Search

Abstract Background While studies of non-model organisms are critical for many research areas, such as evolution, development, and environmental biology, they present particular challenges for both experimental and computational genomic level research. Resources such as mass-produced microarrays and the computational tools linking these data to functional annotation at the system and pathway level are rarely available for non-model species. This type of "systems-level" analysis is critical to the understanding of patterns of gene expression that underlie biological processes. Results We describe a bioinformatics pipeline known as FunnyBase that has been used to store, annotate, and analyze 40,363 expressed sequence tags (ESTs) from the heart and liver of the fish, Fundulus heteroclitus. Primary annotations based on sequence similarity are linked to networks of systematic annotation in Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) and can be queried and computationally utilized in downstream analyses. Steps are taken to ensure that the annotation is self-consistent and that the structure of GO is used to identify higher level functions that may not be annotated directly. An integrated framework for cDNA library production, sequencing, quality control, expression data generation, and systems-level analysis is presented and utilized. In a case study, a set of genes, that had statistically significant regression between gene expression levels and environmental temperature along the Atlantic Coast, shows a statistically significant (P < 0.001) enrichment in genes associated with amine metabolism. Conclusion The methods described have application for functional genomics studies, particularly among non-model organisms. The web interface for FunnyBase can be accessed at http://genomics.rsmas.miami.edu/funnybase/super_craw4/. Data and source code are available by request at jpaschall@bioinfobase.umkc.edu.

As states, cities, tribes, and private interests cope with climate damages and seek to increase preparedness and resilience, they will need to navigate myriad choices and options available to them. Making these choices in ways that identify pathways for climate action that support their development objectives will require constructive public dialogue, community participation, and flexible and ongoing access to science- and experience-based knowledge. In 2016, a Federal Advisory Committee (FAC) was convened to recommend how to conduct a sustained National Climate Assessment (NCA) to increase the relevance and usability of assessments for informing action. The FAC was disbanded in 2017, but members and additional experts reconvened to complete the report that is presented here. A key recommendation is establishing a new nonfederal ‘‘climate assessment consortium’’ to increase the role of state/local/tribal government and civil society in assessments. The expanded process would 1) focus on applied problems faced by practitioners, 2) organize sustained partnerships for collaborative learning across similar projects and case studies to identify effective tested practices, and 3) assess and improve knowledge-based methods for project implementation. Specific recommendations include evaluating climate models and data using user-defined metrics; improving benefit–cost assessment and supporting decision-making under uncertainty; and accelerating application of tools and methods such as citizen science, artificial intelligence, indicators, and geospatial analysis. The recommendations are the result of broad consultation and present an ambitious agenda for federal agencies, state/local/tribal jurisdictions, universities and the research sector, professional associations, nongovernmental and community-based organizations, and private-sector firms.

As states, cities, tribes, and private interests cope with climate damages and seek to increase preparedness and resilience, they will need to navigate myriad choices and options available to them. Making these choices in ways that identify pathways for climate action that support their development objectives will require constructive public dialogue, community participation, and flexible and ongoing access to science- and experience-based knowledge. In 2016, a Federal Advisory Committee (FAC) was convened to recommend how to conduct a sustained National Climate Assessment (NCA) to increase the relevance and usability of assessments for informing action. The FAC was disbanded in 2017, but members and additional experts reconvened to complete the report that is presented here. A key recommendation is establishing a new nonfederal ‘‘climate assessment consortium’’ to increase the role of state/local/tribal government and civil society in assessments. The expanded process would 1) focus on applied problems faced by practitioners, 2) organize sustained partnerships for collaborative learning across similar projects and case studies to identify effective tested practices, and 3) assess and improve knowledge-based methods for project implementation. Specific recommendations include evaluating climate models and data using user-defined metrics; improving benefit–cost assessment and supporting decision-making under uncertainty; and accelerating application of tools and methods such as citizen science, artificial intelligence, indicators, and geospatial analysis. The recommendations are the result of broad consultation and present an ambitious agenda for federal agencies, state/local/tribal jurisdictions, universities and the research sector, professional associations, nongovernmental and community-based organizations, and private-sector firms.

We estimate the economic benefits of avoiding reductions in drinking water quality due to sea level rise accruing to North Carolina (NC) coastal tourists. Using stated preference methods and responses from recent coastal visitors, we find that tourists are 2%, 8%, and 11% less likely to take an overnight trip if drinking water tastes slightly, moderately, or very salty at their chosen destination. The majority of those who decline a trip would take a trip to another NC beach without water quality issues, others would take another type of recreational trip, with a minority opting to stay home. Willingness to pay for an overnight beach trip declines with the salty taste of drinking water. We find evidence of attribute non‐attendance in the stated preference data, which impacts the regression model and estimates of the willingness to pay for trips. Combining economic and hydrological models, annual aggregate benefit losses due to low drinking water quality could be as high as $232 million by 2040. Key Points: We estimate the benefits to North Carolina coastal tourists of avoiding reductions in drinking water quality due to sea level riseWillingness to pay for an overnight beach trip declines with the salty taste of drinking waterAnnual aggregate benefit losses due to low drinking water quality could be as high as $232 million in 2040 [ABSTRACT FROM AUTHOR]

Using a Bayesian approach we compare anecdotal tsunami runup observations from the 29 December 1820 Flores Sea earthquake with close to 200 000 tsunami simulations to determine the most probable earthquake parameters causing the tsunami. Using a dual hypothesis of the source earthquake either originating from the Flores Thrust or the Walanae/Selayar Fault, we found that neither source perfectly matches the observational data, particularly while satisfying seismic constraints of the region. Instead both posteriors have shifted to the edge of the prior indicating that the actual earthquake may have run along both faults. [ABSTRACT FROM AUTHOR]

In numerical studies of thermal convection that includes a layer of lighter surface fluid, the light fluid naturally forms clusters that bulge downward at downwelling sites. A curious result is that in some cases, the clusters have maximum bulging downward near the sides of the cluster instead of a single bulge downward centred above the downwelling. The fluid mechanics leading to this 'double bulge' formation is analysed. To accomplish this, a simplified model replaces the thermally driven convection cells with driving cells with a fixed speed. Adding a layer of dense fluid on the bottom to the previous configuration leads to bulges along the top and bottom. More importantly, this allows a new scaling that reduces the number of governing parameters from four to three and even to two in this study. The mechanism for the double bulges comes from buoyancy of the clusters. This produces localized vorticity at the sides of the cluster that has the opposite sign of the driving cells. When this vorticity is approximately the same order of magnitude as the driving cell vorticity, a divergence in the middle of each cluster leads to the double bulges. The effect can be so great that the underlying flow cells are tilted so that vertical motion is reversed under the middle of each bulge. [ABSTRACT FROM AUTHOR]

Numerical calculations of two component cellular convection with a lighter component diffusing down from the top are a simple model of the convection of rocky planets with a crust. The crust either is mixed down, floats along the top as blobs (continents separated by ocean basins), or forms layers. The calculations are for very viscous fluid with density variations from temperature and the lighter component representing the crust. If variations are approximately the same size, the lighter component collects along the top into H‐shaped blobs/clusters that have a flat midsection with two lobes on each end. Elevations are calculated for a free upper surface and the shape resembles continent and ocean floor topography with level interiors and thickening (mountains) at the edges produced by sinking at the margins. Between each pair of clusters, thermal and concentration boundary layers resemble ocean basins with spreading centers. Convection is unsteady but introducing internal decay of the lighter concentration produces steady flow. Internal heating produces similar results along with periodic drifting and merging of blobs like some geological cycles. The fact that these features arise without phase changes or viscosity variation implies that blobs of continent‐like crust might be widely found on rocky planets. Plain Language Summary: A simple numerical model of fluid flow has circulation cells driven by buoyancy. The cells are propelled by convection cells like mantle convection. Along the top, a model of a crust with lower density accumulates into a row of shapes. These resemble continents separated by ocean basins. Each accumulation is shaped like a wide capital letter H with a middle plateau and thickening (like mountains) at both ends. Cold, dense surface fluid plunges down next to each end like ocean trenches and subduction zones. These accumulations extend above the fluid surface because of their low density. Midway between each pair of these accumulations, hot fluid rises from the bottom and spreads out. The surface is depressed like ocean basins although the center is slightly elevated like mid‐ocean ridges. Forming these features from flow of a single constant viscosity fluid has not been previously done so the dynamics are discussed. Key Points: Convection cells with lighter fluid diffusing down from the top produce shapes like continents and ocean basins for certain parametersAdding internal heating produces cycles of splitting, drifting, and merging like the Wilson cycleThe calculations are simple and include two diffusivities for temperature and composition. A MATLAB code is included [ABSTRACT FROM AUTHOR]