Transient fertilization of a post-Sturtian Snowball ocean margin with dissolved phosphate by clay minerals

Marine sedimentary rocks deposited across the Neoproterozoic Cryogenian Snowball interval, ~720-635 million years ago, suggest that post-Snowball fertilization of shallow continental margin seawater with phosphorus accelerated marine primary productivity, ocean-atmosphere oxygenation, and ultimately the rise of animals. However, the mechanisms that sourced and delivered bioavailable phosphate from land to the ocean are not fully understood. Here we demonstrate a causal relationship between clay mineral production by the melting Sturtian Snowball ice sheets and a short-lived increase in seawater phosphate bioavailability by at least 20-fold and oxygenation of an immediate post-Sturtian Snowball ocean margin. Bulk primary sediment inputs and inferred dissolved seawater phosphate dynamics point to a relatively low marine phosphate inventory that limited marine primary productivity and seawater oxygenation before the Sturtian glaciation, and again in the later stages of the succeeding interglacial greenhouse interval.

Changes in groundwater trace element concentrations before seismic and volcanic activities in Iceland during 2010-2018

We analysed temporal variations of trace element concentrations in groundwater from a 101 m-deep borehole (HA01) in northern Iceland during 2010-2018 and compared them with seismic and volcanic events that occurred in the same period to identify potential hydrogeochemical precursors. An increase of B, Al, V, Li and Mo concentrations started from eight months to one month before the 2014 Bárðarbunga eruption (~115 km from HA01), a major rifting event in central Iceland, while Ga and V concentrations began to increase one day and one month after the onset of the event, respectively. We also found that concentrations of some trace elements (Li, B, Ga, Mo, Sr, Rb and Fe) significantly increased before an M_w 5.0 earthquake that occurred ~80 km from the borehole in 2018. However, other notable hydrogeochemical changes were detected during the monitoring period without apparent correlation with the seismic and volcanic events in the region. This study shows that the systematic long-term hydrogeochemical monitoring in seismic and volcanic areas is critical to advance the science of seismic and eruptive precursors. Furthermore, the use of statistical tools, such as Principal Component Analysis (PCA) and Change Point (CP) detection can help identify the most useful chemical elements and validate the trend variability of those elements in the time series, reducing arbitrary choices of pre-seismic and pre-volcanic hydrogeochemical anomalies as potential precursors.

Lockdown Measures Which Reduced Greenhouse Gas Emissions With Little Negative Impact on Quality of Life

Lockdown measures in response to the new Covid-19 virus have caused the largest ever fall of annual greenhouse gas emissions. A key question that we attempt to answer in this study is which, if any, of these measures can be productively encouraged post-lockdown in efforts to sustain at least part of this reduction in emissions. Sweden is uniquely suited for our study because the voluntary nature of lockdown in Sweden allowed us to assess the level of compliance to recommendations and its effects on greenhouse gas emissions. First, we assessed the change of perceived quality of life (QOL) among 746 individuals from Stockholm region due to adhering to lockdown measures. Second, we calculated the associated change of annual per capita greenhouse emissions. We found that avoiding travel for work, avoiding purchasing, and avoiding restaurants had the least negative effect on QOL, and at the same time the largest positive effect on carbon dioxide equivalent (CO2e) emission reductions. We conclude that these are potential leverage points for stimulating behavioral change that has a positive climatic impact.

Why on earth did I buy that? A study of regretted appliance purchases

If targets to reduce greenhouse gas emissions and thereby tackle climate change are to be achieved, it will be necessary to reduce both embodied energy costs (e.g. in terms of producing and manufacturing the products and services that society consumes) and operational energy costs. Reducing the number of purchases that people regret could be a first step in changing the overall dynamic of consumption patterns. This research looks at some potentially adverse effects of consumption on well-being (e.g. negative emotions), applying social practice theory to give insights into why people make purchases that they feel negatively about. This paper draws from: (i) findings of a national survey of over 2000 respondents which found that 53% of adults had reported regretting purchasing an electrical device at some point, and that 23% regretted making such a purchase within the past year; and (ii) a series of walking interviews around people's homes that provide detailed insights into the nature and extent of regretted purchases of electrical goods (e.g. resentment at built-in obsolescence, frustration at the pace of technological change). By combining the qualitative and quantitative data, we develop a typology of regretted consumption and explore the underlying factors that lead to such purchases. The paper concludes with a discussion of the policy implications of this research.This article is part of the themed issue 'Material demand reduction'.

Genome sequence of vanilla distortion mosaic virus infecting Coriandrum sativum

The 9573-nucleotide genome of a potyvirus was sequenced from a Coriandrum sativum plant from India with viral symptoms. On analysis, this virus was shown to have greater than 85 % nucleotide sequence identity to vanilla distortion mosaic virus (VDMV). Analysis of the putative coat protein sequence confirmed that this virus was in fact VDMV, with greater than 91 % amino acid sequence identity. The genome appears to encode a 3083-amino-acid polyprotein potentially cleaved into the 10 mature proteins expected in potyviruses. Phylogenetic analysis confirmed that VDMV is a distinct but ungrouped member of the genus Potyvirus.

Magmatic origin of giant 'Kiruna-type' apatite-iron-oxide ores in central Sweden

Iron is the most important metal for modern industry and Sweden is by far the largest iron-producer in Europe, yet the genesis of Sweden's main iron-source, the ‘Kiruna-type’ apatite-iron-oxide ores, remains enigmatic. We show that magnetites from the largest central Swedish ‘Kiruna-type’ deposit at Grängesberg have δ¹⁸O values between −0.4 and +3.7‰, while the 1.90−1.88 Ga meta-volcanic host rocks have δ¹⁸O values between +4.9 and +9‰. Over 90% of the magnetite data are consistent with direct precipitation from intermediate to felsic magmas or magmatic fluids at high-temperature (δ¹⁸O_mgt > +0.9‰, i.e. ortho-magmatic). A smaller group of magnetites (δ¹⁸O_mgt ≤ +0.9‰), in turn, equilibrated with high-δ¹⁸O, likely meteoric, hydrothermal fluids at low temperatures. The central Swedish ‘Kiruna-type’ ores thus formed dominantly through magmatic iron-oxide precipitation within a larger volcanic superstructure, while local hydrothermal activity resulted from low-temperature fluid circulation in the shallower parts of this system.

Canna yellow streak virus: a new potyvirus associated with severe streaking symptoms in canna

A new potyvirus has been found in canna. A 1700-nucleotide region at the 3' end of the genomic RNA has been sequenced from two isolates. The sequence reveals the virus to be a distinct member of the genus Potyvirus but most closely related to Johnsongrass mosaic virus. A specific primer pair was designed that enabled canna material to be screened specifically for this virus. The virus was consistently found in cannas showing severe virus symptoms. This virus has been found in different canna varieties from the UK, Belgium, Netherlands, France and Israel. The name Canna yellow streak virus (CaYSV) has been proposed for this new virus.

Barriers for accrual to clinical trials in adult patients (pts) with thoracic malignancies

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Background: Despite recent advances in the treatment of pts with thoracic malignancies, the outcome continues to be poor. Only about 3% of all adult oncology pts enroll in clinical trials compared to approximately 50% of pediatric pts. The proportion of adult pts enrolled in clinical trials is low, even in tertiary cancer centers. It is critical to understand the barriers for accrual to clinical trials. Methods: We reviewed the outpatient charts of all pts with thoracic malignancies (non-small cell lung cancer [NSCLC], small cell lung cancer, and esophageal cancer) referred to the thoracic medical oncology group at our institution from 11/1/2004 to 10/31/2005. Available and appropriate clinical trials are presented to the pts routinely and reasons for non-enrollment are documented. We collected information on histology, stage, performance status (PS) and co-morbid conditions. Appropriate studies at the time of initial consultation were noted from database. Results: Of 284 consecutive patient charts reviewed, 13 pts (4.6%) did not require therapy, 6 pts (2.1%) were deemed to have a non-thoracic primary on review, and 15 pts (5.3%) had already initiated therapy at the time of consultation. Of the remaining 250 evaluable pts, 88 pts (35.2%) were not enrolled because of lack of available appropriate clinical trials at the time of initial consultation. The most common categories were adjuvant therapy for early stage NSCLC and advanced esophageal cancer. Twenty-one pts (8.4%) enrolled onto a clinical trial. The most common reasons for not participating in a clinical trial include: ineligibility due to PS (28 pts, 11.2%), geographic issues (23 pts, 9.2%), patient refusal (16 pts, 6.4%) and co-morbid conditions (9 pts, 3.6%). Ten pts (4.0%) were lost to follow up. Conclusions: 1. Lack of appropriate and available clinical trials and poor PS are the two most common reasons for lack of patient enrollment in clinical trials at our institution. 2. It is critical to develop innovative clinical trials for pts with advanced esophageal cancer, adjuvant therapy in early stage NSCLC, and poor PS. 3. More work is needed to understand patient perception about clinical trials.

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SCH 503034, a mechanism-based inhibitor of hepatitis C virus NS3 protease, suppresses polyprotein maturation and enhances the antiviral activity of alpha interferon in replicon cells

Cleavage of the hepatitis C virus (HCV) polyprotein by the viral NS3 protease releases functional viral proteins essential for viral replication. Recent studies by Foy and coworkers strongly suggest that NS3-mediated cleavage of host factors may abrogate cellular response to alpha interferon (IFN-alpha) (E. Foy, K. Li, R. Sumpter, Jr., Y.-M. Loo, C. L. Johnson, C. Wang, P. M. Fish, M. Yoneyama, T. Fujita, S. M. Lemon, and M. Gale, Jr., Proc. Natl. Acad. Sci. USA 102:2986-2991, 2005, and E. Foy, K. Li, C. Wang, R. Sumpter, Jr., M. Ikeda, S. M. Lemon, and M. Gale, Jr., Science 300:1145-1148, 2003). Blockage of NS3 protease activity therefore is expected to inhibit HCV replication by both direct suppression of viral protein production as well as by restoring host responsiveness to IFN. Using structure-assisted design, a ketoamide inhibitor, SCH 503034, was generated which demonstrated potent (overall inhibition constant, 14 nM) time-dependent inhibition of the NS3 protease in cell-free enzyme assays as well as robust in vitro activity in the HCV replicon system, as monitored by immunofluorescence and real-time PCR analysis. Continuous exposure of replicon-bearing cell lines to six times the 90% effective concentration of SCH 503034 for 15 days resulted in a greater than 4-log reduction in replicon RNA. The combination of SCH 503034 with IFN was more effective in suppressing replicon synthesis than either compound alone, supporting the suggestion of Foy and coworkers that combinations of IFN with protease inhibitors would lead to enhanced therapeutic efficacy.

The use of real-time RT-PCR (TaqMan®) and post-ELISA virus release for the detection of Beet necrotic yellow vein virus types containing RNA 5 and its comparison with conventional RT-PCR

Real-time RT-PCR (TaqMan) assays were developed for the specific detection of Beet necrotic yellow vein virus (BNYVV). The two assays designed were a broad-spectrum one that detected RNA 2 from all types and a second designed to detect types containing RNA 5. The assays were validated against a range of different isolates from Europe and the Far East. These real-time assays were compared to a conventional RT-PCR assay for the detection of RNA 5. Sensitivity comparisons showed that for the detection of RNA 5, TaqMan was 10,000 times more sensitive than the conventional RT-PCR assay. Further improvements were made to the test procedure by using post-ELISA virus release (VR), as an alternative to RNA extraction. This significantly increased the speed of processing samples and reduced the staff input required, allowing the TaqMan assay to be used routinely as part of an annual survey of UK field samples.

Evolution not revolution? The struggle for the recognition and development of patient education in the UK

In this paper, a review of patient education in the United Kingdom (UK) is presented. Some of the reasons for the development of patient education are identified and its relationship to other educational activities in health care settings is discussed. The gap between the theory and practice of UK patient education is then examined and emerging new practices are considered. The concluding section of the paper identifies a number of important questions to ask when considering the future development of patient education. These are relevant questions for patients, practitioners, researchers and politicians.

RNA-dependent RNA polymerase activity encoded by GB virus-B non-structural protein 5B

Phylogenetic analysis and polyprotein organization comparison have shown that GB virus-B (GBV-B) is closely related to hepatitis C virus (HCV). In this study, the coding region for GBV-B non-structural protein 5B (NS5B) was isolated by reverse transcription-polymerase chain reaction (RT-PCR) from pooled serum of GBV-B-infected tamarins. Expression of soluble GBV-B NS5B protein in Escherichia coli was achieved by removal of a 19-amino acid hydrophobic domain at the C-terminus of the protein. The truncated GBV-B NS5B (NS5BDeltaCT19) was purified to homogeneity and shown to possess an RNA-dependent RNA polymerase (RdRp) activity in both gel-based and scintillation proximity assays. NS5BDeltaCT19 required the divalent cation Mn2+ for enzymatic activity, at an optimal concentration of 15 mM. Interestingly, Mg2+, at concentrations up to 20 mM, did not support the GBV-B NS5B activity. This differs from HCV NS5B where both Mn2+ and Mg2+ can support RdRp activity. Zn2+ was found to inhibit the activity of GBV-B NS5B, with a 50% inhibitory concentration (IC50) of 5-10 microM. Higher concentrations of monovalent salts (NaCl or KCl > 100 mM) and glycerol (> 3%) were also inhibitory. NS5BDeltaCT19 was able to bind to RNA homopolymers, but utilized most efficiently poly(C), the one with the lowest binding affinity for RNA synthesis. Mutational analysis of GBV-B NS5B demonstrated the importance of several conserved sequence motifs for enzymatic activity. Based on sequence homology ( approximately 37% identity and 52% similarity) between GBV-B and HCV NS5B proteins, the active GBV-B RdRp provides a good surrogate assay system for HCV polymerase studies.

Generation and characterization of a hepatitis C virus NS3 protease-dependent bovine viral diarrhea virus

Unique to pestiviruses, the N-terminal protein encoded by the bovine viral diarrhea virus (BVDV) genome is a cysteine protease (Npro) responsible for a self-cleavage that releases the N terminus of the core protein (C). This unique protease is dispensable for viral replication, and its coding region can be replaced by a ubiquitin gene directly fused in frame to the core. To develop an antiviral assay that allows the assessment of anti-hepatitis C virus (HCV) NS3 protease inhibitors, a chimeric BVDV in which the coding region of Npro was replaced by that of an NS4A cofactor-tethered HCV NS3 protease domain was generated. This cofactor-tethered HCV protease domain was linked in frame to the core protein of BVDV through an HCV NS5A-NS5B junction site and mimicked the proteolytic function of Npro in the release of BVDV core for capsid assembly. A similar chimeric construct was built with an inactive HCV NS3 protease to serve as a control. Genomic RNA transcripts derived from both chimeric clones, P(H/B) (wild-type HCV NS3 protease) and P(H/B(S139A)) (mutant HCV NS3 protease) were then transfected into bovine cells (MDBK). Only the RNA transcripts from the P(H/B) clone yielded viable viruses, whereas the mutant clone, P(H/B(S139A)), failed to produce any signs of infection, suggesting that the unprocessed fusion protein rendered the BVDV core protein defective in capsid assembly. Like the wild-type BVDV (NADL), the chimeric virus was cytopathic and formed plaques on the cell monolayer. Sequence and biochemical analyses confirmed the identity of the chimeric virus and further revealed variant viruses due to growth adaptation. Growth analysis revealed comparable replication kinetics between the wild-type and the chimeric BVDVs. Finally, to assess the genetic stability of the chimeric virus, an Npro-null BVDV (BVDV-Npro in which the entire Npro coding region was deleted) was produced. Although cytopathic, BVDV-Npro was highly defective in viral replication and growth, a finding consistent with the observed stability of the chimeric virus after serial passages.

Nucleoside triphosphatase and RNA helicase activities associated with GB virus B nonstructural protein 3

GB virus B (GBV-B) is a positive-stranded RNA virus that belongs to the Flaviviridae family. This virus is closely related to hepatitis C virus (HCV) and causes acute hepatitis in tamarins (Saguinus species). Nonstructural protein 3 (NS3) of GBV-B contains sequence motifs predictive of three enzymatic activities: serine protease, nucleoside triphosphatase (NTPase), and RNA helicase. The N-terminal serine protease has been characterized and shown to share similar substrate specificity with the HCV NS3 protease. In this report, a full-length GBV-B NS3 protein was expressed in Escherichia coli and purified to homogeneity. This recombinant protein was shown to possess polynucleotide-stimulated NTPase and double-stranded RNA (dsRNA) unwinding activities. Both activities were abolished by a single amino acid substitution, from the Lys (K) residue in the conserved walker motif A (or Ia) "AXXXXGK(210)S" to an Ala (A), confirming that they are intrinsic to GBV-B NS3. Kinetic parameters (K(m) and k(cat)) for hydrolysis of various NTPs or dNTPs were obtained. The dsRNA unwinding activity depends on the presence of divalent metal ions and ATP and requires an RNA duplex substrate with 3' unpaired regions (RNAs with 5' unpaired regions only or with blunt ends are not suitable substrates for this enzyme). This indicates that GBV-B NS3 RNA helicase unwinds dsRNA in the 3' to 5' direction. Direct interaction of the GBV-B NS3 protein with a single-stranded RNA was established using a gel-based RNA bandshift assay. Finally, a homology model of GBV-B NS3 RNA helicase domain based on the 3-dimensional structure of the HCV NS3 helicase that shows a great similarity in overall structure and surface charge distribution between the two proteins was proposed.

Generation of transmissible hepatitis C virions from a molecular clone in chimpanzees

Multiple alignments of hepatitis C virus (HCV) polyproteins from six different genotypes identified a total of 22 nonconsensus mutations in a clone derived from the Hutchinson (H77) isolate. These mutations, collectively, may have contributed to the failure in generating a "functionally correct" or "infectious" clone in earlier attempts. A consensus clone was constructed after systematic repair of these mutations, which yielded infectious virions in a chimpanzee after direct intrahepatic inoculation of in vitro transcribed RNAs. This RNA-infected chimpanzee has developed hepatitis and remained HCV positive for more than 11 months. To further verify this RNA-derived infectivity, a second naive chimpanzee was injected intravenously with serum collected from the first chimpanzee. Infectivity analysis of the second chimpanzee demonstrated that the HCV infection was successfully transmitted, which validated unequivocally the infectivity of our repaired molecular clone. Amino acid sequence comparisons revealed that our repaired infectious clone had 4 mismatches with the isogenic clone reported by Kolykhalov et al. (1997, Science 277, 570-574) and 8 mismatches with that reported by Yanagi et al. (1997, Proc. Natl. Acad. Sci. USA 94, 8738-8743). At the RNA level, more mismatches (43 and 67, respectively) were identified; most of them were synonymous substitutions. Further comparisons with 16 isolates from different genotypes demonstrated that our repaired clone shares greater consensus than the reported isogenic clones. This approach of generating infectious HCV RNA validates the importance of amino acid sequence consensus in relation to the biology of HCV.

SCH 43478 and analogs: in vitro activity and in vivo efficacy of novel agents for herpesvirus type 2

SCH 43478 and analogs are a class of non-nucleoside antiviral agents that have potent and selective activity against herpes simplex virus type 2 (HSV-2). The IC50 for these compounds in plaque reduction analysis using Vero cells ranges from 0.8 to 2.0 microg/ml. All compounds have a LC50 > 100 microg/ml in cytotoxicity analysis. Mechanism of action studies suggest that these molecules have an effect on the transactivation of viral immediate early (alpha) gene expression. Time of addition studies indicate that antiviral activity of these analogs is limited to the initial 2-3 h after infection and is not due to inhibition of viral adsorption or penetration. Analysis of HSV protein expression demonstrates that SCH 49286 inhibits the accumulation of viral immediate early (alpha) gene products. SCH 43478 demonstrates statistically significant efficacy (P < 0.05) in the guinea pig genital model of HSV infection. Following subcutaneous administration in a therapeutic treatment regimen, SCH 43478 (90 mg/kg/day) is efficacious in reducing the number and severity of lesions and the neurological complications of acute HSV infection. Thus, SCH 43478 and analogs are anti-herpesvirus agents with a unique mechanism of action.

Structure of poliovirus type 2 Lansing complexed with antiviral agent SCH48973: comparison of the structural and biological properties of three poliovirus serotypes

BACKGROUND

Polioviruses are human pathogens and the causative agents of poliomyelitis. Polioviruses are icosahedral single-stranded RNA viruses, which belong to the picornavirus family, and occur as three distinct serotypes. All three serotypes of poliovirus can infect primates, but only type 2 can infect mice. The crystal structures of a type 1 and a type 3 poliovirus are already known. Structural studies of poliovirus type 2 Lansing (PV2L) were initiated to try to enhance our understanding of the differences in host range specificity, antigenicity and receptor binding among the three serotypes of poliovirus.

RESULTS

The crystal structure of the mouse neurovirulent PV2L complexed with a potent antiviral agent, SCH48973, was determined at 2.9 A resolution. Structural differences among the three poliovirus serotypes occur primarily in the loop regions of the viral coat proteins (VPs), most notably in the loops of VP1 that cluster near the fivefold axes of the capsid, where the BC loop of PV2L is disordered. Unlike other known structures of enteroviruses, the entire polypeptide chain of PV2L VP4 is visible in the electron density and RNA bases are observed stacking with conserved aromatic residues (Tyr4020 and Phe4046) of VP4. The broad-spectrum antiviral agent SCH48973 is observed binding in a pocket within the beta-barrel of VP1, in approximately the same location that natural 'pocket factors' bind to polioviruses. SCH48973 forms predominantly hydrophobic interactions with the pocket residues.

CONCLUSIONS

Some of the conformational changes required for infectivity and involved in the control of capsid stability and neurovirulence in mice may occur in the vicinity of the fivefold axis of the poliovirus, where there are significant structural differences among the three poliovirus serotypes in the surface exposed loops of VP1 (BC, DE, and HI). A surface depression is located at the fivefold axis of PV2L that is not present in the other two poliovirus serotypes. The observed interaction of RNA with VP4 supports the observation that loss of VP4 ultimately leads to the loss of viral RNA. A model is proposed that suggests dual involvement of the virion fivefold and pseudo-threefold axes in receptor-mediated initiation of infection by picornaviruses.

Who profits from not-for-profits: a reconsideration

'Who profits from nonprofits?' asked Herzlinger and Krasker in a recent Harvard Business Review article. Their study examined whether not-for-profit hospitals achieve the intended social goals for which they are subsidised by society. In this paper, we report a reconsideration of Herzlinger and Krasker's question. Using a larger data set and a different statistical method, our findings are at variance with those of Herzlinger and Krasker and in general agreement with their critics.

Atopy in parents of children dying with sudden infant death syndrome

36 parents of infants who had died suddenly did not differ in frequency of atopic symptoms, immediate skin tests, IgE, IgE antibody, immunoglobulin G, A, and M, or yeast opsonisation, from 36 matched controls, although atopy was common (about half had atopy in both groups.

The atopic syndrome: in vitro immunological characteristics of clinically defined subgroups of atopic subjects

Total IgE, selected specific IgE antibody levels, C2 and yeast opsonization were measured in four clinically defined subgroups of atopic patients who had previously been HLA-typed. Each group was characterized by a distinctive mean total IgE level and profile of specific IgE responses. All groups gave comparable levels of IgE antibodies to Timothy grass pollen but in patients initially presenting with infantile eczema and who subsequently developed asthma and/or hay fever, IgE antibodies to bovine milk proteins, egg ovalbumin and cat dander were frequently observed whereas in patients initially presenting with hay fever later in life these antibodies were usually absent. Computer assisted analysis failed to show any association between IgE antibody responses and (a) the HLA phenotypes A1,B8 and A3,B7 (b) C2 levels and (c) the yeast opsonization index.