High-throughput comparison of gene fitness among related bacteria

BACKGROUND: The contribution of a gene to the fitness of a bacterium can be assayed by whether and to what degree the bacterium tolerates transposon insertions in that gene. We use this fact to compare the fitness of syntenic homologous genes among related Salmonella strains and thereby reveal differences not apparent at the gene sequence level. RESULTS: A transposon Tn5 derivative was used to construct mutants in Salmonella Typhimurium ATCC14028 (STM1) and Salmonella Typhi Ty2 (STY1), which were then grown in rich media. The locations of 234,152 and 53,556 integration sites, respectively, were mapped by sequencing. These data were compared to similar data available for a different Ty2 isolate (STY2) and essential genes identified in E. coli K-12 (ECO). Of 277 genes considered essential in ECO, all had syntenic homologs in STM1, STY1, and STY2, and all but nine genes were either devoid of transposon insertions or had very few. For three of these nine genes, part of the annotated gene lacked transposon integrations (yejM, ftsN and murB). At least one of the other six genes, trpS, had a potentially functionally redundant gene encoded elsewhere in Salmonella but not in ECO. An additional 165 genes were almost entirely devoid of transposon integrations in all three Salmonella strains examined, including many genes associated with protein and DNA synthesis. Four of these genes (STM14_1498, STM14_2872, STM14_3360, and STM14_5442) are not found in E. coli. Notable differences in the extent of gene selection were also observed among the three different Salmonella isolates. Mutations in hns, for example, were selected against in STM1 but not in the two STY strains, which have a defect in rpoS rendering hns nonessential. CONCLUSIONS: Comparisons among transposon integration profiles from different members of a species and among related species, all grown in similar conditions, identify differences in gene contributions to fitness among syntenic homologs. Further differences in fitness profiles among shared genes can be expected in other selective environments, with potential relevance for comparative systems biology

Characterization of Queso Fresco during Storage at 4 and 10°C

Abstract Queso Fresco, a popular Hispanic cheese variety, was prepared and its chemical, rheological, textural, functional, and sensory aspects were evaluated during storage at 4 and 10°C to determine changes in quality. Decreases in lactose and pH levels were observed and attributed to activity by spoilage microorganisms. The appearance of volatile compounds derived from lipids indicated that lipolysis was taking place, and some proteolysis was also noted. Minor variations in texture profile, torsion, color, and melt analyses were seen throughout 8 wk of storage. No microstructural changes were observed. A consumer taste panel generally liked laboratory-made and two commercially-made cheeses, and could not distinguish one of the commercial samples from the laboratory sample. The results provide a basis for assessing the quality traits of Queso Fresco during storage

The Fermi GBM Gamma-Ray Burst Spectral Catalog: Four Years Of Data

In this catalog we present the updated set of spectral analyses of GRBs detected by the Fermi Gamma-Ray Burst Monitor (GBM) during its first four years of operation. It contains two types of spectra, time-integrated spectral fits and spectral fits at the brightest time bin, from 943 triggered GRBs. Four different spectral models were fitted to the data, resulting in a compendium of more than 7500 spectra. The analysis was performed similarly, but not identically to Goldstein et al. 2012. All 487 GRBs from the first two years have been re-fitted using the same methodology as that of the 456 GRBs in years three and four. We describe, in detail, our procedure and criteria for the analysis, and present the results in the form of parameter distributions both for the observer-frame and rest-frame quantities. The data files containing the complete results are available from the High-Energy Astrophysics Science Archive Research Center (HEASARC).Comment: Accepted for publication in ApJ

National CO\u3csub\u3e2\u3c/sub\u3e budgets (2015-2020) inferred from atmospheric CO\u3csub\u3e2\u3c/sub\u3e observations in support of the global stocktake

Accurate accounting of emissions and removals of CO2 is critical for the planning and verification of emission reduction targets in support of the Paris Agreement. Here, we present a pilot dataset of country-specific net carbon exchange (NCE; fossil plus terrestrial ecosystem fluxes) and terrestrial carbon stock changes aimed at informing countries\u27 carbon budgets. These estimates are based on top-down NCE outputs from the v10 Orbiting Carbon Observatory (OCO-2) modeling intercomparison project (MIP), wherein an ensemble of inverse modeling groups conducted standardized experiments assimilating OCO-2 column-Averaged dry-Air mole fraction (XCO2) retrievals (ACOS v10), in situ CO2 measurements or combinations of these data. The v10 OCO-2 MIP NCE estimates are combined with bottom-up estimates of fossil fuel emissions and lateral carbon fluxes to estimate changes in terrestrial carbon stocks, which are impacted by anthropogenic and natural drivers. These flux and stock change estimates are reported annually (2015-2020) as both a global 1gg×g1g gridded dataset and a country-level dataset and are available for download from the Committee on Earth Observation Satellites\u27 (CEOS) website: 10.48588/npf6-sw92 . Across the v10 OCO-2 MIP experiments, we obtain increases in the ensemble median terrestrial carbon stocks of 3.29-4.58gPgCO2yr-1 (0.90-1.25gPgCyr-1). This is a result of broad increases in terrestrial carbon stocks across the northern extratropics, while the tropics generally have stock losses but with considerable regional variability and differences between v10 OCO-2 MIP experiments. We discuss the state of the science for tracking emissions and removals using top-down methods, including current limitations and future developments towards top-down monitoring and verification systems

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine

[This corrects the article DOI: 10.1186/s13054-016-1208-6.]

Morphodynamic trends of the Ribb River, Ethiopia, prior to dam construction

The meandering Ribb River flows in northwest Ethiopia to Lake Tana, the source of the Blue Nile River. The river has already undergone changes due to several human interventions, such as embanking, sand mining, water extraction and lake level regulation for hydropower. At present, a dam and a weir are under construction to store and divert water for irrigation. This will strongly alter both water and sediment discharges to the downstream river reaches, causing adjustments to the morphology. Assessing the current morphodynamic trends is the first necessary step to study the future effects and find ways to mitigate them. This paper presents an analysis of the current and past river based on newly collected data, aerial photographs, SPOT and Google Earth images. The riverbed changes are derived from historical staff gauge height analysis. The effects of sediment mining and water extraction are assessed using the theory of morphodynamic equilibrium. The findings of the analysis show a reduction of sediment transport capacity in the downstream direction, which has resulted in intense sediment deposition, resulting in blockage of the Lower River reach and subsequent channel avulsion. The effects of Lake Tana level regulation on the observed processes appear to be minor.Water ResourcesEnvironmental Fluid Mechanic

Incrementally baked global illumination

Global Illumination is affected by the slightest change in a 3D scene, requiring a complete reevaluation of the distributed light. In cases where real-time algorithms are not applicable due to high demands on the achievable accuracy, this recomputation from scratch results in artifacts like flickering or noise, disturbing the visual appearance and negatively affecting interactive lighting design workflows. We propose a novel system tackling this problem by providing incremental updates of a baked global illumination solution after scene modifications, and a re-convergence after a few seconds. Using specifically targeted incremental data structures and prioritization strategies in a many-light global illumination algorithm, we compute a differential update from one illumination state to another. We further demonstrate the use of a novel error balancing strategy making it possible to prioritize the illumination updates.Comp Graphics & Visualisatio

Graphene Isotope Superlattices with Strongly Diminished Thermal Conductivity for Thermoelectric Applications

Graphene has a high intrinsic thermal conductivity and a high electron mobility. The thermal conductivity of graphene can be significantly reduced when different carbon isotopes are mixed, which can enhance the performance of thermoelectric devices. Here we synthesize isotopic 12C/13C random mixes and isotope superlattices (SLs) with periods ranging from 46 to 225 nm by chemical vapor deposition. Raman optothermal conductivity measurements of these SL structures show an approximately 50% reduction in thermal conductivity compared to pristine 12C graphene. This average reduction is similar to the random isotope mix. The reduction of the thermal conductivity in the SL is well described by a model of pristine graphene and an additional quasi-one-dimensional periodic interfacial thermal resistance of (2.5 ± 0.5) × 10-11 m2 K W-1 for the 12C/13C boundary. This is consistent with a large anisotropic thermal conductivity in the SL, where the thermal conductivity depends on the orientation of the 12C/13C boundary. Accepted Author ManuscriptQN/Steeneken La

Real-space Raman spectroscopy of graphene isotope superlattices

We report the Raman spectroscopy of C12/C13 graphene isotope superlattices (SLs) synthesized by chemical vapor deposition. At large periods the Raman spectrum corresponds to the sum of the bulk C12 and C13 contributions. However, at small periods we observe the formation of mixed C12/C13 modes for Raman processes that involve two phonons, which results in the tripling of the 2D and 2D′ Raman peaks. This tripling can be well understood in the framework of real-space Raman spectroscopy, where the two emitted phonons stem from different regions of the SL. The intensity of the mixed peak increases as the SL half-period approaches the mean free path of the photoexcited electron-hole pairs. By varying the SL period between 6 and 225 nm we have a direct measure of the photoexcited electron mean free path, which is found to be 18 nm for suspended graphene and 7 nm for graphene on SiO2 substrates.QN/Steeneken La