Refining the planktic foraminiferal I/Ca proxy:Results from the Southeast Atlantic Ocean

Profound changes in upper ocean oxygenation have taken place in recent decades and are expected to continue in the future, but the complexity of the processes driving these changes has yet to be fully unraveled. Planktic foraminiferal I/Ca is a promising tool to reconstruct the extent of past upper ocean oxygenation, but a thorough assessment is necessary to evaluate both its potential and its limitations. We used foraminifers from Holocene core-tops (Southeast Atlantic Ocean) to document planktic I/Ca across a range of oceanographic conditions. Subsurface O2 concentrations may be the dominant control on planktic foraminiferal I/Ca and planktic I/Ca decreases rapidly at low O2 conditions (O2 < ∼70–100 µmol/kg). We thus document that low planktic I/Ca can be used empirically to indicate hypoxia in the upper water column, but questions remain as to the mechanistic understanding of the relation between seawater iodine speciation change, its O2 threshold and foraminiferal I/Ca. Planktic I/Ca records from core GeoB1720-2 (Benguela Upwelling System, SE Atlantic) suggest that hypoxic waters were present near the site persistently during the last 240 ka, without clear glacial-interglacial variability

Calcification, Dissolution and Test Properties of Modern Planktonic Foraminifera From the Central Atlantic Ocean

The mass of well-preserved calcite in planktonic foraminifera shells provides an indication of the calcification potential of the surface ocean. Here we report the shell weight of 8 different abundant planktonic foraminifera species from a set of core-top sediments along the Mid-Atlantic Ridge. The analyses showed that near the equator, foraminifera shells of equivalent size weigh on average 1/3 less than those from the middle latitudes. The carbonate preservation state of the samples was assessed by high resolution X-ray microcomputed tomographic analyses of Globigerinoides ruber and Globorotalia truncatulinoides specimens. The specimen preservation was deemed good and does not overall explain the observed shell mass variations. However, G. ruber shell weights might be to some extent compromised by residual fine debris internal contamination. Deep dwelling species possess heavier tests than their surface-dwelling counterparts, suggesting that the weight of the foraminifera shells changes as a function of the depth habitat. Ambient seawater carbonate chemistry of declining carbonate ion concentration with depth cannot account for this interspecies difference. The results suggest a depth regulating function for plankton calcification, which is not dictated by water column acidity

Calcification, dissolution and test properties of modern planktonic foraminifera from the central Atlantic Ocean

This research was supported in part by a Royal Society Newton International postdoctoral Fellowship to SZ from the Royal Society of London. JWBR acknowledges funding from the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement 805246). We also acknowledge support from U.K. NERC Grant (PUCCA) NE/V011049/1.The mass of well-preserved calcite in planktonic foraminifera shells provides an indication of the calcification potential of the surface ocean. Here we report the shell weight of 8 different abundant planktonic foraminifera species from a set of core-to sediments along the Mid-Atlantic Ridge. The analyses showed that near the equator, foraminifera shells of equivalent size weigh on average 1/3 less than those from the middle latitudes. The carbonate preservation state of the samples was assessed by high resolution X-ray microcomputed tomographic analyses of Globigerinoides ruber and Globorotalia truncatulinoides specimens. The specimen preservation was deemed good and does not overall explain the observed shell mass variations. However, G. ruber shell weights might be to some extent compromised by residual fine debris internal contamination. Deep dwelling species possess heavier tests than their surface-dwelling counterparts, suggesting that the weight of the foraminifera shells changes as a function of the depth habitat. Ambient seawater carbonate chemistry of declining carbonate ion concentration with depth cannot account for this interspecies difference. The results suggest a depth regulating function for plankton calcification, which is not dictated by water column acidity.Publisher PDFPeer reviewe

D-4F, an apoA-1 mimetic, decreases airway hyperresponsiveness, inflammation, and oxidative stress in a murine model of asthma

Asthma is characterized by oxidative stress and inflammation of the airways. Although proinflammatory lipids are involved in asthma, therapies targeting them remain lacking. Ac-DWFKAFYDKVAEKFKEAFNH2 (4F) is an apolipoprotein (apo)A-I mimetic that has been shown to preferentially bind oxidized lipids and improve HDL function. The objective of the present study was to determine the effects of 4F on oxidative stress, inflammation, and airway resistance in an established murine model of asthma. We show here that ovalbumin (OVA) -sensitization increased airway hyperresponsiveness, eosinophil recruitment, and collagen deposition in lungs of C57BL/6J mice by a mechanism that could be reduced by 4F. OVA sensitization induced marked increases in transforming growth factor (TGF)β-1, fibroblast specific protein (FSP)-1, anti-T15 autoantibody staining, and modest increases in 4-hydroxynonenal (4-HNE) Michael\u27s adducts in lungs of OVA-sensitized mice. 4F decreased TGFβ-1, FSP-1, anti-T15 autoantibody, and 4-HNE adducts in the lungs of the OVA-sensitized mice. Eosinophil peroxidase (EPO) activity in bronchial alveolar lavage fluid (BALF), peripheral eosinophil counts, total IgE, and proinflammatory HDL (p-HDL) were all increased in OVA-sensitized mice. 4F decreased BALF EPO activity, eosinophil counts, total IgE, and p-HDL in these mice. These data indicate that 4F reduces pulmonary inflammation and airway resistance in an experimental murine model of asthma by decreasing oxidative stress

Transcriptomic analysis of cutaneous squamous cell carcinoma reveals a multi-gene prognostic signature associated with metastasis.

BackgroundMetastasis of cutaneous squamous cell carcinoma (cSCC) is uncommon. Current staging methods are reported to have sub-optimal performances in metastasis prediction. Accurate identification of patients with tumours at high risk of metastasis would have a significant impact on management.ObjectiveTo develop a robust and validated gene expression profile (GEP) signature for predicting primary cSCC metastatic risk using an unbiased whole transcriptome discovery-driven approach.MethodsArchival formalin-fixed paraffin-embedded primary cSCC with perilesional normal tissue from 237 immunocompetent patients (151 non-metastasising and 86 metastasising) were collected retrospectively from four centres. TempO-seq was used to probe the whole transcriptome and machine learning algorithms were applied to derive predictive signatures, with a 3:1 split for training and testing datasets.ResultsA 20-gene prognostic model was developed and validated, with an accuracy of 86.0%, sensitivity of 85.7%, specificity of 86.1%, and positive predictive value of 78.3% in the testing set, providing more stable, accurate prediction than pathological staging systems. A linear predictor was also developed, significantly correlating with metastatic risk.LimitationsThis was a retrospective 4-centre study and larger prospective multicentre studies are now required.ConclusionThe 20-gene signature prediction is accurate, with the potential to be incorporated into clinical workflows for cSCC

Transcriptomic analysis of cutaneous squamous cell carcinoma reveals a multi-gene prognostic signature associated with metastasis.

BACKGROUND: Metastasis of cutaneous squamous cell carcinoma (cSCC) is uncommon. Current staging methods are reported to have sub-optimal performances in metastasis prediction. Accurate identification of patients with tumours at high risk of metastasis would have a significant impact on management. OBJECTIVE: To develop a robust and validated gene expression profile (GEP) signature for predicting primary cSCC metastatic risk using an unbiased whole transcriptome discovery-driven approach. METHODS: Archival formalin-fixed paraffin-embedded primary cSCC with perilesional normal tissue from 237 immunocompetent patients (151 non-metastasising and 86 metastasising) were collected retrospectively from four centres. TempO-seq was used to probe the whole transcriptome and machine learning algorithms were applied to derive predictive signatures, with a 3:1 split for training and testing datasets. RESULTS: A 20-gene prognostic model was developed and validated, with an accuracy of 86.0%, sensitivity of 85.7%, specificity of 86.1%, and positive predictive value of 78.3% in the testing set, providing more stable, accurate prediction than pathological staging systems. A linear predictor was also developed, significantly correlating with metastatic risk. LIMITATIONS: This was a retrospective 4-centre study and larger prospective multicentre studies are now required. CONCLUSION: The 20-gene signature prediction is accurate, with the potential to be incorporated into clinical workflows for cSCC

Late inception of a resiliently oxygenated upper ocean

This is the author accepted manuscript. The final version is available from American Association for the Advancement of Science via the DOI in this record Rising oceanic and atmospheric oxygen levels through time have been crucial to enhanced habitability of surface Earth environments. Few redox proxies can track secular variations in dissolved oxygen concentrations around threshold levels for metazoan survival in the upper ocean. We present an extensive compilation of iodine-to-calcium ratios (I/Ca) in marine carbonates. Our record supports a major rise in the partial pressure of oxygen in the atmosphere at ~400 million years (Ma) ago and reveals a step change in the oxygenation of the upper ocean to relatively sustainable near-modern conditions at ~200 Ma ago. An Earth system model demonstrates that a shift in organic matter remineralization to greater depths, which may have been due to increasing size and biomineralization of eukaryotic plankton, likely drove the I/Ca signals at ~200 Ma ago.NER

Meridional overturning circulation in the South Atlantic at the last glacial maximum

Author Posting. © American Geophysical Union, 2006. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 7 (2006): Q10N03, doi:10.1029/2005GC001226.The geostrophic shear associated with the meridional overturning circulation is reflected in the difference in density between the eastern and western margins of the ocean basin. Here we examine how the density difference across 30°S in the upper 2 km of the Atlantic Ocean (and thus the magnitude of the shear associated with the overturning circulation) has changed between the last glacial maximum and the present. We use oxygen isotope measurements on benthic foraminifera to reconstruct density. Today, the density in upper and intermediate waters along the eastern margin in the South Atlantic is greater than along the western margin, reflecting the vertical shear associated with the northward flow of surface and intermediate waters and the southward flowing North Atlantic Deep Waters below. The greater density along the eastern margin is reflected in the higher δ 18O values for surface sediment benthic foraminifera than those found on the western margin for the upper 2 km. For the last glacial maximum the available data indicate that the eastern margin foraminifera had similar δ 18O to those on the western margin between 1 and 2 km and that the gradient was reversed relative to today with the higher δ 18O values in the western margin benthic foraminifera above 1 km. If this reversal in benthic foraminifera δ 18O gradient reflects a reversal in seawater density gradient, these data are not consistent with a vigorous but shallower overturning cell in which surface waters entering the Atlantic basin are balanced by the southward export of Glacial North Atlantic Intermediate Water.This work was supported by NSF award OCE-9984989/OCE-0428803 to J.L.-S., NSF award OCE-9986748 to D.W.O. and W.B.C., NSF OCE-0222111 to C.D.C., and SEGRF fellowship at LLNL to J.M

A genome-wide scan for common alleles affecting risk for autism

Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10−8. When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10−8 threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C