Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chakraborty, A., Ruff, S. E., Dong, X., Ellefson, E. D., Li, C., Brooks, J. M., McBee, J., Bernard, B. B., & Hubert, C. R. J. Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres. Proceedings of the National Academy of Sciences of the United States of America, 117(20), (2020): 11029-11037, doi: 10.1073/pnas.2002289117.Marine cold seeps transmit fluids between the subseafloor and seafloor biospheres through upward migration of hydrocarbons that originate in deep sediment layers. It remains unclear how geofluids influence the composition of the seabed microbiome and if they transport deep subsurface life up to the surface. Here we analyzed 172 marine surficial sediments from the deep-water Eastern Gulf of Mexico to assess whether hydrocarbon fluid migration is a mechanism for upward microbial dispersal. While 132 of these sediments contained migrated liquid hydrocarbons, evidence of continuous advective transport of thermogenic alkane gases was observed in 11 sediments. Gas seeps harbored distinct microbial communities featuring bacteria and archaea that are well-known inhabitants of deep biosphere sediments. Specifically, 25 distinct sequence variants within the uncultivated bacterial phyla Atribacteria and Aminicenantes and the archaeal order Thermoprofundales occurred in significantly greater relative sequence abundance along with well-known seep-colonizing members of the bacterial genus Sulfurovum, in the gas-positive sediments. Metabolic predictions guided by metagenome-assembled genomes suggested these organisms are anaerobic heterotrophs capable of nonrespiratory breakdown of organic matter, likely enabling them to inhabit energy-limited deep subseafloor ecosystems. These results point to petroleum geofluids as a vector for the advection-assisted upward dispersal of deep biosphere microbes from subsurface to surface environments, shaping the microbiome of cold seep sediments and providing a general mechanism for the maintenance of microbial diversity in the deep sea.We wish to thank Jody Sandel as well as the crew of R/V GeoExplorer for collection of piston cores, onboard core processing, sample preservation, and shipment. Cynthia Kwan and Oliver Horanszky are thanked for assistance with amplicon library preparation. We also wish to thank Jayne Rattray, Daniel Gittins, and Marc Strous for valuable discussions and suggestions, and Rhonda Clark for research support. Collaborations with Andy Mort from the Geological Survey of Canada, and Richard Hatton from Geoscience Wales are also gratefully acknowledged. This work was financially supported by a Mitacs Elevate Postdoctoral Fellowship awarded to A.C.; an Alberta Innovates-Technology Futures/Eyes High Postdoctoral Fellowship to S.E.R.; and a Natural Sciences and Engineering Research Council Strategic Project Grant, a Genome Canada Genomics Applications Partnership Program grant, a Canada Foundation for Innovation grant (CFI-JELF 33752) for instrumentation, and Campus Alberta Innovates Program Chair funding to C.R.J.H

Guidance and control requirements for high-speed Rollout and Turnoff (ROTO)

This report defines the initial requirements for designing a research high-speed rollout and turnoff (ROTO) guidance and control system applicable to transport class aircraft whose purpose is to reduce the average runway occupancy time (ROT) for aircraft operations. The requirements will be used to develop a ROTO system for both automatic and manual piloted operation under normal and reduced visibility conditions. Requirements were determined for nose wheel/rudder steering, braking/reverse thrust, and the navigation system with the aid of a non-real time, three degree-of-freedom MD-11 simulation program incorporating airframe and gear dynamics. The requirements were developed for speeds up to 70 knots using 30 ft exit geometries under dry and wet surface conditions. The requirements were generated under the assumptions that the aircraft landing system meets the current Category III touchdown dispersion requirements and that aircraft interarrival spacing is 2 nautical miles. This effort determined that auto-asymmetric braking is needed to assist steering for aft center-of-gravity aircraft. This report shows various time-history plots of the aircraft performance for the ROTO operation. This effort also investigated the state-of-the-art in the measurement of the runway coefficient of friction for various runway conditions

Mycobacterial RNA isolation optimized for non-coding RNA: high fidelity isolation of 5S rRNA from Mycobacterium bovis BCG reveals novel post-transcriptional processing and a complete spectrum of modified ribonucleosides

A major challenge in the study of mycobacterial RNA biology is the lack of a comprehensive RNA isolation method that overcomes the unusual cell wall to faithfully yield the full spectrum of non-coding RNA (ncRNA) species. Here, we describe a simple and robust procedure optimized for the isolation of total ncRNA, including 5S, 16S and 23S ribosomal RNA (rRNA) and tRNA, from mycobacteria, using Mycobacterium bovis BCG to illustrate the method. Based on a combination of mechanical disruption and liquid and solid-phase technologies, the method produces all major species of ncRNA in high yield and with high integrity, enabling direct chemical and sequence analysis of the ncRNA species. The reproducibility of the method with BCG was evident in bioanalyzer electrophoretic analysis of isolated RNA, which revealed quantitatively significant differences in the ncRNA profiles of exponentially growing and non-replicating hypoxic bacilli. The method also overcame an historical inconsistency in 5S rRNA isolation, with direct sequencing revealing a novel post-transcriptional processing of 5S rRNA to its functional form and with chemical analysis revealing seven post-transcriptional ribonucleoside modifications in the 5S rRNA. This optimized RNA isolation procedure thus provides a means to more rigorously explore the biology of ncRNA species in mycobacteria.Singapore-MIT Alliance for Research and TechnologyNational Institute of Environmental Health Sciences (ES017010)National Institute of Environmental Health Sciences (ES002109)Singapore-MIT Alliance (Graduate Fellowship)Singapore. National Research Foundatio

Serving the community with trustworthy government information and data: What can we learn from the public librarians?

The role of public librarians in mediating and providing access to government information and data becomes more critical than ever in the face of new threats to the trustworthiness of government information and the availability of data. Interviewing reference librarians in four county library systems, the study tries to find out how library and information science (LIS) education can help future public librarians prepare for their roles in mediating government information and data in the global context

Guidance and Control Design for High-Speed Rollout and Turnoff (ROTO)

A ROTO architecture, braking and steering control law and display designs for a research high speed Rollout and Turnoff (ROTO) system applicable to transport class aircraft are described herein. Minimum surface friction and FMS database requirements are also documented. The control law designs were developed with the aid of a non-real time simulation program incorporating airframe and gear dynamics as well as steering and braking guidance algorithms. An attainable objective of this ROTO system, as seen from the results of this study, is to assure that the studied aircraft can land with runway occupancy times less then 53 seconds. Runway occupancy time is measured from the time the aircraft crosses the runway threshold until its wing tip clears the near side of the runway. Turnoff ground speeds of 70 knots onto 30 degree exits are allowed with dry and wet surface conditions. Simulation time history and statistical data are documented herein. Parameters which were treated as variables in the simulation study include aircraft touchdown weight/speed/location, aircraft CG, runway friction, sensor noise and winds. After further design and development of the ROTO control system beyond the system developed earlier, aft CG MD-11 aircraft no longer require auto-asymmetric braking (steering) and fly-by-wire nose gear steering. However, the auto ROTO nose gear hysteresis must be less than 2 degrees. The 2 sigma dispersion certified for MD-11 CATIIIB is acceptable. Using this longitudinal dispersion, three ROTO exits are recommended at 3300, 4950 and 6750 feet past the runway threshold. The 3300 foot exit is required for MD-81 class aircraft. Designs documented in this report are valid for the assumptions/models used in this simulation. It is believed that the results will apply to the general class of transport aircraft; however further effort is required to validate this assumption for the general case

Probing the equation of state in the AGS energy range with 3-d hydrodynamics

The effect of (i) the phase transition between a quark gluon plasma (QGP) and a hadron gas and (ii) the number of resonance degrees of freedom in the hadronic phase on the single inclusive distributions of 16 different types of produced hadrons for Au+Au collisions at AGS energies is studied. We have used an exact numerical solution of the relativistic hydrodynamical equations without free parameters which, because of its 3-d character, constitutes a considerable improvement over the classical Landau solution. Using two different equations of state (eos) - one containing a phase transition from QGP to the Hadronic Phase and two versions of a purely hadronic eos - we find that the first one gives an overall better description of the Au+Au experimental data at $AGS$ energies. We reproduce and analyse measured meson and proton spectra and also make predictions for anti-protons, deltas, anti-deltas and hyperons. The low m_t enhancement in pi- spectra is explained by baryon number conservation and strangeness equilibration. We also find that negative kaon data are more sensitive to the eos, as well as the K-/pi- ratio. All hyperons and deltas are sensitive to the presence of a phase transition in the forward rapidity region. Anti-protons, Omegas and heavy anti-baryons are sensitive in the whole rapidity range.Comment: 25 pages (.tex) and 9 figures (.ps

Can Implicit Measures Augment Suicide Detection in Youth? The Feasibility and Acceptability of the Death Implicit Association Test Among Pediatric Medical Impatients

Background: Medically ill youth are at increased suicide risk, necessitating early detection. This study aimed to assess the feasibility of administering the Death Implicit Association Test (Death IAT) to pediatric medical inpatients. Methods: Participants completed measures including the Ask Suicide-Screening Questions (ASQ) and the Death IAT. Results: Over 90% of participants found the Death IAT to be acceptable and more than 75% of participants were comfortable completing the task. There was a small, but statistically significant, improvement from pre-survey to post-survey reports of mood (t(174) = 3.02, p = 0.003, d = 0.15). Participants who endorsed a past suicide attempt on the ASQ had significantly higher “suicide” trial D-scores than those without a past suicide attempt (Wilcoxon W = 1312; p = 0.048; d = 0.61). Conclusions: Implementing an IAT measure among pediatric medical inpatients was feasible and acceptable. In exploratory analyses, “suicide” trial IAT D-scores were associated with past suicide attempts, suggesting future studies should examine whether implicit measures may be useful in hospital settings to augment detection of youth suicide risk

Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruginosa

Bacteria respond to environmental stresses using a variety of signaling and gene expression pathways, with translational mechanisms being the least well understood. Here, we identified a tRNA methyltransferase in Pseudomonas aeruginosa PA14, trmJ, which confers resistance to oxidative stress. Analysis of tRNA from a trmJ mutant revealed that TrmJ catalyzes formation of Cm, Um, and, unexpectedly, Am. Defined in vitro analyses revealed that tRNA[superscript Met(CAU)] and tRNA[superscript Trp(CCA)] are substrates for Cm formation, tRNA[superscript Gln(UUG)], tRNA[superscript Pro(UGG)], tRNA[superscript Pro(CGG)] and tRNA[superscript His(GUG)] for Um, and tRNA[superscript Pro(GGG)] for Am. tRNA[superscript Ser(UGA)], previously observed as a TrmJ substrate in Escherichia coli, was not modified by PA14 TrmJ. Position 32 was confirmed as the TrmJ target for Am in tRNA[superscriptPro(GGG)] and Um in tRNA[superscript Gln(UUG)] by mass spectrometric analysis. Crystal structures of the free catalytic N-terminal domain of TrmJ show a 2-fold symmetrical dimer with an active site located at the interface between the monomers and a flexible basic loop positioned to bind tRNA, with conformational changes upon binding of the SAM-analog sinefungin. The loss of TrmJ rendered PA14 sensitive to H2O2 exposure, with reduced expression of oxyR-recG, katB-ankB, and katE. These results reveal that TrmJ is a tRNA:Cm32/Um32/Am32 methyltransferase involved in translational fidelity and the oxidative stress response.National Science Foundation (U.S.) (CHE-1308839)Agilent TechnologiesSingapore-MIT Alliance for Research and Technology (SMART

Thrombolytic removal of intraventricular haemorrhage in treatment of severe stroke: results of the randomised, multicentre, multiregion, placebo-controlled CLEAR III trial

Background: Intraventricular haemorrhage is a subtype of intracerebral haemorrhage, with 50% mortality and serious disability for survivors. We aimed to test whether attempting to remove intraventricular haemorrhage with alteplase versus saline irrigation improved functional outcome. Methods: In this randomised, double-blinded, placebo-controlled, multiregional trial (CLEAR III), participants with a routinely placed extraventricular drain, in the intensive care unit with stable, non-traumatic intracerebral haemorrhage volume less than 30 mL, intraventricular haemorrhage obstructing the 3rd or 4th ventricles, and no underlying pathology were adaptively randomly assigned (1:1), via a web-based system to receive up to 12 doses, 8 h apart of 1 mg of alteplase or 0·9% saline via the extraventricular drain. The treating physician, clinical research staff, and participants were masked to treatment assignment. CT scans were obtained every 24 h throughout dosing. The primary efficacy outcome was good functional outcome, defined as a modified Rankin Scale score (mRS) of 3 or less at 180 days per central adjudication by blinded evaluators. This study is registered with ClinicalTrials.gov, NCT00784134. Findings: Between Sept 18, 2009, and Jan 13, 2015, 500 patients were randomised: 249 to the alteplase group and 251 to the saline group. 180-day follow-up data were available for analysis from 246 of 249 participants in the alteplase group and 245 of 251 participants in the placebo group. The primary efficacy outcome was similar in each group (good outcome in alteplase group 48% vs saline 45%; risk ratio [RR] 1·06 [95% CI 0·88–1·28; p=0·554]). A difference of 3·5% (RR 1·08 [95% CI 0·90–1·29], p=0·420) was found after adjustment for intraventricular haemorrhage size and thalamic intracerebral haemorrhage. At 180 days, the treatment group had lower case fatality (46 [18%] vs saline 73 [29%], hazard ratio 0·60 [95% CI 0·41–0·86], p=0·006), but a greater proportion with mRS 5 (42 [17%] vs 21 [9%]; RR 1·99 [95% CI 1·22–3·26], p=0·007). Ventriculitis (17 [7%] alteplase vs 31 [12%] saline; RR 0·55 [95% CI 0·31–0·97], p=0·048) and serious adverse events (114 [46%] alteplase vs 151 [60%] saline; RR 0·76 [95% CI 0·64–0·90], p=0·002) were less frequent with alteplase treatment. Symptomatic bleeding (six [2%] in the alteplase group vs five [2%] in the saline group; RR 1·21 [95% CI 0·37–3·91], p=0·771) was similar. Interpretation: In patients with intraventricular haemorrhage and a routine extraventricular drain, irrigation with alteplase did not substantially improve functional outcomes at the mRS 3 cutoff compared with irrigation with saline. Protocol-based use of alteplase with extraventricular drain seems safe. Future investigation is needed to determine whether a greater frequency of complete intraventricular haemorrhage removal via alteplase produces gains in functional status