Recent technological advancements have enabled the profiling of a large number of genome-wide features in individual cells. However, single-cell data present unique challenges that require the ...development of specialized methods and software infrastructure to successfully derive biological insights. The Bioconductor project has rapidly grown to meet these demands, hosting community-developed open-source software distributed as R packages. Featuring state-of-the-art computational methods, standardized data infrastructure and interactive data visualization tools, we present an overview and online book (https://osca.bioconductor.org) of single-cell methods for prospective users.
Plasma discharges with a negative triangularity (δ=-0.4) shape have been created in the DIII-D tokamak with a significant normalized beta (β_{N}=2.7) and confinement characteristic of the high ...confinement mode (H_{98y2}=1.2) despite the absence of an edge pressure pedestal and no edge localized modes (ELMs). These inner-wall-limited plasmas have a similar global performance as a positive triangularity (δ=+0.4) ELMing H-mode discharge with the same plasma current, elongation and cross sectional area. For cases both of dominant electron cyclotron heating with T_{e}/T_{i}>1 and dominant neutral beam injection heating with T_{e}/T_{i}=1, turbulent fluctuations over radii 0.5<ρ<0.9 were reduced by 10-50% in the negative triangularity shape compared to the matching positive triangularity shape, depending on the radius and conditions.
Hypervirulent K. pneumoniae (hvKp) is a distinct pathotype that causes invasive community-acquired infections in healthy individuals. Hypermucoviscosity (hmv) is a major phenotype associated with ...hvKp characterized by copious capsule production and poor sedimentation. Dissecting the individual functions of CPS production and hmv in hvKp has been hindered by the conflation of these two properties. Although hmv requires capsular polysaccharide (CPS) biosynthesis, other cellular factors may also be required and some fitness phenotypes ascribed to CPS may be distinctly attributed to hmv. To address this challenge, we systematically identified genes that impact capsule and hmv. We generated a condensed, ordered transposon library in hypervirulent strain KPPR1, then evaluated the CPS production and hmv phenotypes of the 3,733 transposon mutants, representing 72% of all open reading frames in the genome. We employed forward and reverse genetic screens to evaluate effects of novel and known genes on CPS biosynthesis and hmv. These screens expand our understanding of core genes that coordinate CPS biosynthesis and hmv, as well as identify central metabolism genes that distinctly impact CPS biosynthesis or hmv, specifically those related to purine metabolism, pyruvate metabolism and the TCA cycle. Six representative mutants, with varying effect on CPS biosynthesis and hmv, were evaluated for their impact on CPS thickness, serum resistance, host cell association, and fitness in a murine model of disseminating pneumonia. Altogether, these data demonstrate that hmv requires both CPS biosynthesis and other cellular factors, and that hmv and CPS may serve distinct functions during pathogenesis. The integration of hmv and CPS to the metabolic status of the cell suggests that hvKp may require certain nutrients to specifically cause deep tissue infections.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
We present a detailed study of the Faraday depth structure of four bright (>1 Jy), strongly polarized, unresolved radio-loud quasars. The Australia Telescope Compact Array (ATCA) was used to observe ...these sources with 2 GHz of instantaneous bandwidth from 1.1 to 3.1 GHz. This allowed us to spectrally resolve the polarization structure of spatially unresolved radio sources, and by fitting various Faraday rotation models to the data, we conclusively demonstrate that two of the sources cannot be described by a simple rotation measure (RM) component modified by depolarization from a foreground Faraday screen. Our results have important implications for using background extragalactic radio sources as probes of the Galactic and intergalactic magneto-ionic media as we show how RM estimations from narrow-bandwidth observations can give erroneous results in the presence of multiple interfering Faraday components. We postulate that the additional RM components arise from polarized structure in the compact inner regions of the radio source itself and not from polarized emission from galactic or intergalactic foreground regions. We further suggest that this may contribute significantly to any RM time variability seen in RM studies on these angular scales. Follow-up, high-sensitivity very long baseline interferometry (VLBI) observations of these sources will directly test our predictions.
The deep reef refugia hypothesis proposes that deep reefs can act as local recruitment sources for shallow reefs following disturbance. To test this hypothesis, nine polymorphic DNA microsatellite ...loci were developed and used to assess vertical connectivity in 583 coral colonies of the Caribbean depth‐generalist coral Montastraea cavernosa. Samples were collected from three depth zones (≤10, 15–20 and ≥25 m) at sites in Florida (within the Upper Keys, Lower Keys and Dry Tortugas), Bermuda, and the U.S. Virgin Islands. Migration rates were estimated to determine the probability of coral larval migration from shallow to deep and from deep to shallow. Finally, algal symbiont (Symbiodinium spp.) diversity and distribution were assessed in a subset of corals to test whether symbiont depth zonation might indicate limited vertical connectivity. Overall, analyses revealed significant genetic differentiation by depth in Florida, but not in Bermuda or the U.S. Virgin Islands, despite high levels of horizontal connectivity between these geographic locations at shallow depths. Within Florida, greater vertical connectivity was observed in the Dry Tortugas compared to the Lower or Upper Keys. However, at all sites, and regardless of the extent of vertical connectivity, migration occurred asymmetrically, with greater likelihood of migration from shallow to intermediate/deep habitats. Finally, most colonies hosted a single Symbiodinium type (C3), ruling out symbiont depth zonation of the dominant symbiont type as a structuring factor. Together, these findings suggest that the potential for shallow reefs to recover from deep‐water refugia in M. cavernosa is location‐specific, varying among and within geographic locations likely as a consequence of local hydrology.
Abstract
We report on the discovery of FRB 20200120E, a repeating fast radio burst (FRB) with a low dispersion measure (DM) detected by the Canadian Hydrogen Intensity Mapping Experiment FRB project. ...The source DM of 87.82 pc cm
−3
is the lowest recorded from an FRB to date, yet it is significantly higher than the maximum expected from the Milky Way interstellar medium in this direction (∼50 pc cm
−3
). We have detected three bursts and one candidate burst from the source over the period 2020 January–November. The baseband voltage data for the event on 2020 January 20 enabled a sky localization of the source to within ≃14 arcmin
2
(90% confidence). The FRB localization is close to M81, a spiral galaxy at a distance of 3.6 Mpc. The FRB appears on the outskirts of M81 (projected offset ∼20 kpc) but well inside its extended H
i
and thick disks. We empirically estimate the probability of a chance coincidence with M81 to be <10
−2
. However, we cannot reject a Milky Way halo origin for the FRB. Within the FRB localization region, we find several interesting cataloged M81 sources and a radio point source detected in the Very Large Array Sky Survey. We search for prompt X-ray counterparts in Swift Burst Alert Telescope and Fermi/GBM data, and, for two of the FRB 20200120E bursts, we rule out coincident SGR 1806−20-like X-ray bursts. Due to the proximity of FRB 20200120E, future follow-up for prompt multiwavelength counterparts and subarcsecond localization could be constraining of proposed FRB models.
The Observations and Modeling of the Green Ocean Amazon (GoAmazon2014/5) Experiment was carried out in the environs of Manaus, Brazil, in the central region of the Amazon basin for 2 years from ...1 January 2014 through 31 December 2015. The experiment focused on the complex interactions among vegetation, atmospheric chemistry, and aerosol production on the one hand and their connections to aerosols, clouds, and precipitation on the other. The objective was to understand and quantify these linked processes, first under natural conditions to obtain a baseline and second when altered by the effects of human activities. To this end, the pollution plume from the Manaus metropolis, superimposed on the background conditions of the central Amazon basin, served as a natural laboratory. The present paper, as the introduction to the special issue of GoAmazon2014/5, presents the context and motivation of the GoAmazon2014/5 Experiment. The nine research sites, including the characteristics and instrumentation of each site, are presented. The sites range from time point zero (T0) upwind of the pollution, to T1 in the midst of the pollution, to T2 just downwind of the pollution, to T3 furthest downwind of the pollution (70 km). In addition to the ground sites, a low-altitude G-159 Gulfstream I (G-1) observed the atmospheric boundary layer and low clouds, and a high-altitude Gulfstream G550 (HALO) operated in the free troposphere. During the 2-year experiment, two Intensive Operating Periods (IOP1 and IOP2) also took place that included additional specialized research instrumentation at the ground sites as well as flights of the two aircraft. GoAmazon2014/5 IOP1 was carried out from 1 February to 31 March 2014 in the wet season. GoAmazon2014/5 IOP2 was conducted from 15 August to 15 October 2014 in the dry season. The G-1 aircraft flew during both IOP1 and IOP2, and the HALO aircraft flew during IOP2. In the context of the Amazon basin, the two IOPs also correspond to the clean and biomass burning seasons, respectively. The Manaus plume is present year-round, and it is transported by prevailing northeasterly and easterly winds in the wet and dry seasons, respectively. This introduction also organizes information relevant to many papers in the special issue. Information is provided on the vehicle fleet, power plants, and industrial activities of Manaus. The mesoscale and synoptic meteorologies relevant to the two IOPs are presented. Regional and long-range transport of emissions during the two IOPs is discussed based on satellite observations across South America and Africa. Fire locations throughout the airshed are detailed. In conjunction with the context and motivation of GoAmazon2014/5 as presented in this introduction, research articles including thematic overview articles are anticipated in this special issue to describe the detailed results and findings of the GoAmazon2014/5 Experiment.
Addition of molasses and urea was tested as a means of stimulating microbial urea hydrolysis in the Eastern Snake River Plain Aquifer in Idaho. Ureolysis is an integral component of a novel ...remediation approach for divalent trace metal and radionuclide contaminants in groundwater and associated geomedia, where the contaminants are immobilized by coprecipitation in calcite. Generation of carbonate alkalinity from ureolysis promotes calcite precipitation. In calcite-saturated aquifers, this represents a potential long-term contaminant sequestration mechanism. In a single-well experiment, dilute molasses was injected three times over two weeks to promote overall microbial growth, followed by one urea injection. With molasses addition, total cell numbers in the groundwater increased 1−2 orders of magnitude. Estimated ureolysis rates in recovered groundwater samples increased from <0.1 to >25 nmol L−1 hr−1. A quantitative PCR assay for the bacterial ureC gene indicated that urease gene numbers increased up to 170 times above pre-injection levels. Following urea injection, calcite precipitates were recovered. Estimated values for an in situ first order ureolysis rate constant ranged from 0.016 to 0.057 d−1. Although collateral impacts such as reduced permeability were observed, overall results indicated the viability of manipulating biogeochemical processes to promote contaminant sequestration.
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