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An automatic and quantitative approach to the detection and tracking of acoustic scattering layers
Get PDFAcoustic scattering layers are ubiquitous, horizontally extensive aggregations of both vertebrate and invertebrate organisms that play key roles in oceanic ecosystems. However, currently there are no conventions or widely adaptable automatic methods for identifying these often dynamic, spatially complex features, so it is difficult to consistently and efficiently describe and compare results. We developed an automatic scattering layer detection method that can be used to monitor changes in layer depth, width, and internal structure over time. Extensive, contiguous regions of the water column that have echo strengths above a threshold were identified as “background layers.” They correspond to regions of the water column that contain scattering from diffusely distributed organisms. Often, background layers contained contiguous, horizontally extensive features of concentrated acoustic scattering we identified as “strata.” These features were identified by fitting Gaussian curves to the echo envelope of each vertical profile of scattering, and their boundaries were identified as the endpoints of the region containing 95% of the area under the fitted curves. These endpoints were linked horizontally to make continuous tracks. Bottom and top tracks were paired to identify features that sometimes extended horizontally for tens of kilometers. This approach was effective in three disparate ecosystems (the Gulf of California, Monterey Bay, and the Bering Sea), and a sensitivity analysis showed its robustness to changes in input parameters. By allowing a comparable, automated approach to be used across environments, this method promotes the improved classification and characterization of acoustic scattering layers necessary for examining their role in oceanic ecosystems.This is the publisher’s final pdf. The published article is copyrighted by the American Society of Limnology and Oceanography, Inc. and can be found at: http://www.aslo.org/lomethods/
Highly Enantioselective Construction of Polycyclic Spirooxindoles by Organocatalytic 1,3-Dipolar Cycloaddition of 2-Cyclohexenone Catalyzed by Proline-Sulfonamide
Get PDFAn enantioselective 1,3-dipolar cycloaddition of 2-cyclo-hexene-1-one and azomethine ylide generated in situ from isatin and amino ester was developed by employing proline sulfonamide as the catalyst. Consequently, novel polycyclic spirooxindole scaffolds with three contiguous stereocenters were prepared in high yield (up to 95%) with excellent diastereo- (> 20:1 dr) and enantio-selectivity (up to 99% ee).Keywords: Isatin,
Spiro compounds,
Organocatalysis,
Cycloaddition,
Nitrogen heterocycles,
Spirooxindole,
2-cyclohexene-1-one,
Alkaloids,
1,3-dipolar cycloadditio
GrünwaldNiklausBotanyPlantPathologyEphemeralSexualPopulation_SupportingInformation.zip
No full textPhytophthora infestans, the causal agent of late blight disease, has been reported in North America since the mid-nineteenth century. In the United States the lack of or very limited sexual reproduction has resulted in largely clonal populations of P. infestans. In 2010 and 2011, but not in 2012 or 2013, 20 rare and diverse genotypes of P. infestans were detected in a region that centered around central New York State. The ratio of A1 to A2 mating types among these genotypes was close to the 50:50 ratio expected for sexual recombination. These genotypes were diverse at the glucose-6-phosphate isomerase locus, differed in their microsatellite profiles, showed different banding patterns in a restriction fragment length polymorphism assay using a moderately repetitive and highly polymorphic probe (RG57), were polymorphic for four different nuclear genes and differed in their sensitivity to the systemic fungicide mefenoxam. The null hypothesis of linkage equilibrium was not rejected, which suggests the population could be sexual. These new genotypes were monomorphic in their mitochondrial haplotype that was the same as US-22. Through parentage exclusion testing using microsatellite data and sequences of four nuclear genes, recent dominant lineages US-8, US-11, US-23, and US-24 were excluded as possible parents for these genotypes. Further analyses indicated that US-22 could not be eliminated as a possible parent for 14 of the 20 genotypes. We conclude that US-22 could be a parent of some, but not all, of the new genotypes found in 2010 and 2011. There were at least two other parents for this population and the genotypic characteristics of the other parents were identified
Correspondence between Scale Morphometrics and Scale and Otolith Chemistry for Interpreting Juvenile Salmon Life Histories
Get PDFFish scales have long been used to reconstruct fine-scale habitat transitions such as the movement of juvenile fish from freshwater, estuary, and ocean environments. Despite the importance of life history information to fisheries management and conservation, few studies have validated that scale morphology accurately describes fish movement between these habitats. Therefore, we tested the accuracy of using scale morphometric criteria to identify the movement of juvenile Chinook Salmon Oncorhynchus tshawytscha from freshwater to marine portions of the Columbia River estuary by comparing scale morphometric classification, scale chemistry, and otolith chemistry. Nearly one-half of all fish collected in the saline portion of the estuary and approximately one-quarter in the freshwater portion exhibited morphometric patterns (i.e., scale checks and intermediate growth) often associated with periods of estuary rearing. Depending upon the criteria used to define scale checks, otolith chemical results indicated that 33–53% of fish would have been misclassified as estuary residents based solely on their scale patterns. Moreover, many individuals who had resided in strontium-rich estuary water did not form a visible check (37%) on their scales to coincide with estuary entry. We estimated from otolith chemistry that these fish had either entered at or near the size at which scale formation occurs (35–42 mm) or had recently migrated to the saline portion of the estuary (<30 d) before new scale material could be formed and calcified. Scale chemistry alone was a good indicator of entrance into the saline portion of the estuary. Scale chemistry responded to the strontium-enriched salt water, and explained 86% of the variation found in otolith chemistry. Scale morphometric classification did not provide the fine-scale resolution that scale and, even more so, otolith chemistry provided for describing the proportion of juvenile Chinook salmon using the saline portion of the Columbia River estuary
SchmittnerAndreasCEOASEarlyDeglacialAtlantic_Supplement.zip
No full textThe reason for the initial rise in atmospheric
CO₂ during the last deglaciation remains unknown. Most recent
hypotheses invoke Southern Hemisphere processes such
as shifts in midlatitude westerly winds. Coeval changes in
the Atlantic meridional overturning circulation (AMOC) are
poorly quantified, and their relation to the CO₂ increase is
not understood. Here we compare simulations from a global,
coupled climate–biogeochemistry model that includes a detailed
representation of stable carbon isotopes (δ¹³C) with a
synthesis of high-resolution δ¹³C reconstructions from deep-sea
sediments and ice core data. In response to a prolonged
AMOC shutdown initialized from a preindustrial state, modeled
δ¹³C of dissolved inorganic carbon (δ¹³C[subscript DIC]) decreases
in most of the surface ocean and the subsurface Atlantic, with
largest amplitudes (more than 1.5 ‰) in the intermediate-depth
North Atlantic. It increases in the intermediate and
abyssal South Atlantic, as well as in the subsurface Southern,
Indian, and Pacific oceans. The modeled pattern is similar
and highly correlated with the available foraminiferal δ¹³C
reconstructions spanning from the late Last Glacial Maximum
(LGM, ~19.5–18.5 ka BP) to the late Heinrich stadial
event 1 (HS1, ~16.5–15.5 ka BP), but the model overestimates
δ¹³C[subscript DIC] reductions in the North Atlantic. Possible
reasons for the model–sediment-data differences are discussed.
Changes in remineralized δ¹³C[subscript DIC] dominate the total
δ¹³C[subscript DIC] variations in the model but preformed contributions
are not negligible. Simulated changes in atmospheric CO₂
and its isotopic composition (δ¹³C[subscript CO₂]) agree well with ice
core data. Modeled effects of AMOC-induced wind changes
on the carbon and isotope cycles are small, suggesting that
Southern Hemisphere westerly wind effects may have been
less important for the global carbon cycle response during
HS1 than previously thought. Our results indicate that during
the early deglaciation the AMOC decreased for several
thousand years.We propose that the observed early deglacial
rise in atmospheric CO₂ and the decrease in δ¹³C[subscript CO₂] may
have been dominated by an AMOC-induced decline of the
ocean’s biologically sequestered carbon storage
KimKi-JoongChemBioEnvEngPlasmonics-Enhanced.pdf
No full textCombined plasmonic nanocrystals and metal–organic framework
thin-films are fabricated for sensing gases in the near-infrared
range. This nanocomposite thin-film shows a highly sensitive response
in near-infrared absorption, which is attributed to preconcentration
of gas molecules in metal–organic framework pores causing close
proximity to the electromagnetic fields at the plasmonic nanocrystal
surface
TorresLeighFisheriesWildlifePoorTransferabilitySpecies_SupportingInformation.zip
No full textSpecies distribution models (SDMs) are increasingly applied in conservation management
to predict suitable habitat for poorly known populations. High predictive performance of
SDMs is evident in validations performed within the model calibration area (interpolation),
but few studies have assessed SDM transferability to novel areas (extrapolation), particularly
across large spatial scales or pelagic ecosystems. We performed rigorous SDM validation
tests on distribution data from three populations of a long-ranging marine predator, the
grey petrel Procellaria cinerea, to assess model transferability across the Southern Hemisphere
(25-65°S). Oceanographic data were combined with tracks of grey petrels from two
remote sub-Antarctic islands (Antipodes and Kerguelen) using boosted regression trees to
generate three SDMs: one for each island population, and a combined model. The predictive
performance of these models was assessed using withheld tracking data from within
the model calibration areas (interpolation), and from a third population, Marion Island (extrapolation).
Predictive performance was assessed using k-fold cross validation and point
biserial correlation. The two population-specific SDMs included the same predictor variables
and suggested birds responded to the same broad-scale oceanographic influences.
However, all model validation tests, including of the combined model, determined strong interpolation
but weak extrapolation capabilities. These results indicate that habitat use reflects
both its availability and bird preferences, such that the realized distribution patterns
differ for each population. The spatial predictions by the three SDMs were compared with
tracking data and fishing effort to demonstrate the conservation pitfalls of extrapolating
SDMs outside calibration regions. This exercise revealed that SDM predictions would have
led to an underestimate of overlap with fishing effort and potentially misinformed bycatch mitigation efforts. Although SDMs can elucidate potential distribution patterns relative to
large-scale climatic and oceanographic conditions, knowledge of local habitat availability
and preferences is necessary to understand and successfully predict region-specific realized
distribution patterns
Context-dependent survival, fecundity and predicted population-level consequences of brucellosis in African buffalo
Get PDF1. Chronic infections may have negative impacts on wildlife populations, yet their effects are difficult to detect in the absence of long-term population monitoring. Brucella abortus, the bacteria responsible for bovine brucellosis, causes chronic infections and abortions in wild and domestic ungulates, but its impact on population dynamics is not well understood.
2. We report infection patterns and fitness correlates of bovine brucellosis in African buffalo based on (1) 7 years of cross-sectional disease surveys and (2) a 4-year longitudinal study in Kruger National Park (KNP), South Africa. We then used a matrix population model to translate these observed patterns into predicted population-level effects.
3. Annual brucellosis seroprevalence ranged from 8·7% (95% CI = 1·8–15·6) to 47·6% (95% CI = 35·1–60·1) increased with age until adulthood (>6) and varied by location within KNP. Animals were on average in worse condition after testing positive for brucellosis (F = −5·074, P < 0·0001), and infection was associated with a 2·0 (95% CI = 1·1–3·7) fold increase in mortality (χ2 = 2·039, P = 0·036). Buffalo in low body condition were associated with lower reproductive success (F = 2·683, P = 0·034), but there was no association between brucellosis and pregnancy or being observed with a calf.
4. For the range of body condition scores observed in the population, the model-predicted growth rate was λ = 1·11 (95% CI = 1·02–1·21) in herds without brucellosis and λ = 1·00 (95% CI = 0·85–1·16) when brucellosis seroprevalence was 30%.
5. Our results suggest that brucellosis infection can potentially result in reduced population growth rates, but because these effects varied with demographic and environmental conditions, they may remain unseen without intensive, longitudinal monitoring.To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work.
This is the publisher’s final pdf. The published article is copyrighted by The Authors and the British Ecological Society. It is published by John Wiley & Sons, Inc., and can be found at: https://doi.org/10.1111/1365-2656.1235
Assessing the carcinogenic potential of low-dose exposures to chemical mixtures in the environment: the challenge ahead
Get PDFLifestyle factors are responsible for a considerable portion of cancer incidence worldwide, but credible estimates from the World Health Organization and the International Agency for Research on Cancer (IARC) suggest that the fraction of cancers attributable to toxic environmental exposures is between 7% and 19%. To explore the hypothesis that low-dose exposures to mixtures of chemicals in the environment may be combining to contribute to environmental carcinogenesis, we reviewed 11 hallmark phenotypes of cancer, multiple priority target sites for disruption in each area and prototypical chemical disruptors for all targets, this included dose-response characterizations, evidence of low-dose effects and cross-hallmark effects for all targets and chemicals. In total, 85 examples of chemicals were reviewed for actions on key pathways/ mechanisms related to carcinogenesis. Only 15% (13/85) were found to have evidence of a dose-response threshold, whereas 59% (50/85) exerted low-dose effects. No dose-response information was found for the remaining 26% (22/85). Our analysis suggests that the cumulative effects of individual (non-carcinogenic) chemicals acting on different pathways, and a variety of related systems, organs, tissues and cells could plausibly conspire to produce carcinogenic synergies. Additional basic research on carcinogenesis and research focused on low-dose effects of chemical mixtures needs to be rigorously pursued before the merits of this hypothesis can be further advanced. However, the structure of the World Health Organization International Programme on Chemical Safety ‘Mode of Action’ framework should be revisited as it has inherent weaknesses that are not fully aligned with our current understanding of cancer biology
Ocean Acidification Has Multiple Modes of Action on Bivalve Larvae
Get PDFOcean acidification (OA) is altering the chemistry of the world’s oceans at rates unparalleled in the past roughly 1 million years. Understanding the impacts of this rapid change in baseline carbonate chemistry on marine organisms needs a precise, mechanistic understanding of physiological responses to carbonate chemistry. Recent experimental work has shown shell development and growth in some bivalve larvae, have direct sensitivities to calcium carbonate saturation state that is not modulated through organismal acid-base chemistry. To understand different modes of action of OA on bivalve larvae, we experimentally tested how pH, P[subscript]CO2, and saturation state independently affect shell growth and development, respiration rate, and initiation of feeding in Mytilus californianus embryos and larvae. We found, as documented in other bivalve larvae, that shell development and growth were affected by aragonite saturation state, and not by pH or P[subscript]CO2. Respiration rate was elevated under very low pH (~7.4) with no change between pH of ~ 8.3 to ~7.8. Initiation of feeding appeared to be most sensitive to P[subscript]CO2, and possibly minor response to pH under elevated P[subscript]CO2. Although different components of physiology responded to different carbonate system variables, the inability to normally develop a shell due to lower saturation state precludes pH or P[subscript]CO2 effects later in the life history. However, saturation state effects during early shell development will carry-over to later stages, where pH or P[subscript]CO2 effects can compound OA effects on bivalve larvae. Our findings suggest OA may be a multi-stressor unto itself. Shell development and growth of the native mussel, M. californianus, was indistinguishable from the Mediterranean mussel, Mytilus galloprovincialis, collected from the southern U.S. Pacific coast, an area not subjected to seasonal upwelling. The concordance in responses suggests a fundamental OA bottleneck during development of the first shell material affected only by saturation state