Ecological disturbance in tropical peatlands prior to marine Permian-Triassic mass extinction

The Permian-Triassic mass extinction is widely attributed to the global environmental changes caused by the eruption of the Siberian Traps. However, the precise temporal link between marine and terrestrial crises and volcanism is unclear. Here, we report anomalously high mercury (Hg) concentrations in terrestrial strata from southwestern China, synchronous with Hg anomalies in the marine Permian-Triassic type section. The terrestrial sediments also record increased abundance of fossil charcoal coincident with the onset of a negative carbon isotope excursion and the loss of tropical rainforest vegetation, both of which occurred immediately before the peak of Hg concentrations. The organic carbon isotope data show an ∼5‰–6‰ negative excursion in terrestrial organic matter (bulk organic, cuticles, and charcoal), reflecting change in atmospheric CO2 carbon-isotope composition coincident with enhanced wildfire indicated by increased charcoal. Hg spikes provide a correlative tool between terrestrial and marine records along with carbon isotope trends. These data demonstrate that ecological deterioration occurred in tropical peatlands prior to the main marine mass extinction

Memory for medication side effects in younger and older adults: the role of subjective and objective importance

Older adults often experience memory impairments, but can sometimes use selective processing and schematic support to remember important information. The current experiments investigate to what degree younger and healthy older adults remember medication side effects that were subjectively or objectively important to remember. Participants studied a list of common side effects, and rated how negative these effects were if they were to experience them, and were then given a free recall test. In Experiment 1, the severity of the side effects ranged from mild (e.g., itching) to severe (e.g., stroke), and in Experiment 2, certain side effects were indicated as critical to remember (i.e., “contact your doctor if you experience this”). There were no age differences in terms of free recall of the side effects, and older adults remembered more severe side effects relative to mild effects. However, older adults were less likely to recognize critical side effects on a later recognition test, relative to younger adults. The findings suggest that older adults can selectively remember medication side effects, but have difficulty identifying familiar but potentially critical side effects, and this has implications for monitoring medication use in older age

Green Sturgeon Physical Habitat Use in the Coastal Pacific Ocean

The green sturgeon (Acipenser medirostris) is a highly migratory, oceanic, anadromous species with a complex life history that makes it vulnerable to species-wide threats in both freshwater and at sea. Green sturgeon population declines have preceded legal protection and curtailment of activities in marine environments deemed to increase its extinction risk. Yet, its marine habitat is poorly understood. We built a statistical model to characterize green sturgeon marine habitat using data from a coastal tracking array located along the Siletz Reef near Newport, Oregon, USA that recorded the passage of 37 acoustically tagged green sturgeon. We classified seafloor physical habitat features with high-resolution bathymetric and backscatter data. We then described the distribution of habitat components and their relationship to green sturgeon presence using ordination and subsequently used generalized linear model selection to identify important habitat components. Finally, we summarized depth and temperature recordings from seven green sturgeon present off the Oregon coast that were fitted with pop-off archival geolocation tags. Our analyses indicated that green sturgeon, on average, spent a longer duration in areas with high seafloor complexity, especially where a greater proportion of the substrate consists of boulders. Green sturgeon in marine habitats are primarily found at depths of 20–60 meters and from 9.5–16.0°C. Many sturgeon in this study were likely migrating in a northward direction, moving deeper, and may have been using complex seafloor habitat because it coincides with the distribution of benthic prey taxa or provides refuge from predators. Identifying important green sturgeon marine habitat is an essential step towards accurately defining the conditions that are necessary for its survival and will eventually yield range-wide, spatially explicit predictions of green sturgeon distribution

A Generic System for the Expression and Purification of Soluble and Stable Influenza Neuraminidase

The influenza surface glycoprotein neuraminidase (NA) is essential for the efficient spread of the virus. Antiviral drugs such as Tamiflu (oseltamivir) and Relenza (zanamivir) that inhibit NA enzyme activity have been shown to be effective in the treatment of influenza infections. The recent ‘swine flu’ pandemic and world-wide emergence of Tamiflu-resistant seasonal human influenza A(H1N1) H274Y have highlighted the need for the ongoing development of new anti-virals, efficient production of vaccine proteins and novel diagnostic tools. Each of these goals could benefit from the production of large quantities of highly pure and stable NA. This publication describes a generic expression system for NAs in a baculovirus Expression Vector System (BEVS) that is capable of expressing milligram amounts of recombinant NA. To construct NAs with increased stability, the natural influenza NA stalk was replaced by two different artificial tetramerization domains that drive the formation of catalytically active NA homotetramers: GCN4-pLI from yeast or the Tetrabrachion tetramerization domain from Staphylothermus marinus. Both recombinant NAs are secreted as FLAG-tagged proteins to allow for rapid and simple purification. The Tetrabrachion-based NA showed good solubility, increased stability and biochemical properties closer to the original viral NA than the GCN4-pLI based construct. The expressed quantities and high quality of the purified recombinant NA suggest that this expression system is capable of producing recombinant NA for a broad range of applications including high-throughput drug screening, protein crystallisation, or vaccine development

Adjusting Phenotypes by Noise Control

Genetically identical cells can show phenotypic variability. This is often caused by stochastic events that originate from randomness in biochemical processes involving in gene expression and other extrinsic cellular processes. From an engineering perspective, there have been efforts focused on theory and experiments to control noise levels by perturbing and replacing gene network components. However, systematic methods for noise control are lacking mainly due to the intractable mathematical structure of noise propagation through reaction networks. Here, we provide a numerical analysis method by quantifying the parametric sensitivity of noise characteristics at the level of the linear noise approximation. Our analysis is readily applicable to various types of noise control and to different types of system; for example, we can orthogonally control the mean and noise levels and can control system dynamics such as noisy oscillations. As an illustration we applied our method to HIV and yeast gene expression systems and metabolic networks. The oscillatory signal control was applied to p53 oscillations from DNA damage. Furthermore, we showed that the efficiency of orthogonal control can be enhanced by applying extrinsic noise and feedback. Our noise control analysis can be applied to any stochastic model belonging to continuous time Markovian systems such as biological and chemical reaction systems, and even computer and social networks. We anticipate the proposed analysis to be a useful tool for designing and controlling synthetic gene networks

Initial results of coring at Prees, Cheshire Basin, UK (ICDP JET project): towards an integrated stratigraphy, timescale, and Earth system understanding for the Early Jurassic

This is the final version. Available on open access from Copernicus Publications via the DOI in this recordData availability: Full core scan data (https://doi.org/10.5285/91392f09-25d4-454c-aece-56bde0dbf3ba, BGS Core Scanning Facility, 2022) will be available after 1 November 2024 via the Natural Environment Research Council (NERC) National Geoscience Data Centre (https://webapps.bgs.ac.uk/services/ngdc/accessions/index.html#, last access: 12 October 2023). Downhole logging data (https://doi.org/10.5880/ICDP.5065.001​​​​​​​, Wonik, 2023) will be made available via the ICDP (https://www.icdp-online.org/projects/by-continent/europe/jet-uk/, last access: 12 October 2023). The JET Operational Report is published as Hesselbo et al. (2023); full information about the operational dataset, the logging dataset, data availability and the explanatory remarks is available on the ICPD-JET project website: https://www.icdp-online.org/projects/by-continent/europe/jet-uk/ (last access: 12 October 2023). A subset of data, additional biostratigraphic tables, and vector graphics files for Figs. 3–5 are included as the Supplement. Supplementary Data File 1 tabulates the corrected depth scale for Prees 2C. Supplementary Data File 2 summarizes the ammonite-based chronostratigraphy of the Prees 2 cores (ammonite identifications by Kevin N. Page). Supplementary Data File 3 summarizes the ammonite-based chronostratigraphy for the Hettangian to Early Pliensbachian of the Llanbedr (Mochras Farm) borehole (updated by Kevin N. Page). Supplementary Data File 4 tabulates the organic carbon-isotope ratios, TOC, and carbonate content of low-resolution samples taken at the Prees drill site; TOC and carbonate data are calculated using calibration based on portable XRF (Supplementary Data File 5) and a gas source isotope ratio mass spectrometer (Supplementary Data File 6). Supplementary Data File 5 tabulates portable XRF results for bulk rock powders of low-resolution samples taken at the Prees drill site; uncertainties stated in the table are given for the fit to the raw data and do not reflect the true reproducibility of the data. Empty fields indicate values under the detection limit. Sample SSK116001 acted as a repeat sample which was measured 70 times over the course of the data acquisition to determine the repeatability and drift of the instrument. LE stands for “light elements”. Supplementary Data File 6 tabulates gas source isotope ratio mass spectrometry (GS-IRMS) data (oxygen- and carbon-isotope ratios of carbonate as well as carbonate content calculated as calcite) for a set of 24 samples covering the entire core length and reflecting a representative spread of carbonate content. Comparison of GS-IRMS data with p-XRF data was used to create a calibration curve to calculate the carbonate (and TOC) content of all low-resolution samples. Supplementary Data File 7 tabulates pyrolysis data (Rock-Eval 6) for Prees 1 well cuttings and Wilkesley borehole samples. Supplementary Data File 8 contains vector graphics files (.svg) for Figs. 3–5.Drilling for the International Continental Scientific Drilling Program (ICDP) Early Jurassic Earth System and Timescale project (JET) was undertaken between October 2020 and January 2021. The drill site is situated in a small-scale synformal basin of the latest Triassic to Early Jurassic age that formed above the major Permian–Triassic half-graben system of the Cheshire Basin. The borehole is located to recover an expanded and complete succession to complement the legacy core from the Llanbedr (Mochras Farm) borehole drilled through 1967–1969 on the edge of the Cardigan Bay Basin, North Wales. The overall aim of the project is to construct an astronomically calibrated integrated timescale for the Early Jurassic and to provide insights into the operation of the Early Jurassic Earth system. Core of Quaternary age cover and Early Jurassic mudstone was obtained from two shallow partially cored geotechnical holes (Prees 2A to 32.2 m below surface (m b.s.) and Prees 2B to 37.0 m b.s.) together with Early Jurassic and Late Triassic mudstone from the principal hole, Prees 2C, which was cored from 32.92 to 651.32 m (corrected core depth scale). Core recovery was 99.7 % for Prees 2C. The ages of the recovered stratigraphy range from the Late Triassic (probably Rhaetian) to the Early Jurassic, Early Pliensbachian (Ibex Ammonoid Chronozone). All ammonoid chronozones have been identified for the drilled Early Jurassic strata. The full lithological succession comprises the Branscombe Mudstone and Blue Anchor formations of the Mercia Mudstone Group, the Westbury and Lilstock formations of the Penarth Group, and the Redcar Mudstone Formation of the Lias Group. A distinct interval of siltstone is recognized within the Late Sinemurian of the Redcar Mudstone Formation, and the name “Prees Siltstone Member” is proposed. Depositional environments range from playa lake in the Late Triassic to distal offshore marine in the Early Jurassic. Initial datasets compiled from the core include radiography, natural gamma ray, density, magnetic susceptibility, and X-ray fluorescence (XRF). A full suite of downhole logs was also run. Intervals of organic carbon enrichment occur in the Rhaetian (Late Triassic) Westbury Formation and in the earliest Hettangian and earliest Pliensbachian strata of the Redcar Mudstone Formation, where up to 4 % total organic carbon (TOC) is recorded. Other parts of the succession are generally organic-lean, containing less than 1 % TOC. Carbon-isotope values from bulk organic matter have also been determined, initially at a resolution of ∼ 1 m, and these provide the basis for detailed correlation between the Prees 2 succession and adjacent boreholes and Global Stratotype Section and Point (GSSP) outcrops. Multiple complementary studies are currently underway and preliminary results promise an astronomically calibrated biostratigraphy, magnetostratigraphy, and chemostratigraphy for the combined Prees and Mochras successions as well as insights into the dynamics of background processes and major palaeo-environmental changes.ICDPNatural Environment Research Council (NERC)German Research FoundationHungarian Scientific Research FundNational Science Centre, PolandPolish Geological Institut