Changes in Biotic and Abiotic Processes Following Mangrove Clearing

Mangrove forests, important tropical coastal habitats, are in decline worldwide primarily due to removal by humans. Changes to mangrove systems can alter ecosystem properties through direct effects on abiotic factors such as temperature, light and nutrient supply or through changes in biotic factors such as primary productivity or species composition. Despite the importance of mangroves as transitional habitats between land and sea, little research has examined changes that occur when they are cleared. We examined changes in a number of biotic and abiotic factors following the anthropogenic removal of red mangroves (Rhizophora mangle) in the Panamanian Caribbean, including algal biomass, algal diversity, algal grazing rates, light penetration, temperature, sedimentation rates and sediment organic content. In this first study examining multiple ecosystem-level effects of mangrove disturbance, we found that areas cleared of mangroves had higher algal biomass and richness than intact mangrove areas. This increase in algal biomass and richness was likely due to changes in abiotic factors (e.g. light intensity, temperature), but not biotic factors (fish herbivory). Additionally the algal and cyanobacterial genera dominating mangrove-cleared areas were rare in intact mangroves and included a number of genera that compete with coral for space on reefs. Interestingly, sedimentation rates did not differ between intact and cleared areas, but the sediments that accumulated in intact mangroves had higher organic content. These findings are the first to demonstrate that anthropogenic clearing of mangroves changes multiple biotic and abiotic processes in mangrove forests and that some of these changes may influence adjacent habitats such as coral reefs and seagrass beds. Additional research is needed to further explore the community and ecosystem-level effects of mangrove clearing and their influence on adjacent habitats, but it is clear that mangrove conservation is an important aspect of managing tropical coastal systems

Protective Capactiy of Mangroves During Tropical Storms: A Case Study from \u27Wilma\u27 and \u27Gamma\u27 in Belize

Globally threatened mangrove forest habitat is often considered an important buffer protecting coastlines from wave and storm impacts and coastal erosion. However, there is little empirical data quantifying the protective effects of mangroves during storms, primarily because of the difficulty of predicting where and when a storm will intersect the shoreline, to facilitate data collection before and after storm events. In 2005, opportunistic results from an ongoing study quantifying differences between intact and cleared mangrove areas on Turneffe Atoll, Belize, provided such pre- and post-storm data from tropical storms ‘Wilma’ (later a Category 5 Hurricane) and ‘Gamma’. We compared differences in equipment retention rates of 3 types of experimental devices previously installed in adjacent intact and cleared mangrove areas. Retention rates were greater in intact mangrove areas, empirically demonstrating the protective capacity of mangroves during moderate magnitude storm events. The results support the assumption that removal of mangroves diminishes coastal protection not only during catastrophic storm events such as hurricanes or tsunamis, but also during less energetic but more frequent events, such as tropical storms. This highlights the importance of improved coastal zone management, as storm events may increase in frequency and intensity with changing climate, and coastal mangrove forest habitats continue to decline in size and number

Bridging the Marine-Terrestrial Disconnect to Improve Marine Coastal Zone Science and Management

Coastal zone ecosystems sit between larger terrestrial and marine environments and, therefore, are strongly affected by processes occurring in both systems. Marine coastal zone systems provide a range of benefits to humans, and yet many have been significantly degraded as a result of direct and indirect human impacts. Management efforts have been hampered by disconnects both between management and scientific research and across linked marine–terrestrial systems. Management jurisdictions often start or end at the shoreline, and multiple agencies at different levels of government often have overlapping or conflicting management goals or priorities, or suffer from a lack of knowledge or interest. Scientists also often fail to consider connections among linked marine–terrestrial systems, and communication among agencies, among scientists in different disciplines, and between scientists and managers is often inadequate. However, despite the institutional and scientific challenges inherent in improving coastal zone management, there are examples of increased coordination and cooperation among different organizations. We discuss a number of examples— including where the marine–terrestrial and science–management disconnects persist and where better integration has led to successes in coastal zone management—and provide recommendations to scientists and managers on how to better link their efforts in science and management across marine and terrestrial systems

Electrodynamics of Media

Contains research objectives and reports on two research projects.Joint Services Electronics Programs (U. S. Army, U. S. Navy, and U. S. Air Force) under Contract DA 28-043-AMC-02536(E)National Science Foundation (Grant GK-3370

A Dynamical Mean Field Theory for the Study of Surface Diffusion Constants

We present a combined analytical and numerical approach based on the Mori projection operator formalism and Monte Carlo simulations to study surface diffusion within the lattice-gas model. In the present theory, the average jump rate and the susceptibility factor appearing are evaluated through Monte Carlo simulations, while the memory functions are approximated by the known results for a Langmuir gas model. This leads to a dynamical mean field theory (DMF) for collective diffusion, while approximate correlation effects beyond DMF are included for tracer diffusion. We apply our formalism to three very different strongly interacting systems and compare the results of the new approach with those of usual Monte Carlo simulations. We find that the combined approach works very well for collective diffusion, whereas for tracer diffusion the influence of interactions on the memory effects is more prominent.Comment: 13 pages LaTeX and 6 PostScript figures, style files included. To appear in Surface Science Letter

Pearling and Pinching: Propagation of Rayleigh Instabilities

A new category of front propagation problems is proposed in which a spreading instability evolves through a singular configuration before saturating. We examine the nature of this front for the viscous Rayleigh instability of a column of one fluid immersed in another, using the marginal stability criterion to estimate the front velocity, front width, and the selected wavelength in terms of the surface tension and viscosity contrast. Experiments are suggested on systems that may display this phenomenon, including droplets elongated in extensional flows, capillary bridges, liquid crystal tethers, and viscoelastic fluids. The related problem of propagation in Rayleigh-like systems that do not fission is also considered.Comment: Revtex, 7 pages, 4 ps figs, PR

Variability in Isotope Discrimination Factors in Coral Reef Fishes: Implications for Diet and Food Web Reconstruction

Interpretation of stable isotope ratios of carbon and nitrogen (δ13C and δ15N) is generally based on the assumption that with each trophic level there is a constant enrichment in the heavier isotope, leading to diet-tissue discrimination factors of 3.4‰ for 15N (ΔN) and ∼0.5‰ for 13C (ΔC). Diet-tissue discrimination factors determined from paired tissue and gut samples taken from 152 individuals from 26 fish species at Ningaloo Reef, Western Australia demonstrate a large amount of variability around constant values. While caution is necessary in using gut contents to represent diet due to the potential for high temporal variability, there were significant effects of trophic position and season that may also lead to variability in ΔN under natural conditions. Nitrogen enrichment increased significantly at higher trophic levels (higher tissue δ15N), with significantly higher ΔN in carnivorous species. Changes in diet led to significant changes in ΔN, but not tissue δ15N, between seasons for several species: Acanthurus triostegus, Chromis viridis, Parupeneus signatus and Pomacentrus moluccensis. These results confirm that the use of meta-analysis averages for ΔN is likely to be inappropriate for accurately determining diets and trophic relationships using tissue stable isotope ratios. Where feasible, discrimination factors should be directly quantified for each species and trophic link in question, acknowledging the potential for significant variation away from meta-analysis averages and, perhaps, controlled laboratory diets and conditions

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding

Regulatory proteins can bind to different sets of genomic targets in various cell types or conditions. To reliably characterize such condition-specific regulatory binding we introduce MultiGPS, an integrated machine learning approach for the analysis of multiple related ChIP-seq experiments. MultiGPS is based on a generalized Expectation Maximization framework that shares information across multiple experiments for binding event discovery. We demonstrate that our framework enables the simultaneous modeling of sparse condition-specific binding changes, sequence dependence, and replicate-specific noise sources. MultiGPS encourages consistency in reported binding event locations across multiple-condition ChIP-seq datasets and provides accurate estimation of ChIP enrichment levels at each event. MultiGPS's multi-experiment modeling approach thus provides a reliable platform for detecting differential binding enrichment across experimental conditions. We demonstrate the advantages of MultiGPS with an analysis of Cdx2 binding in three distinct developmental contexts. By accurately characterizing condition-specific Cdx2 binding, MultiGPS enables novel insight into the mechanistic basis of Cdx2 site selectivity. Specifically, the condition-specific Cdx2 sites characterized by MultiGPS are highly associated with pre-existing genomic context, suggesting that such sites are pre-determined by cell-specific regulatory architecture. However, MultiGPS-defined condition-independent sites are not predicted by pre-existing regulatory signals, suggesting that Cdx2 can bind to a subset of locations regardless of genomic environment. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2–5.National Science Foundation (U.S.) (Graduate Research Fellowship under Grant 0645960)National Institutes of Health (U.S.) (grant P01 NS055923)Pennsylvania State University. Center for Eukaryotic Gene Regulatio

RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins

Metazoan genomes encode hundreds of RNA-binding proteins (RBPs). These proteins regulate post-transcriptional gene expression and have critical roles in numerous cellular processes including mRNA splicing, export, stability and translation. Despite their ubiquity and importance, the binding preferences for most RBPs are not well characterized. In vitro and in vivo studies, using affinity selection-based approaches, have successfully identified RNA sequence associated with specific RBPs; however, it is difficult to infer RBP sequence and structural preferences without specifically designed motif finding methods. In this study, we introduce a new motif-finding method, RNAcontext, designed to elucidate RBP-specific sequence and structural preferences with greater accuracy than existing approaches. We evaluated RNAcontext on recently published in vitro and in vivo RNA affinity selected data and demonstrate that RNAcontext identifies known binding preferences for several control proteins including HuR, PTB, and Vts1p and predicts new RNA structure preferences for SF2/ASF, RBM4, FUSIP1 and SLM2. The predicted preferences for SF2/ASF are consistent with its recently reported in vivo binding sites. RNAcontext is an accurate and efficient motif finding method ideally suited for using large-scale RNA-binding affinity datasets to determine the relative binding preferences of RBPs for a wide range of RNA sequences and structures

Environmental and Genetic Determinants of Colony Morphology in Yeast

Nutrient stresses trigger a variety of developmental switches in the budding yeast Saccharomyces cerevisiae. One of the least understood of such responses is the development of complex colony morphology, characterized by intricate, organized, and strain-specific patterns of colony growth and architecture. The genetic bases of this phenotype and the key environmental signals involved in its induction have heretofore remained poorly understood. By surveying multiple strain backgrounds and a large number of growth conditions, we show that limitation for fermentable carbon sources coupled with a rich nitrogen source is the primary trigger for the colony morphology response in budding yeast. Using knockout mutants and transposon-mediated mutagenesis, we demonstrate that two key signaling networks regulating this response are the filamentous growth MAP kinase cascade and the Ras-cAMP-PKA pathway. We further show synergistic epistasis between Rim15, a kinase involved in integration of nutrient signals, and other genes in these pathways. Ploidy, mating-type, and genotype-by-environment interactions also appear to play a role in the controlling colony morphology. Our study highlights the high degree of network reuse in this model eukaryote; yeast use the same core signaling pathways in multiple contexts to integrate information about environmental and physiological states and generate diverse developmental outputs