Gene expression in the deep biosphere

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in Nature 499 (2013): 205-208, doi:10.1038/nature12230.Scientific ocean drilling has revealed a deep biosphere of widespread microbial life in sub-seafloor sediment. Microbial metabolism in the marine subsurface likely plays an important role in global biogeochemical cycles1-3 but deep biosphere activities are not well understood1. Here, we describe and analyze the first subseafloor metatranscriptomes from anaerobic Peru Margin sediment up to 159 meters below seafloor (mbsf) represented by over 1 billion cDNA sequence reads. Anaerobic metabolism of amino acids, carbohydrates, and lipids appear to be dominant metabolic processes, and profiles of dissimilatory sulfite reductase (Dsr) transcripts are consistent with porewater sulfate concentration profiles1. Moreover, transcripts involved in cell division increase as a function of microbial cell concentration, indicating that increases in subseafloor microbial abundance are a function of cell division across all three domains of life. These data support calculations1 and models4 of subseafloor microbial metabolism and represent the first holistic picture of deep biosphere activities.This work was fostered by a Center for Dark Energy Biosphere Investigations (CDEBI) grant OCE-0939564 to WO and a NSF IOS grant 1238801 to JFB.2013-12-1

Observing Galaxy Evolution in the Context of Large-Scale Structure

Galaxies form and evolve in the context of their local and large-scale environments. Their baryonic content that we observe with imaging and spectroscopy is intimately connected to the properties of their dark matter halos, and to their location in the "cosmic web" of large-scale structure. Very large spectroscopic surveys of the local universe (e.g., SDSS and GAMA) measure galaxy positions (location within large-scale structure), statistical clustering (a direct constraint on dark matter halo masses), and spectral features (measuring physical conditions of the gas and stars within the galaxies, as well as internal velocities). Deep surveys with the James Webb Space Telescope (JWST) will revolutionize spectroscopic measurements of redshifts and spectral properties for galaxies out to the epoch of reionization, but with numerical statistics and over cosmic volumes that are too small to map large-scale structure and to constrain halo properties via clustering. Here, we consider advances in understanding galaxy evolution that would be enabled by very large spectroscopic surveys at high redshifts: very large numbers of galaxies (outstanding statistics) over large co-moving volumes (large-scale structure on all scales) over broad redshift ranges (evolution over most of cosmic history). The required observational facility can be established as part of the probe portfolio by NASA within the next decade.Comment: 8 pages (including cover page and references), 3 figures. Science white paper submitted to Astro2020. arXiv admin note: substantial text overlap with arXiv:1802.0153

Smoking Cessation Among Women with and at Risk for HIV: Are They Quitting?

Cigarette smoking is an important risk factor for adverse health events in HIV-infected populations. While recent US population-wide surveys report annual sustained smoking cessation rates of 3.4–8.5%, prospective data are lacking on cessation rates for HIV-infected smokers. To determine the sustained tobacco cessation rate and predictors of cessation among women with or at risk for HIV infection. Prospective cohort study. A total of 747 women (537 HIV-infected and 210 HIV-uninfected) who reported smoking at enrollment (1994–1995) in the Women’s Interagency HIV Study (WIHS) and remained in follow-up after 10 years. The participants were mostly minority (61% non-Hispanic Blacks and 22% Hispanics) and low income (68% with reported annual incomes of less than or equal to $12,000). The primary outcome was defined as greater than 12 months continuous cessation at year 10. Multivariate logistic regression was used to identify independent baseline predictors of subsequent tobacco cessation. A total of 121 (16%) women reported tobacco cessation at year 10 (annual sustained cessation rate of 1.8%, 95% CI 1.6–2.1%). Annual sustained cessation rates were 1.8% among both HIV-positive and HIV-negative women (p = 0.82). In multivariate analysis, the odds of tobacco cessation were significantly higher in women with more years of education (p trend = 0.02) and of Hispanic origin (OR = 1.87, 95% CI = 1.4–2.9) compared to Black women. Cessation was significantly lower in current or former illicit drug users (OR = 0.42 95% CI = 0.24–0.74 and OR = 0.65, 95% CI = 0.49–0.86, respectively, p trend = 0.03) and women reporting a higher number of cigarettes per day at baseline (p trend < 0.001). HIV-infected and at-risk women in this cohort have lower smoking cessation rates than the general population. Given the high prevalence of smoking, the high risk of adverse health events from smoking, and low rates of cessation, it is imperative that we increase efforts and overcome barriers to help these women quit smoking

Deep sequencing of subseafloor eukaryotic rRNA reveals active fungi across marine subsurface provinces

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e56335, doi:10.1371/journal.pone.0056335.The deep marine subsurface is a vast habitat for microbial life where cells may live on geologic timescales. Because DNA in sediments may be preserved on long timescales, ribosomal RNA (rRNA) is suggested to be a proxy for the active fraction of a microbial community in the subsurface. During an investigation of eukaryotic 18S rRNA by amplicon pyrosequencing, unique profiles of Fungi were found across a range of marine subsurface provinces including ridge flanks, continental margins, and abyssal plains. Subseafloor fungal populations exhibit statistically significant correlations with total organic carbon (TOC), nitrate, sulfide, and dissolved inorganic carbon (DIC). These correlations are supported by terminal restriction length polymorphism (TRFLP) analyses of fungal rRNA. Geochemical correlations with fungal pyrosequencing and TRFLP data from this geographically broad sample set suggests environmental selection of active Fungi in the marine subsurface. Within the same dataset, ancient rRNA signatures were recovered from plants and diatoms in marine sediments ranging from 0.03 to 2.7 million years old, suggesting that rRNA from some eukaryotic taxa may be much more stable than previously considered in the marine subsurface.This work was performed with funding from the Center for Dark Energy Biosphere Investigations (C-DEBI) to William Orsi (OCE-0939564) and The Ocean Life Institute (WHOI) to Virginia Edgcomb (OLI-27071359)

Physical and biogeochemical controls on the variability in surface pH and calcium carbonate saturation states in the Atlantic sectors of the Arctic and Southern Oceans

Polar oceans are particularly vulnerable to ocean acidification due to their low temperatures and reduced buffering capacity, and are expected to experience extensive low pH conditions and reduced carbonate mineral saturations states (Ω) in the near future. However, the impact of anthropogenic CO2 on pH and Ω will vary regionally between and across the Arctic and Southern Oceans. Here we investigate the carbonate chemistry in the Atlantic sector of two polar oceans, the Nordic Seas and Barents Sea in the Arctic Ocean, and the Scotia and Weddell Seas in the Southern Ocean, to determine the physical and biogeochemical processes that control surface pH and Ω. High-resolution observations showed large gradients in surface pH (0.10–0.30) and aragonite saturation state (Ωar) (0.2–1.0) over small spatial scales, and these were particularly strong in sea-ice covered areas (up to 0.45 in pH and 2.0 in Ωar). In the Arctic, sea-ice melt facilitated bloom initiation in light-limited and iron replete (dFe>0.2 nM) regions, such as the Fram Strait, resulting in high pH (8.45) and Ωar (3.0) along the sea-ice edge. In contrast, accumulation of dissolved inorganic carbon derived from organic carbon mineralisation under the ice resulted in low pH (8.05) and Ωar (1.1) in areas where thick ice persisted. In the Southern Ocean, sea-ice retreat resulted in bloom formation only where terrestrial inputs supplied sufficient iron (dFe>0.2 nM), such as in the vicinity of the South Sandwich Islands where enhanced pH (8.3) and Ωar (2.3) were primarily due to biological production. In contrast, in the adjacent Weddell Sea, weak biological uptake of CO2 due to low iron concentrations (dFe<0.2 nM) resulted in low pH (8.1) and Ωar (1.6). The large spatial variability in both polar oceans highlights the need for spatially resolved surface data of carbonate chemistry variables but also nutrients (including iron) in order to accurately elucidate the large gradients experienced by marine organisms and to understand their response to increased CO2 in the future

Albiglutide and cardiovascular outcomes in patients with type 2 diabetes and cardiovascular disease (Harmony Outcomes): a double-blind, randomised placebo-controlled trial

Background: Glucagon-like peptide 1 receptor agonists differ in chemical structure, duration of action, and in their effects on clinical outcomes. The cardiovascular effects of once-weekly albiglutide in type 2 diabetes are unknown. We aimed to determine the safety and efficacy of albiglutide in preventing cardiovascular death, myocardial infarction, or stroke. Methods: We did a double-blind, randomised, placebo-controlled trial in 610 sites across 28 countries. We randomly assigned patients aged 40 years and older with type 2 diabetes and cardiovascular disease (at a 1:1 ratio) to groups that either received a subcutaneous injection of albiglutide (30–50 mg, based on glycaemic response and tolerability) or of a matched volume of placebo once a week, in addition to their standard care. Investigators used an interactive voice or web response system to obtain treatment assignment, and patients and all study investigators were masked to their treatment allocation. We hypothesised that albiglutide would be non-inferior to placebo for the primary outcome of the first occurrence of cardiovascular death, myocardial infarction, or stroke, which was assessed in the intention-to-treat population. If non-inferiority was confirmed by an upper limit of the 95% CI for a hazard ratio of less than 1·30, closed testing for superiority was prespecified. This study is registered with ClinicalTrials.gov, number NCT02465515. Findings: Patients were screened between July 1, 2015, and Nov 24, 2016. 10 793 patients were screened and 9463 participants were enrolled and randomly assigned to groups: 4731 patients were assigned to receive albiglutide and 4732 patients to receive placebo. On Nov 8, 2017, it was determined that 611 primary endpoints and a median follow-up of at least 1·5 years had accrued, and participants returned for a final visit and discontinuation from study treatment; the last patient visit was on March 12, 2018. These 9463 patients, the intention-to-treat population, were evaluated for a median duration of 1·6 years and were assessed for the primary outcome. The primary composite outcome occurred in 338 (7%) of 4731 patients at an incidence rate of 4·6 events per 100 person-years in the albiglutide group and in 428 (9%) of 4732 patients at an incidence rate of 5·9 events per 100 person-years in the placebo group (hazard ratio 0·78, 95% CI 0·68–0·90), which indicated that albiglutide was superior to placebo (p&lt;0·0001 for non-inferiority; p=0·0006 for superiority). The incidence of acute pancreatitis (ten patients in the albiglutide group and seven patients in the placebo group), pancreatic cancer (six patients in the albiglutide group and five patients in the placebo group), medullary thyroid carcinoma (zero patients in both groups), and other serious adverse events did not differ between the two groups. There were three (&lt;1%) deaths in the placebo group that were assessed by investigators, who were masked to study drug assignment, to be treatment-related and two (&lt;1%) deaths in the albiglutide group. Interpretation: In patients with type 2 diabetes and cardiovascular disease, albiglutide was superior to placebo with respect to major adverse cardiovascular events. Evidence-based glucagon-like peptide 1 receptor agonists should therefore be considered as part of a comprehensive strategy to reduce the risk of cardiovascular events in patients with type 2 diabetes. Funding: GlaxoSmithKline

Eukaryotic genera affiliated with rRNA sequences detected in subsurface samples.

<p>Eukaryotic genera affiliated with rRNA sequences detected in subsurface samples.</p

Canonical correspondence analysis of fungal OTUs from marine subsurface samples.

<p>Black circles are proportional to the number of fungal OTUs detected in each sample. Red and blue circles are proportional parametric (CatchAll) and nonparametric (Chao1) richness estimates (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056335#pone.0056335.s007" target="_blank">Table S2</a>). Vectors represent sulfide, TOC, and DIC correlations. The p-value resulting from an MRPP test for effect of DIC, TOC, and sulfide on fungal distributions is shown in the lower right corner of the biplot. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056335#pone-0056335-t001" target="_blank">Table 1</a> for sample information.</p