Correlative multi-scale cryo-imaging unveils SARS-CoV-2 assembly and egress.

Funder: Medical Research CouncilSince the outbreak of the SARS-CoV-2 pandemic, there have been intense structural studies on purified viral components and inactivated viruses. However, structural and ultrastructural evidence on how the SARS-CoV-2 infection progresses in the native cellular context is scarce, and there is a lack of comprehensive knowledge on the SARS-CoV-2 replicative cycle. To correlate cytopathic events induced by SARS-CoV-2 with virus replication processes in frozen-hydrated cells, we established a unique multi-modal, multi-scale cryo-correlative platform to image SARS-CoV-2 infection in Vero cells. This platform combines serial cryoFIB/SEM volume imaging and soft X-ray cryo-tomography with cell lamellae-based cryo-electron tomography (cryoET) and subtomogram averaging. Here we report critical SARS-CoV-2 structural events - e.g. viral RNA transport portals, virus assembly intermediates, virus egress pathway, and native virus spike structures, in the context of whole-cell volumes revealing drastic cytppathic changes. This integrated approach allows a holistic view of SARS-CoV-2 infection, from the whole cell to individual molecules

Examination of Late Palaeolithic archaeological sites in northern Europe for the preservation of cryptotephra layers

We report the first major study of cryptotephra (non-visible volcanic ash layers) on Late Palaeolithic archaeological sites in northern Europe. Examination of 34 sites dating from the Last Termination reveals seven with identifiable cryptotephra layers. Preservation is observed in minerogenic and organic deposits, although tephra is more common in organic sediments. Cryptotephra layers normally occur stratigraphically above or below the archaeology. Nearby off-site palaeoclimate archives (peat bogs and lakes <0.3 km distant) were better locations for detecting tephra. However in most cases the archaeology can only be correlated indirectly with such cryptotephras. Patterns affecting the presence/absence of cryptotephra include geographic position of sites relative to the emitting volcanic centre; the influence of past atmospherics on the quantity, direction and patterns of cryptotephra transport; the nature and timing of local site sedimentation; sampling considerations and subsequent taphonomic processes. Overall, while tephrostratigraphy has the potential to improve significantly the chronology of such sites many limiting factors currently impacts the successful application

The RESET project: constructing a European tephra lattice for refined synchronisation of environmental and archaeological events during the last c. 100 ka

This paper introduces the aims and scope of the RESET project (. RESponse of humans to abrupt Environmental Transitions), a programme of research funded by the Natural Environment Research Council (UK) between 2008 and 2013; it also provides the context and rationale for papers included in a special volume of Quaternary Science Reviews that report some of the project's findings. RESET examined the chronological and correlation methods employed to establish causal links between the timing of abrupt environmental transitions (AETs) on the one hand, and of human dispersal and development on the other, with a focus on the Middle and Upper Palaeolithic periods. The period of interest is the Last Glacial cycle and the early Holocene (c. 100-8 ka), during which time a number of pronounced AETs occurred. A long-running topic of debate is the degree to which human history in Europe and the Mediterranean region during the Palaeolithic was shaped by these AETs, but this has proved difficult to assess because of poor dating control. In an attempt to move the science forward, RESET examined the potential that tephra isochrons, and in particular non-visible ash layers (cryptotephras), might offer for synchronising palaeo-records with a greater degree of finesse. New tephrostratigraphical data generated by the project augment previously-established tephra frameworks for the region, and underpin a more evolved tephra 'lattice' that links palaeo-records between Greenland, the European mainland, sub-marine sequences in the Mediterranean and North Africa. The paper also outlines the significance of other contributions to this special volume: collectively, these illustrate how the lattice was constructed, how it links with cognate tephra research in Europe and elsewhere, and how the evidence of tephra isochrons is beginning to challenge long-held views about the impacts of environmental change on humans during the Palaeolithic. © 2015 Elsevier Ltd.RESET was funded through Consortium Grants awarded by the Natural Environment Research Council, UK, to a collaborating team drawn from four institutions: Royal Holloway University of London (grant reference NE/E015905/1), the Natural History Museum, London (NE/E015913/1), Oxford University (NE/E015670/1) and the University of Southampton, including the National Oceanography Centre (NE/01531X/1). The authors also wish to record their deep gratitude to four members of the scientific community who formed a consultative advisory panel during the lifetime of the RESET project: Professor Barbara Wohlfarth (Stockholm University), Professor Jørgen Peder Steffensen (Niels Bohr Institute, Copenhagen), Dr. Martin Street (Romisch-Germanisches Zentralmuseum, Neuwied) and Professor Clive Oppenheimer (Cambridge University). They provided excellent advice at key stages of the work, which we greatly valued. We also thank Jenny Kynaston (Geography Department, Royal Holloway) for construction of several of the figures in this paper, and Debbie Barrett (Elsevier) and Colin Murray Wallace (Editor-in-Chief, QSR) for their considerable assistance in the production of this special volume.Peer Reviewe

Isotope Variations of Dissolved Zn in the Rio Grande Watershed, USA: The Role of Adsorption on Zn Isotope Composition

In order to better understand the factors influencing zinc (Zn) isotope composition in hydrological systems, we analyzed the δ66Zn of dissolved Zn in the streams and groundwater of the Upper and Middle Rio Grande watershed in Colorado and New Mexico, United States. The stream water samples have a wider variation of δ66Zn (-0.57 to +0.41‰ relative to the JMC 3-0749-Lyon standard) than groundwater samples (-0.13 to +0.12‰) and than samples from streams that are in close proximity to abandoned mining sites (+0.24 to +0.40‰). Regional changes of bedrock geology, from primarily igneous rocks to primarily sedimentary rocks, have no resolvable effect on the δ66Zn of aqueous samples. Instead, an increase in water pH from 7.5 to 8.5 corresponds to a considerable decrease in the δ66Zn of dissolved Zn (R2=-0.37, p=0.003, n=22). Consequently, we link the observed Zn isotope variations to the process of adsorption of Zn onto suspended sediment and bedrock minerals (average Δ66Znadsorbed-dissolved = +0.31‰). Our results are in good agreement with previous experimental and empirical studies suggesting that Zn adsorption leads to a residual dissolved pool enriched in light Zn isotopes. Given that anthropogenic Zn sources can also be responsible for lowering of δ66Zn, and may overlap with the pH/adsorption effect on δ66Zn, the latter needs to be carefully considered in future studies to differentiate between natural and anthropogenic factors influencing Zn isotopes in this and other aquatic systems

Efflorescence As a Source of Hydrated Sulfate Minerals in Valley Settings on Mars

A distinctive sulfur cycle dominates many geological processes on Mars and hydrated sulfate minerals are found in numerous topographic settings with widespread occurrences on the Martian surface. However, many of the key processes controlling the hydrological transport of sulfur, including sulfur sources, climate and the depositional history that led to precipitation of these minerals, remain unclear. In this paper, we use a model for the formation of sulfate efflorescent salts (Mg-Ca-Na sulfates) in the Rio Puerco watershed of New Mexico, a terrestrial analog site from the semiarid Southwest U.S., to assess the origin and environmental conditions that may have controlled deposition of hydrated sulfates in Valles Marineris on Mars. Our terrestrial geochemical results (δ34S of -36.0 to +11.1‰) show that an ephemeral arid hydrological cycle that mobilizes sulfur present in the bedrock as sulfides, sulfate minerals, and dry/wet atmospheric deposition can lead to widespread surface accumulations of hydrated sulfate efflorescences. Repeating cycles of salt dissolution and reprecipitation appear to be major processes that migrate sulfate efflorescences to sites of surface deposition and ultimately increase the aqueous SO42- flux along the watershed (average 41,273 metric tons/yr). We suggest that similar shallow processes may explain the occurrence of hydrated sulfates detected on the scarps and valley floors of Valles Marineris on Mars. Our estimates of salt mass and distribution are in accord with studies that suggest a rather short-lived process of sulfate formation (minimum rough estimate ~100 to 1000 years) and restriction by prevailing arid conditions on Mars

Isotopic Studies of the Upper and Middle Rio Grande. Part 1 - Importance of Sulfide Weathering in the Riverine Sulfate Budget

In order to characterize the sulfide-derived SO4 fluxes in the Rio Grande, we collected seasonally (from 2009 to 2011) riverine, agricultural drain and groundwater samples and analyzed them for their major element chemistries and the δ34S and δ18O of dissolved SO4. The observed variation of δ34S (- 4 to + 8‰) and δ18O (- 2 to + 7‰) in the Rio Grande mainly resulted from mixing between sulfide- and sulfate-derived SO4 of volcanic and sedimentary origin. Our S isotope mass balance suggests that the average sulfide-derived SO4 flux usually accounted for 83-94% (± 10-20%) of the sulfate source in the upstream Rio Grande and decreased downstream to 45-51% because of increasing contributions of sulfate-derived SO4. The sulfide-derived SO4 was related to snow melt in the high elevation watersheds and recycling of surficial sulfate-rich salts by episodic water activity in dry areas at lower elevations. Additionally, elevated bedrock sulfide contents in volcanic and some sedimentary terrains of the studied area have been recognized as important factors contributing to sulfide-derived SO4 in the Rio Grande

The Sources and Budget for Dissolved Sulfate in a Fractured Carbonate Aquifer, Southern Sacramento Mountains, New Mexico, USA

Climate change in the SW USA is likely to involve drier conditions and higher surface temperatures. In order to better understand the evolution of water chemistry and the sources of aqueous SO4 in these semi-arid settings, chemical and S isotope compositions were determined of springs, groundwater, and bedrock associated with a Permian fractured carbonate aquifer located in the southern Sacramento Mountains, New Mexico, USA. The results suggest that the evolution of water chemistry in the semi-arid carbonate aquifer is mainly controlled by dedolomitization of bedrock, which was magnified by increasing temperature and increasing dissolution of gypsum/anhydrite along the groundwater flow path. The δ34S of dissolved SO4 in spring and groundwater samples varied from +9.0‰ to +12.8‰, reflecting the mixing of SO4 from the dissolution of Permian gypsum/anhydrite (+12.3‰ to +13.4‰) and oxidation of sulfide minerals (-24.5‰ to -4.2‰). According to S isotope mass balance constraints, the contribution of sulfide-derived SO4 was considerable in the High Mountain recharge areas, accounting for up to ~10% of the total SO4 load. However, sulfide weathering decreased in importance in the lower reaches of the watershed. A smaller SO4 input of ~2-4% was contributed by atmospheric wet deposition. This study implies that the δ34S variation of SO4 in semi-arid environments can be complex, but that S isotopes can be used to distinguish among the different sources of weathering. Here it was found that H2SO4 dissolution due to sulfide oxidation contributes up to 5% of the total carbonate weathering budget, while most of the SO4 is released from bedrock sources during dedolomitization

The Polar Sulfur Cycle in the Werenskioldbreen, Spitsbergen: Possible Implications for Understanding the Deposition of Sulfate Minerals in the North Polar Region of Mars

In this study we investigated the polar cycling of sulfur (S) associated with the Werenskioldbreen glacier in Spitsbergen (Svalbard). Sulfide-derived S comprised 0.02-0.42 wt% of the fine-grained fraction of proglacial sediments. These sediments originated from glacial erosion of Precambrian sulfide-rich quartz and carbonate veins. In summer 2008, the δ34S of dissolved SO4 in glacier melt waters (+9‰ to +17‰) was consistent with SO4 generation from oxidation of primary sulfide minerals in the bedrock (+9‰ to +16‰). The calculated monthly SO4 load was ~6881 kg/month/km2 in the main glacier stream. Subsequent evaporation and freezing of glacial waters lead to precipitation, accumulation, and temporary storage of sulfate salt efflorescences in the proglacial zone. These salts are presumably ephemeral, as they dissolve during annual snow/glacial melt events.Hydrated sulfates such as gypsum are also important constituents of the low-elevation areas around the polar ice cap of Planum Boreum on Mars. The origin of this gypsum on Mars might be better understood by using the investigated polar S cycle in Spitsbergen as a foundation. Assuming a trace sulfide content in the basaltic bedrock on Mars, the weathering of sulfides within the fine, porous texture of the ancient aeolian strata (basal unit) underlying Planum Boreum could have created elevated SO4 fluxes (and gypsum precipitation) during episodic thawing/melting events in the past. Limited water activity and prevailing dry conditions on the surface of Mars are the likely factors that accounted for the larger accumulation and preservation of polar gypsum on the surface and its broad aeolian distribution around Planum Boreum. This suggestion is also supported by an experiment showing that gypsum sand can be transported, under dry conditions, over great distances (~2000 km) without a significant loss of mass

Isotopic Studies of the Upper and Middle Rio Grande. Part 2 - Salt Loads and Human Impacts in South New Mexico and West Texas

Increasing groundwater and soil salinity is a threat to the land and water resources in arid regions. Global warming will likely increase salinity of dryland river systems. In order to characterize salt loading into the semi-arid portion of the Rio Grande in south New Mexico and west Texas, we sampled seasonally (2009-2011) the river, agricultural drains, and saline groundwater. In addition to major element chemistry, these samples were analyzed for sulfur and oxygen isotope compositions (δ34S and δ18O) of dissolved SO4 and in some cases for nitrogen and oxygen isotope compositions (delta;15N and δ18O) of dissolved NO3. Uranium isotopes (234U/238U activity ratio) were also measured for selected samples. The natural inflow of basinal brines/groundwater (δ34S of + 8 to + 11‰) in the semi-arid Rio Grande study area was minor in the investigated seasons and could not be detected by the δ34S mass balance. However, we did find localized increases of δ34S (+ 2 to + 5‰) in the Rio Grande that were attributable to salt loads from the intersections of agricultural drains with the water table of a natural salt flat and associated evaporative brine (δ34S of + 12‰) in the shallow subsurface. In the areas, with higher water use for land irrigation, the δ34S of the river and drain water was relatively consistent (from ~ 0 to + 2‰) compared to the δ18O (from ~+ 2 to + 6‰). Most likely, this resulted from application of S-rich fertilizers (e.g., ammonium sulfates, elemental S, sulfuric acid) with low δ34S (- 2 to + 4‰) and high δ18O (+ 9 to + 16‰). Additionally, we observed considerably lower δ18O (SO4) in the Rio Grande and agricultural drains (\u3e 7‰) compared to geologic and anthropogenic SO4 sources (+ 9 to + 16‰), which likely resulted from microbial recycling of SO4 in soil of the irrigated land related to assimilatory sulfate reduction. Shallow recharge to the Rio Grande was also inferred from the lower 234U/238U activity ratios (1.62 to 1.88) compared to deeper groundwater (2.54 to 2.64) and the distinctive delta;15N and δ18O values of nitrates (+ 5 to + 25‰ and - 5 to + 15‰, respectively) typical for septic effluents that are undergoing denitrification. Agricultural practices during flood irrigation intensify evaporation of the Rio Grande surface water and considerably increase water salinity. This process is also important in the evolution of water chemistry toward a Na-SO4-Cl-rich composition and precipitation of secondary calcite in soil profiles

The geochemistry of Irish rivers

Study region: Ireland Study focus: Multiple studies have established that catchment geology and weathering regime strongly influence surface water chemistry, and that geochemical cycling can vary due to seasonal climatic conditions. However, fewer studies have focused on the influence these controls in a holistic manner. We relate the water chemistry of a country-wide Irish river survey to atmospheric input, underlying geology, and the influence of bogs. Climatic conditions were defined by an atypically wet winter and an unusually dry summer, providing the opportunity to investigate river chemistry variation across hydrologic conditions. Sampling included 21 of Ireland’s 22 largest rivers ranked by discharge, first-order and second-order streams draining bog lands, a second-order stream draining a limestone catchment, and downstream transects along the River Shannon. All samples were analyzed for major elements, selected trace elements, and nutrients, and a subset was analyzed for δ34SSO4. New hydrological insights: Most catchments were dominated by carbonate weathering with little contribution from the weathering of aluminosilicates. River water composition also varied geographically along the prevailing wind direction due to inputs from marine aerosols, with additional weathering components important in some systems. Seasonal influences could be seen in the chemistry of the headwaters of the River Shannon, while the lower reaches of the river exhibited less variable behavior throughout seasonal changes, likely due to the influence of lakes in the River Shannon system