Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities
. Exploration of this vast sequence space has been limited to a comparative analysis ...against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database
. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.
Excess phytoplankton production, which contributes to hypoxic conditions, is nitrogen limited in the Chesapeake Bay during the summer months. Therefore, understanding the flux of ammonia by direct ...deposition to the biologically active surface layer is critical to understanding the nutrient dynamics of the bay. This paper presents the results of a 2-yr study measuring gaseous ammonia (NH3) and aerosol ammonium (NH4 +) in Baltimore and Solomons, MD, from which direct atmospheric loading of total ammonia (Nt = NH3 + NH4 +) to the Chesapeake Bay is estimated. Mean atmospheric concentrations of total ammonia for Baltimore and Solomons were 2.7 ± 1.7 and 1.0 ± 0.8 μg of N m-3, respectively. Monte Carlo estimates of gross dry deposition ranged from <100 to 4900 μg of N m-2 d-1. However, based upon water quality parameters, Monte Carlo estimates of gross volatilization of NH3 were calculated to range from <100 to 7700 μg of N m-2 d-1. The resulting net air−sea exchange flux varied seasonally from a net deposition into the water during the winter to a net volatilizing into the atmosphere during the summer. A total of 60% of the paired air−water samples had flux estimates that were not significantly different than equilibrium at the 90% confidence interval. The gross deposition, gross volatilization, and net air−sea fluxes were greater and more variable in Baltimore relative to the rural site. Atmospheric ammonia concentrations decrease during the winter at the rural site. However, the net exchange is still into the water due to an exponential decrease in NH3eq with temperature. These results indicate that the nitrogen-limited Chesapeake Bay can act as a source of ammonia to the local atmosphere.
Polycyclic aromatic hydrocarbons (PAHs), mutagenic compounds predominantly derived from combustion, have been used as markers of combustion sources to the atmosphere. Marine aerosol collected aboard ...the NOAA R/V Ronald Brown during the Aerosols99 and the Indian Ocean Experiment (INDOEX) projects was analyzed for PAHs to assess the continental impact of combustion‐derived particulate matter on the Atlantic and Indian Ocean atmospheres. PAH concentrations in the Atlantic and southern Indian Ocean atmospheres were consistent and low, ranging from <0.45 pg/m3 for coronene to 30 pg/m3 for 9, 10‐dimethylanthracene. PAH concentrations increased ten fold as the ship crossed the Intertropical Convergence Zone (ITCZ) into the northern Indian Ocean, indicating an increased anthropogenic influence. PAH concentrations over the northern Indian Ocean atmosphere were approximately an order of magnitude greater than those in the northern Atlantic Ocean atmosphere. PAH composition profiles over the northern Indian Ocean were specific to wind regimes and influenced by a combination of biomass and fossil fuel combustion. This was supported by significant correlations between select PAHs and organic carbon (OC), elemental carbon (EC), SO4−2 and K+ for particular wind regimes. Indeno1,2,3‐cdpyrene/EC ratios used as a combustion source marker suggest that fossil fuel combustion, rather than biomass burning, is the predominant source of PAHs to the Northern Hemisphere Indian Ocean atmosphere. Interestingly, fossil fuel consumption in the Indian sub‐continent is a fraction of that in Europe and the United States but the soot and PAH levels in the adjacent Northern Indian Ocean atmosphere are significantly greater than those in the Northern Atlantic atmosphere.
Boundary spanning is a focused effort to facilitate the exchange of knowledge and information between producers (i.e., analysts, scientists, researchers, etc.) and users (i.e., decision-makers, ...policy makers, managers, etc.) in support of evidence-informed decision-making. Here we provide specific examples of approaches and products by a boundary spanning organization as part of a regional ecosystem-based management program. These examples illustrate a range of potential boundary spanning activities while also describing a more holistic boundary system that employs several complimentary and related approaches to improve the use of knowledge in decision-making across interfaces separating different institutions. This system is supported by, and indeed requires, a larger institutional framework that provides scaffolding upon which the boundary spanning operates. As described, the institutional framework is often not supplied solely by a single boundary spanning organization, but rather by a suite of cooperating institutions. Last, we discuss approaches to evaluating the various impacts of boundary spanning.
•Boundary spanning systems provide multiple opportunities to improve knowledge use.•Vignettes illustrate range of approaches to cross diverse institutional interfaces.•Coordinating institutions create a framework to support boundary spanning.•Alternative measure of boundary spanning impacts should be considered.
Lake Superior's food web was analyzed in 1994 for hydrophobic organochlorine contaminants (OCs) including toxaphene, chlordane and metabolites, hexachlorocyclohexanes, hexachlorobenzene, dieldrin, ...and polychlorinated biphenyl congeners. Toxaphene was the dominant organochlorine contaminant in the Lake Superior food web, with concentrations 2−15 times higher than total PCBs. Among the biota studied, wet weight toxaphene levels were highest in bloaters (Coregonus hoyi) at 1100 ± 270 ng/g (mean ± 1 standard deviation) and lowest in Mysis relicta (32 ± 804 ng/g). Total PCB concentrations ranged more than a factor of 20 on a wet weight basis but less than a factor of 6 on a lipid weight basis. The lipid content of the organisms explains 81% of the variability in wet weight t-PCB, with trophic position exerting a smaller influence. Using path analysis and regression techniques, the main influence of trophic position on t-PCBs was shown to be due to the concurrent increase in lipid content with trophic position. The relative distributions of organochlorines among trophic levels were very similar, despite the 3 orders of magnitude range in OC hydrophobicity. Unlike our work in Lake Baikal, the accumulation of OCs in the Lake Superior food web was not significantly (p < 0.05) related to the log octanol/water (K ow) partition coefficient, suggesting either that organochlorines in this food web equilibrate with surrounding dissolved OCs rapidly relative to dietary uptake or that the OC assimilation efficiency of predators does not vary with log K ow. Based on OC concentrations in benthic amphipods, we conclude that settling particles are an important source of OCs to deep water organisms in Lake Superior.
Concentrations of 14 polycyclic aromatic hydrocarbons (PAH) and 35 polychlorinated biphenyls (PCB) were measured in the surface waters and atmosphere of Superior lake to estimate the direction and ...magnitude of their fluxes across the air-water interface. Total atmospheric PCB and PAH concentrations were 1.2 and 3.9 ng per m3, respectively. Fugacity gradients, compound-specific equilibrium and mass-transfer parameters were measured. Superior lake was degassing organic contaminants during the summer months. Mean volatilization fluxes of total PCB (19 ng per m2.day) were similar to estimates of gross atmospheric deposition to the lake. This supported the hypothesis of nonequilibrium steady-state PCB exchange across the air-water interface. There is a bibliography of 64 references.
Objectives To examine the distribution of birth weight in children with nonalcoholic fatty liver disease (NAFLD) compared with the general US population, and to investigate the relationship between ...birth weight and severity of NAFLD. Study design A multicenter, cross-sectional study of children with biopsy-proven NAFLD enrolled in the Nonalcoholic Steatohepatitis Clinical Research Network Database. Birth weight was categorized as low birth weight (LBW), normal birth weight (NBW), or high birth weight (HBW) and compared with the birth weight distribution in the general US population. The severity of liver histology was assessed by birth weight category. Results Children with NAFLD (n = 538) had overrepresentation of both LBW and HBW compared with the general US population (LBW, 9.3%; NBW, 75.8%; HBW, 14.9% vs LBW, 6.1%; NBW, 83.5%; HBW 10.5%; P < .0001). Children with HBW had significantly greater odds of having more severe steatosis (OR, 1.82, 95% CI. 1.15-2.88) and nonalcoholic steatohepatitis (OR, 2.03; 95% CI, 1.21-3.40) compared with children with NBW. In addition, children with NAFLD and LBW had significantly greater odds of having advanced fibrosis (OR, 2.23; 95% CI, 1.08-4.62). Conclusion Birth weight involves maternal and in utero factors that may have long-lasting consequences. Children with both LBW and HBW may be at increased risk for developing NAFLD. Among children with NAFLD, those with LBW or HBW appear to be at increased risk for more severe disease.
Objective: Success of achalasia therapy is difficult to determine because repeated physiologic study is impractical and symptoms are subjective. Timed barium esophagography directly measures ...esophageal emptying and is simple to perform. This study (1) evaluates the assessment of myotomy by timed barium esophagography and (2) compares it with premyotomy and postmyotomy symptoms. Methods: Fifty patients ingested 250 mL low-density barium and had upright films at 1, 2, and 5 minutes premyotomy. Forty-five underwent repeat timed barium esophagography 8 weeks (median) postmyotomy. Premyotomy and postmyotomy height and width of the barium column were compared and related to symptoms. Results: At 1, 2, and 5 minutes premyotomy, median barium column height was 19, 17, and 15 cm, and width was 5.2, 4.8, and 4.5 cm, respectively. Surgery reduced these to 7.0, 5.0, and 1.0 cm and to 3.5, 3.0, and 1.0 cm, respectively (P <.001). Postmyotomy complete esophageal emptying was seen in 29%, 36%, and 49% at 1, 2, and 5 minutes. Postmyotomy height was unrelated (r ~ 0.2) to premyotomy height but was directly related to premyotomy width (r = 0.3-0.5; P <.05); postmyotomy width was directly related to premyotomy width (r ~ 0.6; P <.001). Premyotomy dysphagia was more severe when little change in width occurred from 1 to 5 minutes (r = 0.26, P =.07). Premyotomy regurgitation was more severe the higher the barium column (r ~ 0.4, P <.007). Surgery relieved symptoms in the majority of patients (grade 2-5 dysphagia from 72% to 4%, grade 2-5 regurgitation from 79% to 4%). Postmyotomy symptoms were unrelated to the timed barium esophagogram. Conclusions: (1) The timed barium esophagogram gives objective confirmation of successful myotomy. (2) Symptoms are unreliable in assessing esophageal emptying. (J Thorac Cardiovasc Surg 2000;120:935-46)
Urban-industrial areas exhibit atmospheric concentrations of organic contaminants that are often > 5−10× regional background. Increased emissions of PCBs into the urban-industrial atmosphere leads to ...enhanced depositional fluxes to proximate waters. In this study, the increased air−water exchange inputs of PCB congeners into southern Lake Michigan driven by elevated atmospheric concentrations emanating from the Chicago, IL/Gary, IN air plume was studied. Intensive experiments were conducted in May and July 1994 and January 1995. The gaseous ΣPCB concentrations at the overlake site 15-km from Chicago ranged from 132 to 1120 pg/m3 with higher concentrations occurring in warm periods and when winds were from southerly and westerly quadrants. Dissolved phase ΣPCB concentrations ranged from 48 to 302 pg/L with concentrations in winter ∼2.5× higher than summer concentrations. Instantaneous net air−water exchange fluxes ranged from −32 (absorption) to + 59 ng/m2-d with absorptive flux highest in summer when winds were from the urban area and gas-phase concentrations were highest. Air and surface water temperatures and wind direction were the dominant factors influencing the magnitude and direction of air−water exchange fluxes. The modeled net air−water exchange flux of ΣPCB in the southern quarter of Lake Michigan was −18 ug/m2-yr (net absorption) in 1994, corresponding to 140 kg/yr net input.
Myotomy for achalasia disrupts the lower esophageal sphincter, improving emptying at the expense of reflux. We hypothesized that surgical palliation of achalasia requires balancing desirable ...improvement in esophageal emptying with undesirable production of gastroesophageal reflux. Therefore, we objectively studied the physiologic effects of adding Dor fundoplication to Heller myotomy.
From December 1996 to June 2004, 149 patients underwent Heller myotomy; 88 (59%) had additional Dor fundoplication. The adequacy of myotomy was assessed by premyotomy to postmyotomy change in lower esophageal sphincter pressures, esophageal emptying by change in timed barium esophagram, and gastroesophageal reflux by postoperative 24-hour pH monitoring.
For adequacy of myotomy, postmyotomy resting lower esophageal sphincter pressure was higher with (median, 18 mm Hg) than without (median, 13 mm Hg) Dor fundoplication (
P = .002), as was residual lower esophageal sphincter pressure (median, 4.6 vs 1.8 mm Hg;
P = .01). For esophageal emptying, postmyotomy barium height and width were similar with or without Dor fundoplication (
P > .1). For gastroesophageal reflux, percentage of upright time with a pH of less than 4 was lower with (median, 0.4%) than without (median, 2.9%) Dor fundoplication (
P = .005), and percentage of supine time with a pH of less than 4 was lower with (median, 0%) than without (median, 5.8%) Dor fundoplication (
P = .007).
The addition of Dor fundoplication reduces the adequacy of myotomy without impairing emptying and reduces reflux. Heller myotomy and Dor fundoplication balance emptying and reflux and therefore should be the surgical treatment of choice for achalasia.
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