Recent Decisions

Comments on recent decisions by William C. Rindone, Ray F. Drexler, Eugene G. Griffin, Ronald Patrick Smith, and John G. Curran

Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20.

UnlabelledThe genomes of sulfate-reducing bacteria remain poorly characterized, largely due to a paucity of experimental data and genetic tools. To meet this challenge, we generated an archived library of 15,477 mapped transposon insertion mutants in the sulfate-reducing bacterium Desulfovibrio alaskensis G20. To demonstrate the utility of the individual mutants, we profiled gene expression in mutants of six regulatory genes and used these data, together with 1,313 high-confidence transcription start sites identified by tiling microarrays and transcriptome sequencing (5' RNA-Seq), to update the regulons of Fur and Rex and to confirm the predicted regulons of LysX, PhnF, PerR, and Dde_3000, a histidine kinase. In addition to enabling single mutant investigations, the D. alaskensis G20 transposon mutants also contain DNA bar codes, which enables the pooling and analysis of mutant fitness for thousands of strains simultaneously. Using two pools of mutants that represent insertions in 2,369 unique protein-coding genes, we demonstrate that the hypothetical gene Dde_3007 is required for methionine biosynthesis. Using comparative genomics, we propose that Dde_3007 performs a missing step in methionine biosynthesis by transferring a sulfur group to O-phosphohomoserine to form homocysteine. Additionally, we show that the entire choline utilization cluster is important for fitness in choline sulfate medium, which confirms that a functional microcompartment is required for choline oxidation. Finally, we demonstrate that Dde_3291, a MerR-like transcription factor, is a choline-dependent activator of the choline utilization cluster. Taken together, our data set and genetic resources provide a foundation for systems-level investigation of a poorly studied group of bacteria of environmental and industrial importance.ImportanceSulfate-reducing bacteria contribute to global nutrient cycles and are a nuisance for the petroleum industry. Despite their environmental and industrial significance, the genomes of sulfate-reducing bacteria remain poorly characterized. Here, we describe a genetic approach to fill gaps in our knowledge of sulfate-reducing bacteria. We generated a large collection of archived, transposon mutants in Desulfovibrio alaskensis G20 and used the phenotypes of these mutant strains to infer the function of genes involved in gene regulation, methionine biosynthesis, and choline utilization. Our findings and mutant resources will enable systematic investigations into gene function, energy generation, stress response, and metabolism for this important group of bacteria

Roles of IL-6-gp130 Signaling in Vascular Inflammation

Interleukin-6 (IL-6) is a well-established, independent indicator of multiple distinct types of cardiovascular disease and all-cause mortality. In this review, we present current understanding of the multiple roles that IL-6 and its signaling pathways through glycoprotein 130 (gp130) play in cardiovascular homeostasis. IL-6 is highly inducible in vascular tissues through the actions of the angiotensin II (Ang II) peptide, where it acts in a paracrine manner to signal through two distinct mechanisms, the first being a classic membrane receptor initiated pathway and the second, a trans-signaling pathway, being able to induce responses even in tissues lacking the IL-6 receptor. Recent advances and new concepts in how its intracellular signaling pathways operate via the Janus kinase (JAK)-Signal Transducer and Activator of Transcription (STAT) are described. IL-6 has diverse actions in multiple cell types of cardiovascular importance, including endothelial cells, monocytes, platelets, hepatocytes and adipocytes. We discuss central roles of IL-6 in endothelial dysfunction, cellular inflammation by affecting monocyte activation/differentiation, cellular cytoprotective functions from reactive oxygen species (ROS) stress, modulation of pro-coagulant state, myocardial growth control, and its implications in metabolic control and insulin resistance. These multiple actions indicate that IL-6 is not merely a passive biomarker, but actively modulates adaptive and pathological responses to cardiovascular stress

AXTAR: Mission Design Concept

The Advanced X-ray Timing Array (AXTAR) is a mission concept for X-ray timing of compact objects that combines very large collecting area, broadband spectral coverage, high time resolution, highly flexible scheduling, and an ability to respond promptly to time-critical targets of opportunity. It is optimized for submillisecond timing of bright Galactic X-ray sources in order to study phenomena at the natural time scales of neutron star surfaces and black hole event horizons, thus probing the physics of ultradense matter, strongly curved spacetimes, and intense magnetic fields. AXTAR's main instrument, the Large Area Timing Array (LATA) is a collimated instrument with 2-50 keV coverage and over 3 square meters effective area. The LATA is made up of an array of supermodules that house 2-mm thick silicon pixel detectors. AXTAR will provide a significant improvement in effective area (a factor of 7 at 4 keV and a factor of 36 at 30 keV) over the RXTE PCA. AXTAR will also carry a sensitive Sky Monitor (SM) that acts as a trigger for pointed observations of X-ray transients in addition to providing high duty cycle monitoring of the X-ray sky. We review the science goals and technical concept for AXTAR and present results from a preliminary mission design study.Comment: 19 pages, 10 figures, to be published in Space Telescopes and Instrumentation 2010: Ultraviolet to Gamma Ray, Proceedings of SPIE Volume 773

The Identification of the X-ray Counterpart to PSR J2021+4026

We report the probable identification of the X-ray counterpart to the gamma-ray pulsar PSR J2021+4026 using imaging with the Chandra X-ray Observatory ACIS and timing analysis with the Fermi satellite. Given the statistical and systematic errors, the positions determined by both satellites are coincident. The X-ray source position is R.A. 20h21m30.733s, Decl. +40 deg 26 min 46.04sec (J2000) with an estimated uncertainty of 1.3 arsec combined statistical and systematic error. Moreover, both the X-ray to gamma-ray and the X-ray to optical flux ratios are sensible assuming a neutron star origin for the X-ray flux. The X-ray source has no cataloged infrared-to-visible counterpart and, through new observations, we set upper limits to its optical emission of i' >23.0 mag and r' > 25.2mag. The source exhibits an X-ray spectrum with most likely both a powerlaw and a thermal component. We also report on the X-ray and visible light properties of the 43 other sources detected in our Chandra observation.Comment: Accepted for publication in the Astrophysical Journa

Global emissions of refrigerants HCFC-22 and HFC-134a: Unforeseen seasonal contributions

HCFC-22 (CHClF[subscript 2]) and HFC-134a (CH[subscript 2]FCF[subscript 3]) are two major gases currently used worldwide in domestic and commercial refrigeration and air conditioning. HCFC-22 contributes to stratospheric ozone depletion, and both species are potent greenhouse gases. In this work, we study in situ observations of HCFC-22 and HFC-134a taken from research aircraft over the Pacific Ocean in a 3-y span [HIaper-Pole-to-Pole Observations (HIPPO) 2009–2011] and combine these data with long-term ground observations from global surface sites [National Oceanic and Atmospheric Administration (NOAA) and Advanced Global Atmospheric Gases Experiment (AGAGE) networks]. We find the global annual emissions of HCFC-22 and HFC-134a have increased substantially over the past two decades. Emissions of HFC-134a are consistently higher compared with the United Nations Framework Convention on Climate Change (UNFCCC) inventory since 2000, by 60% more in recent years (2009–2012). Apart from these decadal emission constraints, we also quantify recent seasonal emission patterns showing that summertime emissions of HCFC-22 and HFC-134a are two to three times higher than wintertime emissions. This unforeseen large seasonal variation indicates that unaccounted mechanisms controlling refrigerant gas emissions are missing in the existing inventory estimates. Possible mechanisms enhancing refrigerant losses in summer are (i) higher vapor pressure in the sealed compartment of the system at summer high temperatures and (ii) more frequent use and service of refrigerators and air conditioners in summer months. Our results suggest that engineering (e.g., better temperature/vibration-resistant system sealing and new system design of more compact/efficient components) and regulatory (e.g., reinforcing system service regulations) steps to improve containment of these gases from working devices could effectively reduce their release to the atmosphere

Modelling the growth of atmospheric nitrous oxide using a global hierarchical inversion

Nitrous oxide is a potent greenhouse gas (GHG) and ozone-depleting substance, whose atmospheric abundance has risen throughout the contemporary record. In this work, we carry out the first global hierarchical Bayesian inversion to solve for nitrous oxide emissions, which includes prior emissions with truncated Gaussian distributions and Gaussian model errors, in order to examine the drivers of the atmospheric surface growth rate. We show that both emissions and climatic variability are key drivers of variations in the surface nitrous oxide growth rate between 2011 and 2020. We derive increasing global nitrous oxide emissions, which are mainly driven by emissions between 0 and 30∘ N, with the highest emissions recorded in 2020. Our mean global total emissions for 2011–2020 of 17.2 (16.7–17.7 at the 95 % credible intervals) Tg N yr−1, comprising of 12.0 (11.2–12.8) Tg N yr−1 from land and 5.2 (4.5–5.9) Tg N yr−1 from ocean, agrees well with previous studies, but we find that emissions are poorly constrained for some regions of the world, particularly for the oceans. The prior emissions used in this and other previous work exhibit a seasonal cycle in the extra-tropical Northern Hemisphere that is out of phase with the posterior solution, and there is a substantial zonal redistribution of emissions from the prior to the posterior. Correctly characterizing the uncertainties in the system, for example in the prior emission fields, is crucial for deriving posterior fluxes that are consistent with observations. In this hierarchical inversion, the model-measurement discrepancy and the prior flux uncertainty are informed by the data, rather than solely through “expert judgement”. We show cases where this framework provides different plausible adjustments to the prior fluxes compared to inversions using widely adopted, fixed uncertainty constraints.</p

Modelling the growth of atmospheric nitrous oxide using a global hierarchical inversion

Nitrous oxide is a potent greenhouse gas (GHG) and ozone-depleting substance, whose atmospheric abundance has risen throughout the contemporary record. In this work, we carry out the first global hierarchical Bayesian inversion to solve for nitrous oxide emissions, which includes prior emissions with truncated Gaussian distributions and Gaussian model errors, in order to examine the drivers of the atmospheric surface growth rate. We show that both emissions and climatic variability are key drivers of variations in the surface nitrous oxide growth rate between 2011 and 2020. We derive increasing global nitrous oxide emissions, which are mainly driven by emissions between 0 and 30∘ N, with the highest emissions recorded in 2020. Our mean global total emissions for 2011–2020 of 17.2 (16.7–17.7 at the 95 % credible intervals) Tg N yr−1, comprising of 12.0 (11.2–12.8) Tg N yr−1 from land and 5.2 (4.5–5.9) Tg N yr−1 from ocean, agrees well with previous studies, but we find that emissions are poorly constrained for some regions of the world, particularly for the oceans. The prior emissions used in this and other previous work exhibit a seasonal cycle in the extra-tropical Northern Hemisphere that is out of phase with the posterior solution, and there is a substantial zonal redistribution of emissions from the prior to the posterior. Correctly characterizing the uncertainties in the system, for example in the prior emission fields, is crucial for deriving posterior fluxes that are consistent with observations. In this hierarchical inversion, the model-measurement discrepancy and the prior flux uncertainty are informed by the data, rather than solely through “expert judgement”. We show cases where this framework provides different plausible adjustments to the prior fluxes compared to inversions using widely adopted, fixed uncertainty constraints.</p

Developments in Agricultural Soil Quality and Health: Reflections by the Research Committee on Soil Organic Matter Management

The North Central Education and Research Activity Committee (NCERA-59) was formed in 1952 to address how soil organic matter formation and management practices affect soil structure and productivity. It is in this capacity that we comment on the science supporting soil quality and associated soil health assessment for agricultural lands with the goal of hastening progress in this important field. Even though the suite of soil quality indicators being applied by U.S. soil health efforts closely mirrors the “minimum data set” we developed and recommended in the mid-1990s, we question whether the methods or means for their selection and development are sufficient to meet current and emerging soil health challenges. The rush to enshrine a standard suite of dated measures may be incompatible with longer-term goals. Legitimate study of soil health considers soil change accrued over years to decades that influence on- and off-site function. Tailoring of methods to local conditions is needed to effectively apply and interpret indicators for different soil resource regions and land uses. Adherence to a set suite of methods selected by subjective criteria should be avoided, particularly when we do not yet have adequate data or agreed upon interpretive frameworks for many so-called “Tier 1” biological indicators used in soil health assessment. While pooling data collected by producer-groups is one of the most exciting new trends in soil health, standardizing methods to meet broad inventory goals could compromise indicator use for site or application-specific problem solving. Changes in our nation’s research landscape are shifting responsibility for soil stewardship from national and state government backed entities to public-private partnerships. As a result, it is critical to ensure that the data needed to assess soil health are generated by reproducible methods selected through a transparent process, and that data are readily available for public and private sector use. Appropriate methods for engagement need to be applied by public-private research partnerships as they establish and expand coordinated research enterprises that can deliver fact-based interpretation of soil quality indicators within the type of normative soil health framework conceived by USDA over 20 years ago. We look to existing examples as we consider how to put soil health information into the hands of practitioners in a manner that protects soils’ services

Developments in Agricultural Soil Quality and Health: Reflections by the Research Committee on Soil Organic Matter Management

The North Central Education and Research Activity Committee (NCERA-59) was formed in 1952 to address how soil organic matter formation and management practices affect soil structure and productivity. It is in this capacity that we comment on the science supporting soil quality and associated soil health assessment for agricultural lands with the goal of hastening progress in this important field. Even though the suite of soil quality indicators being applied by U.S. soil health efforts closely mirrors the “minimum data set” we developed and recommended in the mid-1990s, we question whether the methods or means for their selection and development are sufficient to meet current and emerging soil health challenges. The rush to enshrine a standard suite of dated measures may be incompatible with longer-term goals. Legitimate study of soil health considers soil change accrued over years to decades that influence on- and off-site function. Tailoring of methods to local conditions is needed to effectively apply and interpret indicators for different soil resource regions and land uses. Adherence to a set suite of methods selected by subjective criteria should be avoided, particularly when we do not yet have adequate data or agreed upon interpretive frameworks for many so-called “Tier 1” biological indicators used in soil health assessment. While pooling data collected by producer-groups is one of the most exciting new trends in soil health, standardizing methods to meet broad inventory goals could compromise indicator use for site or application-specific problem solving. Changes in our nation’s research landscape are shifting responsibility for soil stewardship from national and state government backed entities to public-private partnerships. As a result, it is critical to ensure that the data needed to assess soil health are generated by reproducible methods selected through a transparent process, and that data are readily available for public and private sector use. Appropriate methods for engagement need to be applied by public-private research partnerships as they establish and expand coordinated research enterprises that can deliver fact-based interpretation of soil quality indicators within the type of normative soil health framework conceived by USDA over 20 years ago. We look to existing examples as we consider how to put soil health information into the hands of practitioners in a manner that protects soils’ services