techniques. We further explored the key factors with respect to their occurrence in the environment such as concentration levels, polymer composition, size distribution, shape and colour characteristics. The sources of airborne microplastics were also summarized. The results show that microplastics are ubiquitous in all atmospheric compartments including street dust and indoor and outdoor air at various concentrations, which is influenced by the community’s lifestyle choices, anthropogenic activities and meteorological conditions. Various forms of microplastics including spherules, film, fragments, fibres and granules were identified with fibrous microplastics being the most dominant. Additionally, microplastics of 20 different polymers and varying colour characteristic have been reported in studies focusing on airborne microplastic contamination. The size distribution of microplastics varied among the studied air compartments; however, they were mostly distributed towards the smaller size ranges, less than 1 mm. Our review highlights a need to consider atmospheric pathways in addition to soil and water migration dispersion processes for any holistic assessments of microplastic threats to the biosphere. Moreover, standardization of airborne microplastic sampling methods is needed to optimize the effectiveness of future work in this area.
Journal Article
Architecture of the chikungunya virus replication organelle
by
Kumar, Pravin
,
Laurent, Timothée
,
Zare, Farnaz
in
Alphavirus
,
Chikungunya virus
,
cryo-electron tomography
2022
Alphaviruses are mosquito-borne viruses that cause serious disease in humans and other mammals. Along with its mosquito vector, the Alphaviru s chikungunya virus (CHIKV) has spread explosively in the last 20 years, and there is no approved treatment for chikungunya fever. On the plasma membrane of the infected cell, CHIKV generates dedicated organelles for viral RNA replication, so-called spherules. Whereas structures exist for several viral proteins that make up the spherule, the architecture of the full organelle is unknown. Here, we use cryo-electron tomography to image CHIKV spherules in their cellular context. This reveals that the viral protein nsP1 serves as a base for the assembly of a larger protein complex at the neck of the membrane bud. Biochemical assays show that the viral helicase-protease nsP2, while having no membrane affinity on its own, is recruited to membranes by nsP1. The tomograms further reveal that full-sized spherules contain a single copy of the viral genome in double-stranded form. Finally, we present a mathematical model that explains the membrane remodeling of the spherule in terms of the pressure exerted on the membrane by the polymerizing RNA, which provides a good agreement with the experimental data. The energy released by RNA polymerization is found to be sufficient to remodel the membrane to the characteristic spherule shape.
Journal Article