Molybdenum isotope constraints on the origin of vanadium hyper-enrichments in Ediacaran-Phanerozoic marine mudrocks

Vanadium is an important redox-sensitive trace metal for paleoenvironmental reconstructions. Modern organic-rich sediments persistently contain sediment V enrichments 500 μg/g. Previous studies propose that ancient V enrichments of these magnitudes (“V hyper-enrichments”) were deposited from hyper-sulfidic bottom-waters with higher H2S levels (≥10 mM) than observed in modern euxinic basins. To test the importance of hyper-sulfidic conditions for generating V hyper-enrichments, we compare V concentrations with Mo isotope (δ98Mo) compositions from mudrock samples ranging in age from Ediacaran to Pleistocene. In the modern ocean, sediments deposited from strongly euxinic bottom waters ([H2S]aq > 11 μM) closely record global seawater δ98Mo because conversion of molybdate to tri- and tetra-thiomolybdate is quantitative. By contrast, large Mo isotope fractionations occur during Mo adsorption to Fe-Mn particulates or because of incomplete formation of the most sulfidic thiomolybdates in weakly euxinic settings ([H2S]aq < 11 μM), which both favor removal of lighter-mass Mo isotopes to sediments. We find multiple examples when mudrocks with V hyper-enrichments are associated with a wide range of δ98Mo for a single time interval, including values at or below oceanic input δ98Mo (0.3–0.7‰). This observation suggests significant isotopic offset from reasonable seawater values (typically ≥1.0‰). Thus, we conclude that hyper-sulfidic conditions were not responsible for many V hyper-enrichments in Ediacaran–Phanerozoic mudrocks. Instead, sediment V hyper-enrichments can be explained by high Fe-Mn particulate fluxes to weakly euxinic sediments or by moderately restricted euxinic settings with strongly euxinic ([H2S]aq > 11 μM but not necessarily > 10 mM) or weakly euxinic (with slow clastic sedimentation rates and high organic carbon fluxes) bottom waters where vigorous water exchange provides a continuous V supply from the open ocean

Coccolithophores: Functional Biodiversity, Enzymes and Bioprospecting

Emiliania huxleyi is a single celled, marine phytoplankton with global distribution. As a key species for global biogeochemical cycling, a variety of strains have been amassed in various culture collections. Using a library consisting of 52 strains of E. huxleyi and an ‘in house’ enzyme screening program, we have assessed the functional biodiversity within this species of fundamental importance to global biogeochemical cycling, whilst at the same time determining their potential for exploitation in biocatalytic applications. Here, we describe the screening of E. huxleyi strains, as well as a coccolithovirus infected strain, for commercially relevant biocatalytic enzymes such as acid/alkali phosphodiesterase, acid/alkali phosphomonoesterase, EC1.1.1-type dehydrogenase, EC1.3.1-type dehydrogenase and carboxylesterase

Second Workshop on Estimation with the RDBES data model (WKRDB-EST2; outputs from 2020 meeting)

This report shows how the new RDBES that is currently in development will be better able to support the recast EU Data Collection Framework (Regulation (EU) 2017/1004) than the existing RDB. The RDBES is an essential platform for MS and RCGs to fulfil their obligations towards documenting and improving data quality and designing and implementing regional sampling designs. The evaluation of data precision was performed using two complementary techniques. For relatively simple sampling designs it is possible to use analytical functions to calculate the precision (or a related statistical measure such as variance) of a statistical estimate. These calculations and implementations of them in R code are presented in this report. For more complicated sampling designs, the use of analytical functions is usually not feasible. In these cases, it is necessary to evaluate precision using numerical techniques, the main one of which is bootstrapping. This report discussed when bootstrapping is appropriate and gives several worked examples describing how bootstrapping can be applied in different cases. The evaluation of bias is a difficult subject and is hard to quantify. The approach followed in this report was to build on the previous work available in the ICES literature and identify and enumerate the main common sources of bias in catch sampling programs they describe. The information was collated and an evaluation performed as to whether data stored using the RDBES data format and reports issues from them can inform about the potential for bias in catch estimates. A set of example reports was coded that demonstrates the utility of the RDBES in relation to bias issues and can already help member states to identify how deviations in their sampling programmes and sampling variability may potentially lead to bias in their catch estimates

Overview of HST observa7ons of Jupiter’s ultraviolet aurora during Juno orbits 3 to 7

Jupiter’s permanent ultraviolet auroral emissions have been systematically monitored from Earth orbit with the Hubble Space Telescope (HST) during an 8-month period. The Girst part of this HST large program (GO-14634) was meant to support the NASA Juno prime mission during orbits PJ03 through PJ07. The HST program will resume in Feb 2018, in time for Juno’s PJ11 perijove, right after HST’s solar and lunar avoidance periods. HST observations are designed to provide a Jovian auroral activity background for all instruments on-board Juno and for the numerous ground based and space based observatories participating to the Juno mission. In particular, several HST visits were programmed in order to obtain as many simultaneous observations with Juno-UVS as possible, sometimes in the same hemisphere, sometimes in the opposite one. In addition, the timing of some HST visits was set to take advantage of Juno’s multiple crossings of the current sheet and of the magnetic Gield lines threading the auroral emissions. These observations are obtained with the Space Telescope Imaging Spectrograph (STIS) in time-tag mode, they consist in spatially resolved movies of Jupiter’s highly dynamic aurora with timescales ranging from seconds to several days. Here, we present an overview of the present -numerous- HST results. They demonstrate that while Jupiter is always showing the same basic auroral components, it is also displaying an ever-changing auroral landscape. The complexity of the auroral morphology is such that no two observations are alike. Still, in this apparent chaos some patterns emerge. This information is giving clues on magnetospheric processes at play at the local and global scales, the latter being only accessible to remote sensing instruments such as HST

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Background The first epidemic wave of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over one-third of care homes reported an outbreak, while there was limited testing of hospital patients discharged to care homes. Aim To investigate patients discharged from hospitals as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave. Methods A clinical review was performed for all patients discharges from hospitals to care homes from 1st March 2020 to 31st May 2020. Episodes were ruled out based on coronavirus disease 2019 (COVID-19) test history, clinical assessment at discharge, whole-genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis using Cluster Investigation and Virus Epidemiological Tool software. Patient timelines were obtained using electronic hospital records. Findings In total, 787 patients discharged from hospitals to care homes were identified. Of these, 776 (99%) were ruled out for subsequent introduction of SARS-CoV-2 into care homes. However, for 10 episodes, the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data were available. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission, leading to 10 positive cases in their care home. Conclusion The majority of patients discharged from hospitals were ruled out for introduction of SARS-CoV-2 into care homes, highlighting the importance of screening all new admissions when faced with a novel emerging virus and no available vaccine

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

AbstractUnderstanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.</jats:p