Bacteria in the 16S rRNA clade SAR86 are among the most abundant uncultivated constituents of microbial assemblages in the surface ocean for which little genomic information is currently available. ...Bioinformatic techniques were used to assemble two nearly complete genomes from marine metagenomes and single-cell sequencing provided two more partial genomes. Recruitment of metagenomic data shows that these SAR86 genomes substantially increase our knowledge of non-photosynthetic bacteria in the surface ocean. Phylogenomic analyses establish SAR86 as a basal and divergent lineage of γ-proteobacteria, and the individual genomes display a temperature-dependent distribution. Modestly sized at 1.25-1.7 Mbp, the SAR86 genomes lack several pathways for amino-acid and vitamin synthesis as well as sulfate reduction, trends commonly observed in other abundant marine microbes. SAR86 appears to be an aerobic chemoheterotroph with the potential for proteorhodopsin-based ATP generation, though the apparent lack of a retinal biosynthesis pathway may require it to scavenge exogenously-derived pigments to utilize proteorhodopsin. The genomes contain an expanded capacity for the degradation of lipids and carbohydrates acquired using a wealth of tonB-dependent outer membrane receptors. Like the abundant planktonic marine bacterial clade SAR11, SAR86 exhibits metabolic streamlining, but also a distinct carbon compound specialization, possibly avoiding competition.
Planktonic Marine Archaea Santoro, Alyson E; Richter, R. Alexander; Dupont, Christopher L
Annual review of marine science,
01/2019, Letnik:
11, Številka:
1
Journal Article
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Archaea are ubiquitous and abundant members of the marine plankton. Once thought of as rare organisms found in exotic extremes of temperature, pressure, or salinity, archaea are now known in nearly ...every marine environment. Though frequently referred to collectively, the planktonic archaea actually comprise four major phylogenetic groups, each with its own distinct physiology and ecology. Only one group-the marine Thaumarchaeota-has cultivated representatives, making marine archaea an attractive focus point for the latest developments in cultivation-independent molecular methods. Here, we review the ecology, physiology, and biogeochemical impact of the four archaeal groups using recent insights from cultures and large-scale environmental sequencing studies. We highlight key gaps in our knowledge about the ecological roles of marine archaea in carbon flow and food web interactions. We emphasize the incredible uncultivated diversity within each of the four groups, suggesting there is much more to be done.
Enhancing Photorealism Enhancement Richter, Stephan R.; Alhaija, Hassan Abu; Koltun, Vladlen
IEEE transactions on pattern analysis and machine intelligence,
2023-Feb.-1, 2023-Feb, 2023-2-1, 20230201, Letnik:
45, Številka:
2
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We present an approach to enhancing the realism of synthetic images. The images are enhanced by a convolutional network that leverages intermediate representations produced by conventional rendering ...pipelines. The network is trained via a novel adversarial objective, which provides strong supervision at multiple perceptual levels. We analyze scene layout distributions in commonly used datasets and find that they differ in important ways. We hypothesize that this is one of the causes of strong artifacts that can be observed in the results of many prior methods. To address this we propose a new strategy for sampling image patches during training. We also introduce multiple architectural improvements in the deep network modules used for photorealism enhancement. We confirm the benefits of our contributions in controlled experiments and report substantial gains in stability and realism in comparison to recent image-to-image translation methods and a variety of other baselines.
A highly enantioselective and diastereoselective total synthesis of the diterpenoid (−)-mitrephorone A is presented. Key to the synthesis are stereocontrolled 1,4-semihydrogenation of a 1,3-diene ...to a tetrasubstituted double bond, enzyme-catalyzed malonate desymmetrization, and highly diastereoselective nitrile oxide cycloaddition. The streamlined strategy is a considerable improvement to those reported earlier in terms of diastereo- and enantioselectivity. For the first time, the combination of modern Pd-cross-coupling with Cr-catalyzed reduction allows for rapid access to tetrasubstituted olefins with full stereocontrol.
Design and synthesis of a minimal bacterial genome Hutchison, Clyde A.; Chuang, Ray-Yuan; Noskov, Vladimir N. ...
Science (American Association for the Advancement of Science),
03/2016, Letnik:
351, Številka:
6280
Journal Article
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We used whole-genome design and complete chemical synthesis to minimize the 1079-kilobase pair synthetic genome of Mycoplasma mycoides JCVI-syn1.0. An initial design, based on collective knowledge of ...molecular biology combined with limited transposon mutagenesis data, failed to produce a viable cell. Improved transposon mutagenesis methods revealed a class of quasi-essential genes that are needed for robust growth, explaining the failure of our initial design. Three cycles of design, synthesis, and testing, with retention of quasi-essential genes, produced JCVI-syn3.0 (531 kilobase pairs, 473 genes), which has a genome smaller than that of any autonomously replicating cell found in nature. JCVI-syn3.0 retains almost all genes involved in the synthesis and processing of macromolecules. Unexpectedly, it also contains 149 genes with unknown biological functions. JCVI-syn3.0 is a versatile platform for investigating the core functions of life and for exploring whole-genome design.
Thaumarchaeota are among the most abundant microbial cells in the ocean, but difficulty in cultivating marine Thaumarchaeota has hindered investigation into the physiological and evolutionary basis ...of their success. We report here a closed genome assembled from a highly enriched culture of the ammonia-oxidizing pelagic thaumarchaeon CN25, originating from the open ocean. The CN25 genome exhibits strong evidence of genome streamlining, including a 1.23-Mbp genome, a high coding density, and a low number of paralogous genes. Proteomic analysis recovered nearly 70% of the predicted proteins encoded by the genome, demonstrating that a high fraction of the genome is translated. In contrast to other minimal marine microbes that acquire, rather than synthesize, cofactors, CN25 encodes and expresses near-complete biosynthetic pathways for multiple vitamins. Metagenomic fragment recruitment indicated the presence of DNA sequences >90% identical to the CN25 genome throughout the oligotrophic ocean. We propose the provisional name "Candidatus Nitrosopelagicus brevis" str. CN25 for this minimalist marine thaumarchaeon and suggest it as a potential model system for understanding archaeal adaptation to the open ocean.
PM1 (particulate matter with an aerodynamic diameter <1 μm) non-refractory components and black carbon were measured continuously together with additional air quality and atmospheric parameters at an ...urban background site in Barcelona, Spain, during March 2009 (campaign DAURE, Determination of the sources of atmospheric Aerosols in Urban and Rural Environments in the western Mediterranean). Positive matrix factorization (PMF) was conducted on the organic aerosol (OA) data matrix measured by an aerosol mass spectrometer, on both unit mass (UMR) and high resolution (HR) data. Five factors or sources could be identified: LV-OOA (low-volatility oxygenated OA), related to regional, aged secondary OA; SV-OOA (semi-volatile oxygenated OA), a fresher oxygenated OA; HOA (hydrocarbon-like OA, related to traffic emissions); BBOA (biomass burning OA) from domestic heating or agricultural biomass burning activities; and COA (cooking OA). LV-OOA contributed 28% to OA, SV-OOA 27%, COA 17%, HOA 16%, and BBOA 11%. The COA HR spectrum contained substantial signal from oxygenated ions (O:C: 0.21) whereas the HR HOA spectrum had almost exclusively contributions from chemically reduced ions (O:C: 0.03). If we assume that the carbon in HOA is fossil while that in COA and BBOA is modern, primary OA in Barcelona contains a surprisingly high fraction (59%) of non-fossil carbon. This paper presents a method for estimating cooking organic aerosol in ambient datasets based on the fractions of organic mass fragments at m/z 55 and 57: their data points fall into a V-shape in a scatter plot, with strongly influenced HOA data aligned to the right arm and strongly influenced COA data points aligned to the left arm. HR data show that this differentiation is mainly driven by the oxygen-containing ions C3H3O+ and C3H5O+, even though their contributions to m/z 55 and 57 are low compared to the reduced ions C4H7+ and C4H9+. A simple estimation method based on the markers m/z 55, 57, and 44 is developed here and allows for a first-order-estimation of COA in urban air. This study emphasizes the importance of cooking activities for ambient air quality and confirms the importance of chemical composition measurements with a high mass and time resolution.
A network of brain regions have been linked with episodic memory retrieval, but limited progress has been made in identifying the contributions of distinct parts of the network. Here, we utilized ...continuous measures of retrieval to dissociate three components of episodic memory: retrieval success, precision, and vividness. In the fMRI scanner, participants encoded objects that varied continuously on three features: color, orientation, and location. Participants' memory was tested by having them recreate the appearance of the object features using a continuous dial, and continuous vividness judgments were recorded. Retrieval success, precision, and vividness were dissociable both behaviorally and neurally: successful versus unsuccessful retrieval was associated with hippocampal activity, retrieval precision scaled with activity in the angular gyrus, and vividness judgments tracked activity in the precuneus. The ability to dissociate these components of episodic memory reveals the benefit afforded by measuring memory on a continuous scale, allowing functional parcellation of the retrieval network.
Ocean-derived, airborne microbes play important roles in Earth's climate system and human health, yet little is known about factors controlling their transfer from the ocean to the atmosphere. Here, ...we study microbiomes of isolated sea spray aerosol (SSA) collected in a unique ocean-atmosphere facility and demonstrate taxon-specific aerosolization of bacteria and viruses. These trends are conserved within taxonomic orders and classes, and temporal variation in aerosolization is similarly shared by related taxa. We observe enhanced transfer into SSA of Actinobacteria, certain Gammaproteobacteria, and lipid-enveloped viruses; conversely, Flavobacteriia, some Alphaproteobacteria, and Caudovirales are generally under-represented in SSA. Viruses do not transfer to SSA as efficiently as bacteria. The enrichment of mycolic acid-coated Corynebacteriales and lipid-enveloped viruses (inferred from genomic comparisons) suggests that hydrophobic properties increase transport to the sea surface and SSA. Our results identify taxa relevant to atmospheric processes and a framework to further elucidate aerosolization mechanisms influencing microbial and viral transport pathways.
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