Previously, we identified long repeat sequences that are frequently associated with genome rearrangements, including copy number variation (CNV), in many diverse isolates of the human fungal pathogen
...(Todd et al., 2019). Here, we describe the rapid acquisition of novel, high copy number CNVs during adaptation to azole antifungal drugs. Single-cell karyotype analysis indicates that these CNVs appear to arise via a dicentric chromosome intermediate and breakage-fusion-bridge cycles that are repaired using multiple distinct long inverted repeat sequences. Subsequent removal of the antifungal drug can lead to a dramatic loss of the CNV and reversion to the progenitor genotype and drug susceptibility phenotype. These findings support a novel mechanism for the rapid acquisition of antifungal drug resistance and provide genomic evidence for the heterogeneity frequently observed in clinical settings.
The strong, meandering, and eddy‐shedding Gulf Stream is a large oceanic reservoir of both mean and eddy kinetic energy in the northwestern Atlantic. Since 2015, underwater gliders equipped with ...Doppler current profilers have collected over 20,000 absolute velocity profiles in and near the Gulf Stream along the US East Coast. Those observations are used to make three‐dimensional estimates of mean and eddy kinetic energy, substantially expanding the geographic coverage of prior estimates of subsurface kinetic energy in the Gulf Stream. Glider observations are combined via weighted least squares fitting with anisotropic and inhomogeneous length scales to reflect both circulation and sampling density; this averaging technique can be applied to other quantities measured by the gliders. Mean and eddy kinetic energy decay approximately exponentially away from the surface. Vertical decay scales are longest within the high‐speed core of the Gulf Stream and somewhat shorter on the flanks of the Gulf Stream.
Plain Language Summary
Energy is a key metric of the Earth's climate system, of which the ocean is a major part. Kinetic energy, the energy of moving water in the ocean, is partitioned into mean kinetic energy that is associated with the time‐averaged ocean circulation and eddy kinetic energy that is associated with time‐varying motions. Here, a large set of velocity measurements collected by autonomous underwater gliders is used to make three‐dimensional estimates of mean and eddy kinetic energy in and near the Gulf Stream, one of the strongest currents in the global ocean. These new estimates of oceanic kinetic energy serve as a benchmark for numerical simulations of the ocean and climate system to reproduce.
Key Points
Underwater glider observations are used to produce three‐dimensional estimates of mean and eddy kinetic energy in and near the Gulf Stream
Mean and eddy kinetic energy generally decay exponentially with depth and have somewhat longer decay scales within the Gulf Stream
Three‐dimensional mean and eddy kinetic energy fields are available for further analyses and will be updated with future observations
Abstract
Autonomous underwater gliders are conducting high‐resolution surveys within the Gulf Stream along the U.S. East Coast. Glider surveys reveal two mechanisms by which energy is extracted from ...the Gulf Stream as it flows over the Blake Plateau, a portion of the outer continental shelf between Florida and North Carolina where bottom depths are less than 1000 m. Internal waves with vertical velocities exceeding 0.1 m s
−1
and frequencies just below the local buoyancy frequency are routinely found over the Blake Plateau, particularly near the Charleston Bump, a prominent topographic feature. These waves are likely internal lee waves generated by the subinertial Gulf Stream flow over the irregular bathymetry of the outer continental shelf. Bottom mixed layers with O(100) m thickness are also frequently encountered; these thick bottom mixed layers likely form in the lee of topography due to enhanced turbulence generated by O(1) m s
−1
near‐bottom flows.
Key Points
Spray gliders provide high‐resolution surveys of the Gulf Stream along the U.S. East Coast
High‐frequency internal lee waves are generated by Gulf Stream flow over Blake Plateau
Thick bottom mixed layers are common over Blake Plateau
Abstract
The Gulf Stream affects global climate by transporting water and heat poleward. The current’s volume transport increases markedly along the U.S. East Coast. An extensive observing program ...using autonomous underwater gliders provides finescale, subsurface observations of hydrography and velocity spanning more than 15° of latitude along the path of the Gulf Stream, thereby filling a 1500-km-long gap between long-term transport measurements in the Florida Strait and downstream of Cape Hatteras. Here, the glider-based observations are combined with shipboard measurements along Line W near 68°W to provide a detailed picture of the along-stream transport increase. To account for the influences of Gulf Stream curvature and adjacent circulation (e.g., corotating eddies) on transport estimates, upper- and lower-bound transports are constructed for each cross–Gulf Stream transect. The upper-bound estimate for time-averaged volume transport above 1000 m is 32.9 ± 1.2 Sv (1 Sv ≡ 10
6
m
3
s
−1
) in the Florida Strait, 57.3 ± 1.9 Sv at Cape Hatteras, and 75.6 ± 4.7 Sv at Line W. Corresponding lower-bound estimates are 32.3 ± 1.1 Sv in the Florida Strait, 54.5 ± 1.7 Sv at Cape Hatteras, and 69.9 ± 4.2 Sv at Line W. Using the temperature and salinity observations from gliders and Line W, waters are divided into seven classes to investigate the properties of waters that are transported by and entrained into the Gulf Stream. Most of the increase in overall Gulf Stream volume transport above 1000 m stems from the entrainment of subthermocline waters, including upper Labrador Sea Water and Eighteen Degree Water.
Cross‐equator transects occupied by an underwater glider and a research vessel in the western Indian Ocean captured the evolution of equatorial circulation during onset of the boreal summer monsoon ...in 2018. At the end of the winter monsoon in March, surface currents were westward, while the equatorial undercurrent carried salty Arabian Sea High‐Salinity Water eastward. As winds transitioned from westward to eastward during April, an eastward near‐surface Wyrtki Jet developed, while the equatorial undercurrent weakened, vanishing by May. A first‐mode baroclinic Kelvin wave propagated through the survey region after westward winds relaxed. However, the vertical structure of the evolving circulation was inconsistent with the first baroclinic mode, suggesting the influence of higher modes in setting observed vertical structure. The strong equatorial undercurrent at the end of the winter monsoon allowed high‐salinity waters from the western equatorial Indian Ocean to reach the southern Bay of Bengal in summer 2018.
Plain Language Summary
Circulation throughout the Indian Ocean is strongly influenced by the twice‐per‐year reversal of the monsoon winds over the basin. New observations collected using both an autonomous underwater glider and a research vessel in 2018 captured the reversal of layered currents in the upper ocean as the northeast (winter) monsoon gave way to the southwest (summer) monsoon. From March to May, near‐surface currents switched form westward to eastward, while the eastward equatorial undercurrent weakened and vanished. Equatorial planetary waves play a key role in propagating signals, such as those associated with changing monsoon winds, through the equatorial oceans. An eastward propagating Kelvin wave moving at a speed consistent with the first baroclinic mode was detected by satellite, but the observed vertical structure of the changing currents during the monsoon transition was inconsistent with the first baroclinic mode. Higher‐mode waves are suspected to play a role in the evolution of equatorial currents during the monsoon transition. Relatively strong subsurface flow at the end of the winter monsoon carried salty waters originating in the Arabian Sea eastward, leading to a salty subsurface feature in the Bay of Bengal in summer 2018.
Key Points
Autonomous and ship‐based observations capture circulation changes in the western equatorial Indian Ocean during monsoon transition
A first‐mode baroclinic Kelvin wave passed through the region, but observed vertical structure of currents was consistent with higher modes
A strong equatorial undercurrent in March 2018 carried salty waters from the Arabian Sea that later reached the central Bay of Bengal
Although the continental shelf and slope south of New England have been the subject of recent studies that address decadal-scale warming and interannual variability of water mass properties, it is ...not well understood how these changes affect shelf-break exchange processes. In recent years, observations of anomalous shelf and slope conditions obtained from the Ocean Observatories Initiative Pioneer Array and other regional observing programs suggest that onshore intrusions of warm, salty waters are becoming more prevalent. Mean cross-shelf transects constructed from Pioneer Array glider observations collected from April 2014 through December 2016 indicate that slope waters have been warmer and saltier. We examine shelf-break exchange events and anomalous onshore intrusions of warm, salty water associated with warm core rings located near the shelf break in spring 2014 and winter 2017 using observations from the Pioneer Array and other sources. We also describe an additional cross-shelf intrusion of ring water in September 2014 to demonstrate that the occurrence of high-salinity waters extending across the continental shelf is rare. Observations from the Pioneer Array and other sources show warm core ring and Gulf Stream water masses intrude onto the continental shelf more frequently and penetrate further onshore than in previous decades.
Seismic images and glider sections of the Gulf Stream front along the U.S. eastern seaboard capture deep, lens‐shaped submesoscale features. These features have radii of 5–20 km, thicknesses of ...150–300 m, and are located at depths greater than 500 m. These are typical signatures of anticyclonic submesoscale coherent vortices. A submesoscale‐resolving realistic simulation, which reproduces submesoscale coherent vortices with the same characteristics, is used to analyze their generation mechanism. Submesoscale coherent vortices are primarily generated where the Gulf Stream meets the Charleston Bump, a deep topographic feature, due to the frictional effects and intense mixing in the wake of the topography. These submesoscale coherent vortices can transport waters from the Charleston Bump's thick bottom mixed layer over long distances and spread them within the subtropical gyre. Their net effect on heat and salt distribution remains to be quantified.
Plain Language Summary
The interior of the ocean is populated by small‐scale coherent vortices, which redistribute water properties on the scale of basins. These structures are very difficult to observe. They have no surface signature and small dimensions, on the order of 1–50 km, such that they are missed by satellites and sampled only by chance. Furthermore, climate‐scale ocean models do not resolve these type of motions and do not take into account their impacts for the large‐scale transport and distribution of heat, nutrients, and other materials. Understanding and parameterizing these phenomena within models is critical for a better prediction of climate. Here we present new observations of submesoscale coherent vortices from seismic images and glider sections in the region of the Gulf Stream. We use a numerical model at very high resolution to reproduce vortices with the same characteristics and to analyze their generation mechanism. These vortices are generated where the Gulf Stream interacts with a deep topographic feature called the Charleston Bump due to frictional effects and intense mixing in the wake of the topography. These vortices transport waters from the Charleston Bump's thick bottom mixed layer and act to spread them all around the subtropical gyre.
Key Points
Submesoscale lenses of well‐mixed water are observed in seismic reflection images and glider sections across the Gulf Stream
A realistic numerical simulation is used to characterize these lenses as anticyclonic submesoscale coherent vortices
Submesoscale coherent vortices are generated where the Gulf Stream interacts with the Charleston Bump
Whole genome sequencing of human fungal pathogens has revolutionized the speed and accuracy in which sequence variants that cause antifungal resistance can be identified. Genome rearrangements ...resulting in copy number variation (CNV) are a significant source of acquired antifungal drug resistance across diverse fungal species. Some CNVs are transient in nature, while other CNVs are stable and well tolerated even in the absence of antifungal drugs. By visualizing whole genome sequencing read depth as a function of genomic location, CNVs and CNV breakpoints (genomic positions where the copy number changes occur relative to the rest of the genome) are rapidly identified. A similar analysis can be used to visualize allele ratio changes that occur across the genomes of heterozygous fungal species, both in the presence and absence of CNVs. This protocol walks through the bioinformatic analysis of CNVs and allele ratios utilizing free, open-source visualization tools. We provide code to use with an example dataset (matched antifungal drug-sensitive and drug-resistant Candida albicans isolates) and notes on how to expand this protocol to other fungal genomes.
Genome rearrangements resulting in copy number variation (CNV) and loss of heterozygosity (LOH) are frequently observed during the somatic evolution of cancer and promote rapid adaptation of fungi to ...novel environments. In the human fungal pathogen
, CNV and LOH confer increased virulence and antifungal drug resistance, yet the mechanisms driving these rearrangements are not completely understood. Here, we unveil an extensive array of long repeat sequences (65-6499 bp) that are associated with CNV, LOH, and chromosomal inversions. Many of these long repeat sequences are uncharacterized and encompass one or more coding sequences that are actively transcribed. Repeats associated with genome rearrangements are predominantly inverted and separated by up to ~1.6 Mb, an extraordinary distance for homology-based DNA repair/recombination in yeast. These repeat sequences are a significant source of genome plasticity across diverse strain backgrounds including clinical, environmental, and experimentally evolved isolates, and represent previously uncharacterized variation in the reference genome.
Abstract
Invasive fungal infections are a leading global cause of human mortality. Only three major classes of antifungal drugs are widely used, and resistance to all three classes can arise rapidly. ...The most widely prescribed antifungal drug, fluconazole, disseminates rapidly and reaches a wide range of concentrations throughout the body. The impact of drug concentration on the spectrum and effect of mutations acquired during adaptation is not known for any fungal pathogen, and how the specific level of a given stress influences the distribution of beneficial mutations has been poorly explored in general. We evolved 144 lineages from three genetically distinct clinical isolates of Candida albicans to four concentrations of fluconazole (0, 1, 8, and 64 μg/ml) and performed comprehensive phenotypic and genomic comparisons of ancestral and evolved populations. Adaptation to different fluconazole concentrations resulted in distinct adaptive trajectories. In general, lineages evolved to drug concentrations close to their MIC50 (the level of drug that reduces growth by 50% in the ancestor) tended to rapidly evolve an increased MIC50 and acquired distinct segmental aneuploidies and copy number variations. By contrast, lineages evolved to drug concentrations above their ancestral MIC50 tended to acquire a different suite of mutational changes and increased in drug tolerance (the ability of a subpopulation of cells to grow slowly above their MIC50). This is the first evidence that different concentrations of drug can select for different genotypic and phenotypic outcomes in vitro and may explain observed in vivo drug response variation.
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