DNA barcoding identifies a cosmopolitan diet in the ocean sunfish

The ocean sunfish (Mola mola) is the world’s heaviest bony fish reaching a body mass of up to 2.3 tonnes. However, the prey M. mola consumes to fuel this prodigious growth remains poorly known. Sunfish were thought to be obligate gelatinous plankton feeders, but recent studies suggest a more generalist diet. In this study, through molecular barcoding and for the first time, the diet of sunfish in the north-east Atlantic Ocean was characterised. Overall, DNA from the diet content of 57 individuals was successfully amplified, identifying 41 different prey items. Sunfish fed mainly on crustaceans and teleosts, with cnidarians comprising only 16% of the consumed prey. Although no adult fishes were sampled, we found evidence for an ontogenetic shift in the diet, with smaller individuals feeding mainly on small crustaceans and teleost fish, whereas the diet of larger fish included more cnidarian species. Our results confirm that smaller sunfish feed predominantly on benthic and on coastal pelagic species, whereas larger fish depend on pelagic prey. Therefore, sunfish is a generalist predator with a greater diversity of links in coastal food webs than previously realised. Its removal as fisheries’ bycatch may have wider reaching ecological consequences, potentially disrupting coastal trophic interactions.

The Roles of Land and Orography on Precipitation and Ocean Circulation in Global Climate Models

Thesis (Ph.D.)--University of Washington, 2016-08

Breaking Waves on the Ocean Surface

Thesis (Ph.D.)--University of Washington, 2016-08

On the modelling of fire atmosphere/sprinkler spray interacting using an Euler-Lagrange framework

An Euler-Lagrange particle tracking model, developed for simulating fire atmosphere/sprinkler spray interactions, is described. Full details of the model along with the approximations made and restrictions applying are presented. Errors commonly found in previous formulations of the source terms used in this two-phase approach are described and corrected. In order to demonstrate the capabilities of the model it is applied to the simulation of a fire in a long corridor containing a sprinkler. The simulation presented is three-dimensional and transient and considers mass, momentum and energy transfer between the gaseous atmosphere and injected liquid droplets.

Modeling the Arctic Freshwater System and its integration in the global system: Lessons learned and future challenges

Numerous components of the Arctic freshwater system (atmosphere, ocean, cryosphere, terrestrial hydrology) have experienced large changes over the past few decades, and these changes are projected to amplify further in the future. Observations are particularly sparse, both in time and space, in the Polar Regions. Hence, modeling systems have been widely used and are a powerful tool to gain understanding on the functioning of the Arctic freshwater system and its integration within the global Earth system and climate. Here, we present a review of modeling studies addressing some aspect of the Arctic freshwater system. Through illustrative examples, we point out the value of using a hierarchy of models with increasing complexity and component interactions, in order to dismantle the important processes at play for the variability and changes of the different components of the Arctic freshwater system and the interplay between them. We discuss past and projected changes for the Arctic freshwater system and explore the sources of uncertainty associated with these model results. We further elaborate on some missing processes that should be included in future generations of Earth system models and highlight the importance of better quantification and understanding of natural variability, amongst other factors, for improved predictions of Arctic freshwater system change.

Oceanic control of multidecadal variability in an idealized coupled GCM

Idealized ocean models are known to develop intrinsic multidecadal oscillations of the meridional overturning circulation (MOC). Here we explore the role of ocean–atmosphere interactions on this low-frequency variability. We use a coupled ocean–atmosphere model set up in a flat-bottom aquaplanet geometry with two meridional boundaries. The model is run at three different horizontal resolutions (4°, 2° and 1°) in both the ocean and atmosphere. At all resolutions, the MOC exhibits spontaneous variability on multidecadal timescales in the range 30–40 years, associated with the propagation of large-scale baroclinic Rossby waves across the Atlantic-like basin. The unstable region of growth of these waves through the long wave limit of baroclinic instability shifts from the eastern boundary at coarse resolution to the western boundary at higher resolution. Increasing the horizontal resolution enhances both intrinsic atmospheric variability and ocean–atmosphere interactions. In particular, the simulated atmospheric annular mode becomes significantly correlated to the MOC variability at 1° resolution. An ocean-only simulation conducted for this specific case underscores the disruptive but not essential influence of air–sea interactions on the low-frequency variability. This study demonstrates that an atmospheric annular mode leading MOC changes by about 2 years (as found at 1° resolution) does not imply that the low-frequency variability originates from air–sea interactions.

On the stability and spatiotemporal variance distribution of salinity in the upper ocean

Despite recent advances in ocean observing arrays and satellite sensors, there remains great uncertainty in the large-scale spatial variations of upper ocean salinity on the interannual to decadal timescales. Consonant with both broad-scale surface warming and the amplification of the global hydrological cycle, observed global multidecadal salinity changes typically have focussed on the linear response to anthropogenic forcing but not on salinity variations due to changes in the static stability and or variability due to the intrinsic ocean or internal climate processes. Here, we examine the static stability and spatiotemporal variability of upper ocean salinity across a hierarchy of models and reanalyses. In particular, we partition the variance into time bands via application of singular spectral analysis, considering sea surface salinity (SSS), the Brunt Väisälä frequency (N2), and the ocean salinity stratification in terms of the stabilizing effect due to the haline part of N2 over the upper 500m. We identify regions of significant coherent SSS variability, either intrinsic to the ocean or in response to the interannually varying atmosphere. Based on consistency across models (CMIP5 and forced experiments) and reanalyses, we identify the stabilizing role of salinity in the tropics—typically associated with heavy precipitation and barrier layer formation, and the role of salinity in destabilizing upper ocean stratification in the subtropical regions where large-scale density compensation typically occurs.

Dissipation of the energy imparted by mid-latitude storms in the Southern Ocean

The aim of this study is to clarify the role of the Southern Ocean storms on interior mixing and meridional overturning circulation. A periodic and idealized numerical model has been designed to represent the key physical processes of a zonal portion of the Southern Ocean located between 70 and 40° S. It incorporates physical ingredients deemed essential for Southern Ocean functioning: rough topography, seasonally varying air–sea fluxes, and high-latitude storms with analytical form. The forcing strategy ensures that the time mean wind stress is the same between the different simulations, so the effect of the storms on the mean wind stress and resulting impacts on the Southern Ocean dynamics are not considered in this study. Level and distribution of mixing attributable to high-frequency winds are quantified and compared to those generated by eddy–topography interactions and dissipation of the balanced flow. Results suggest that (1) the synoptic atmospheric variability alone can generate the levels of mid-depth dissipation frequently observed in the Southern Ocean (10−10–10−9 W kg−1) and (2) the storms strengthen the overturning, primarily through enhanced mixing in the upper 300 m, whereas deeper mixing has a minor effect. The sensitivity of the results to horizontal resolution (20, 5, 2 and 1 km), vertical resolution and numerical choices is evaluated. Challenging issues concerning how numerical models are able to represent interior mixing forced by high-frequency winds are exposed and discussed, particularly in the context of the overturning circulation. Overall, submesoscale-permitting ocean modeling exhibits important delicacies owing to a lack of convergence of key components of its energetics even when reaching Δx =  1 km.

Ocean acidification in the subpolar North Atlantic: rates and mechanisms controlling pH changes

Repeated hydrographic sections provide critically needed data on and understanding of changes in basin-wide ocean CO2 chemistry over multi-decadal timescales. Here, high-quality measurements collected at twelve cruises carried out along the same track between 1991 and 2015 have been used to determine long-term changes in ocean CO2 chemistry and ocean acidification in the Irminger and Iceland basins of the North Atlantic Ocean. Trends were determined for each of the main water masses present and are discussed in the context of the basin-wide circulation. The pH has decreased in all water masses of the Irminger and Iceland basins over the past 25 years with the greatest changes in surface and intermediate waters (between −0.0010 ± 0.0001 and −0.0018 ± 0.0001 pH units yr−1). In order to disentangle the drivers of the pH changes, we decomposed the trends into their principal drivers: changes in temperature, salinity, total alkalinity (AT) and total dissolved inorganic carbon (both its natural and anthropogenic components). The increase in anthropogenic CO2 (Cant) was identified as the main agent of the pH decline, partially offset by AT increases. The acidification of intermediate waters caused by Cant uptake has been reinforced by the aging of the water masses over the period of our analysis. The pH decrease of the deep overflow waters in the Irminger basin was similar to that observed in the upper ocean and was mainly linked to the Cant increase, thus reflecting the recent contact of these deep waters with the atmosphere.

Marine litter in the upper São Vicente submarine canyon (SW Portugal): abundance, distribution, composition and fauna interactions

Marine litter has become a worldwide environmental problem, tainting all ocean habitats. The abundance, distribution and composition of litter and its interactions with fauna were evaluated in the upper S. Vicente canyon using video images from 3 remote operated vehicle exploratory dives. Litter was present in all dives and the abundance was as high as 3.31 items100m(-1). Mean abundance of litter over rock bottom was higher than on soft substrate. Mean litter abundance was slightly higher than reported for other canyons on the Portuguese margin, but lower in comparison to more urbanized coastal areas of the world. Lost fishing gear was the prevalent type of litter, indicating that the majority of litter originates from maritime sources, mainly fishing activity. Physical contact with sessile fauna and entanglement of specimens were the major impacts of lost fishing gear. Based on the importance of this region for the local fishermen, litter abundance is expected to increase.

Towards a broader understanding of the effects of tidal forcing on the global ocean circulation

The study of tides and their interactions with the complex dynamics of the global ocean represents a crucial challenge in ocean modelling. This thesis aims to deepen this study from a dynamical point of view, analysing what are the tidal effects on the general circulation of the ocean. We perform different experiments of a mesoscale-permitting global ocean model forced by both atmospheric fields and astronomical tidal potential, and we implement two parametrizations to include in the model tidal phenomena that are currently unresolved, with particular emphasis to the topographic wave drag for locally dissipating internal waves. An additional experiment using a mesoscale-resolving configuration is used to compare the simulated tides at different resolutions with observed data. We find that the accuracy of modelled tides strongly depends on the region and harmonic component of interest, even though the increased resolution allows to improve the modelled topography and resolve more intense internal waves. We then focus on the impact of tides in the Atlantic Ocean and find that tides weaken the overturning circulation during the analysed period from 1981 to 2007, even though the interannual differences strongly change in both amplitude and phase. The zonally integrated momentum balance shows that tide changes the water stratification at the zonal boundaries, modifying the pressure and therefore the geostrophic balance over the entire basin. Finally, we describe the overturning circulation in the Mediterranean Sea computing the meridional and zonal streamfunctions both in the Eulerian and residual frameworks. The circulation is characterised by different cells, and their forcing processes are described with particular emphasis to the role of mesoscale and a transient climatic event. We complete the description of the overturning circulation giving evidence for the first time to the connection between meridional and zonal cells.

Iis--integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools.

High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.

Ant-caterpillar Antagonism At The Community Level: Interhabitat Variation Of Tritrophic Interactions In A Neotropical Savanna.

Ant foraging on foliage can substantially affect how phytophagous insects use host plants and represents a high predation risk for caterpillars, which are important folivores. Ant-plant-herbivore interactions are especially pervasive in cerrado savanna due to continuous ant visitation to liquid food sources on foliage (extrafloral nectaries, insect honeydew). While searching for liquid rewards on plants, aggressive ants frequently attack or kill insect herbivores, decreasing their numbers. Because ants vary in diet and aggressiveness, their effect on herbivores also varies. Additionally, the differential occurrence of ant attractants (plant and insect exudates) on foliage produces variable levels of ant foraging within local floras and among localities. Here, we investigate how variation of ant communities and of traits among host plant species (presence or absence of ant attractants) can change the effect of carnivores (predatory ants) on herbivore communities (caterpillars) in a cerrado savanna landscape. We sampled caterpillars and foliage-foraging ants in four cerrado localities (70-460 km apart). We found that: (i) caterpillar infestation was negatively related with ant visitation to plants; (ii) this relationship depended on local ant abundance and species composition, and on local preference by ants for plants with liquid attractants; (iii) this was not related to local plant richness or plant size; (iv) the relationship between the presence of ant attractants and caterpillar abundance varied among sites from negative to neutral; and (v) caterpillars feeding on plants with ant attractants are more resistant to ant predation than those feeding on plants lacking attractants. Liquid food on foliage mediates host plant quality for lepidopterans by promoting generalized ant-caterpillar antagonism. Our study in cerrado shows that the negative effects of generalist predatory ants on herbivores are detectable at a community level, affecting patterns of abundance and host plant use by lepidopterans. The magnitude of ant-induced effects on caterpillar occurrence across the cerrado landscape may depend on how ants use plants locally and how they respond to liquid food on plants at different habitats. This study enhances the relevance of plant-ant and ant-herbivore interactions in cerrado and highlights the importance of a tritrophic perspective in this ant-rich environment.

Contrasting Effects Of Land Use Intensity And Exotic Host Plants On The Specialization Of Interactions In Plant-herbivore Networks.

Human land use tends to decrease the diversity of native plant species and facilitate the invasion and establishment of exotic ones. Such changes in land use and plant community composition usually have negative impacts on the assemblages of native herbivorous insects. Highly specialized herbivores are expected to be especially sensitive to land use intensification and the presence of exotic plant species because they are neither capable of consuming alternative plant species of the native flora nor exotic plant species. Therefore, higher levels of land use intensity might reduce the proportion of highly specialized herbivores, which ultimately would lead to changes in the specialization of interactions in plant-herbivore networks. This study investigates the community-wide effects of land use intensity on the degree of specialization of 72 plant-herbivore networks, including effects mediated by the increase in the proportion of exotic plant species. Contrary to our expectation, the net effect of land use intensity on network specialization was positive. However, this positive effect of land use intensity was partially canceled by an opposite effect of the proportion of exotic plant species on network specialization. When we analyzed networks composed exclusively of endophagous herbivores separately from those composed exclusively of exophagous herbivores, we found that only endophages showed a consistent change in network specialization at higher land use levels. Altogether, these results indicate that land use intensity is an important ecological driver of network specialization, by way of reducing the local host range of herbivore guilds with highly specialized feeding habits. However, because the effect of land use intensity is offset by an opposite effect owing to the proportion of exotic host species, the net effect of land use in a given herbivore assemblage will likely depend on the extent of the replacement of native host species with exotic ones.

Graphene Oxide: A Carrier For Pharmaceuticals And A Scaffold For Cell Interactions.

During the last ten years, graphene oxide has been explored in many applications due to its remarkable electroconductivity, thermal properties and mobility of charge carriers, among other properties. As discussed in this review, the literature suggests that a total characterization of graphene oxide must be conducted because oxidation debris (synthesis impurities) present in the graphene oxides could act as a graphene oxide surfactant, stabilizing aqueous dispersions. It is also important to note that the structure models of graphene oxide need to be revisited because of significant implications for its chemical composition and its direct covalent functionalization. Another aspect that is discussed is the need to consider graphene oxide surface chemistry. The hemolysis assay is recommended as a reliable test for the preliminary assessment of graphene oxide toxicity, biocompatibility and cell membrane interaction. More recently, graphene oxide has been extensively explored for drug delivery applications. An important increase in research efforts in this emerging field is clearly represented by the hundreds of related publications per year, including some reviews. Many studies have been performed to explore the graphene oxide properties that enable it to deliver more than one activity simultaneously and to combine multidrug systems with photothermal therapy, indicating that graphene oxide is an attractive tool to overcome hurdles in cancer therapies. Some strategic aspects of the application of these materials in cancer treatment are also discussed. In vitro studies have indicated that graphene oxide can also promote stem cell adhesion, growth and differentiation, and this review discusses the recent and pertinent findings regarding graphene oxide as a valuable nanomaterial for stem cell research in medicine. The protein corona is a key concept in nanomedicine and nanotoxicology because it provides a biomolecular identity for nanomaterials in a biological environment. Understanding protein corona-nanomaterial interactions and their influence on cellular responses is a challenging task at the nanobiointerface. New aspects and developments in this area are discussed.