The Struggle over the Columbia River Gorge: Establishing and Governing the Country\u27s Largest Scenic Area

This review first considers the historical conditions that coalesced in the late 1970s into the movement calling for federal protection of the Gorge. It then discusses the unlikely and convoluted scenario in which Congress passed and President Ronald Reagan signed into law the Columbia River Gorge National Scenic Area Act in 1986.14 The review then turns to the institutions responsible for implementing the statute: the bi-state Columbia River Gorge Commission; the U.S. Forest Service; six county governments; those agencies’ chief watchdog, the persistent and influential Friends of the Columbia Gorge; and the state legislatures, which control the Commission’s budgets. It then spotlights several Gorge controversies, among them residential developments, commercial uses, a destination resort, a coal power plant, an Indian casino, wind farms, and dam removal. The review concludes with several observations about some enduring themes evident in Durbin’s important case study of this pioneering piece of federal legislation

Smoothed Dissipative Particle Dynamics model for mesoscopic multiphase flows in the presence of thermal fluctuations

Thermal fluctuations cause perturbations of fluid-fluid interfaces and highly nonlinear hydrodynamics in multiphase flows. In this work, we develop a novel multiphase smoothed dissipative particle dynamics model. This model accounts for both bulk hydrodynamics and interfacial fluctuations. Interfacial surface tension is modeled by imposing a pairwise force between SDPD particles. We show that the relationship between the model parameters and surface tension, previously derived under the assumption of zero thermal fluctuation, is accurate for fluid systems at low temperature but overestimates the surface tension for intermediate and large thermal fluctuations. To analyze the effect of thermal fluctuations on surface tension, we construct a coarse-grained Euler lattice model based on the mean field theory and derive a semi-analytical formula to directly relate the surface tension to model parameters for a wide range of temperatures and model resolutions. We demonstrate that the present method correctly models the dynamic processes, such as bubble coalescence and capillary spectra across the interface

Structural phylogeny by profile extraction and multiple superimposition using electrostatic congruence as a discriminator

Phylogenetic analysis of proteins using multiple sequence alignment (MSA) assumes an underlying evolutionary relationship in these proteins which occasionally remains undetected due to considerable sequence divergence. Structural alignment programs have been developed to unravel such fuzzy relationships. However, none of these structure based methods have used electrostatic properties to discriminate between spatially equivalent residues. We present a methodology for MSA of a set of related proteins with known structures using electrostatic properties as an additional discriminator (STEEP). STEEP first extracts a profile, then generates a multiple structural superimposition providing a consolidated spatial framework for comparing residues and finally emits the MSA. Residues that are aligned differently by including or excluding electrostatic properties can be targeted by directed evolution experiments to transform the enzymatic properties of one protein into another. We have compared STEEP results to those obtained from a MSA program (ClustalW) and a structural alignment method (MUSTANG) for chymotrypsin serine proteases. Subsequently, we used PhyML to generate phylogenetic trees for the serine and metallo-β-lactamase superfamilies from the STEEP generated MSA, and corroborated the accepted relationships in these superfamilies. We have observed that STEEP acts as a functional classifier when electrostatic congruence is used as a discriminator, and thus identifies potential targets for directed evolution experiments. In summary, STEEP is unique among phylogenetic methods for its ability to use electrostatic congruence to specify mutations that might be the source of the functional divergence in a protein family. Based on our results, we also hypothesize that the active site and its close vicinity contains enough information to infer the correct phylogeny for related proteins

C4: The New Hampshire Spherulitic Rhyolites: Rocks of Importance to Prehistoric Native Americans

Guidebook for field trips in Western Maine and Northern New Hampshire: New England Intercollegiate Geological Conference, p. 305-316

Patterns of fish utilisation in a tropical Indo-Pacific mangrove-coral seascape, New Caledonia

Mangrove forests are important habitats for fish. However, their utilisation by fish, and the specific values they confer, are still not fully understood. This study describes how fish use mangrove forests in an Indo-Pacific mangrove-coral reef seascape. Sampling was conducted using underwater video cameras (UVCs) to describe spatial and temporal variations in fish assemblages across a small-scale (∼ 2.5 km2) system, and over the tidal and lunar cycle. UVCs were deployed in the two main component habitats of mangrove forests: At the mangrove forest edge, and inside the forest (5 m from the forest edge), to establish patterns of utilisation of fish across the tidal and lunar cycle. Proximity to coral reefs had a strong influence on the mangrove fish community, as most fish recorded were reef-associated. Juveniles of 12 reef species were observed, including two species classified as vulnerable on the IUCN list, and one endemic species. Fish assemblages on the mangrove edge differed significantly from those inside the forest. Most fish utilised the forest edge, with few species making regular use of in-forest habitats, supporting the contention that most fish species remain on the edge and potentially retreat into the forest for opportunistic feeding, or when threatened by larger predators. Species-specific patterns of utilisation varied across the tidal and lunar cycle. Small differences in depth profiles and substrate across the smallscale system had a significant effect on fish assemblages, highlighting the importance of accounting for spatial heterogeneity in these factors. These data provide important information for managers to implement adequate conservation strategies that include broader interconnected habitat mosaics

Hypoxia in mangroves: occurrence and impact on valuable tropical fish habitat

Intertidal mangrove forests are harsh environments that can naturally experience hypoxia in association with low tide. However, we know relatively little about dissolved oxygen (DO) fluctuations and DO-induced responses by fish, although DO is a fundamental water quality parameter. This study examines DO as a potential factor regulating the utilisation of intertidal mangrove forests by fish and consequently their widely recognised feeding, refuge and nursery values. We deployed underwater video cameras, coupled with DO and depth loggers, in a mangrove forest to record changes in fish assemblages in response to tidal variations in DO and other associated environmental parameters. Our results indicate that DO underwent extreme tidal fluctuations, reaching levels as low as 14% saturation. As DO was identified as a significant factor for explaining variability in fish assemblage composition, we further investigated fish responses to DO fluctuations. Higher taxonomic richness and frequencies of occurrence were observed once DO reached 70 %– 80%saturation. More detailed examination revealed speciesspecific responses. Three distinct patterns of mangrove utilisation in response to DO were identified, driven by apparent taxa’s behavioural DO avoidance thresholds. Most taxa did not display any behavioural avoidance, including presence at the lowest DO levels, while other taxa were not observed either below 50 %–60% saturation or below 70 %–80% saturation. This implies that tidal migrations, often observed in intertidal environments, could be the result of differential DO tolerances and are not simply initiated by changes in water depth. Taxa remaining in the mangrove forest even at low DO were on average more frequently observed than the other taxa and were mostly species commonly associated with mangrove habitats. This suggests that being adapted to withstand low DO might be an important condition for using mangrove habitats extensively. The need of being tolerant to low DO could constrain fish utilisation and explain the relatively low species richness often observed in other intertidal mangrove forests

Lunar radiation environment and space weathering from the Cosmic Ray Telescope for the Effects of Radiation (CRaTER)

[1] The Cosmic Ray Telescope for the Effects of Radiation (CRaTER) measures linear energy transfer by Galactic Cosmic Rays (GCRs) and Solar Energetic Particles (SEPs) on the Lunar Reconnaissance Orbiter (LRO) Mission in a circular, polar lunar orbit. GCR fluxes remain at the highest levels ever observed during the space age. One of the largest SEP events observed by CRaTER during the LRO mission occurred on June 7, 2011. We compare model predictions by the Earth-Moon-Mars Radiation Environment Module (EMMREM) for both dose rates from GCRs and SEPs during this event with results from CRaTER. We find agreement between these models and the CRaTER dose rates, which together demonstrate the accuracy of EMMREM, and its suitability for a real-time space weather system. We utilize CRaTER to test forecasts made by the Relativistic Electron Alert System for Exploration (REleASE), which successfully predicts the June 7th event. At the maximum CRaTER-observed GCR dose rate (∼11.7 cGy/yr where Gy is a unit indicating energy deposition per unit mass, 1 Gy = 1 J/kg), GCRs deposit ∼88 eV/molecule in water over 4 billion years, causing significant change in molecular composition and physical structure (e.g., density, color, crystallinity) of water ice, loss of molecular hydrogen, and production of more complex molecules linking carbon and other elements in the irradiated ice. This shows that space weathering by GCRs may be extremely important for chemical evolution of ice on the Moon. Thus, we show comprehensive observations from the CRaTER instrument on the Lunar Reconnaissance Orbiter that characterizes the radiation environment and space weathering on the Moon

MicroRNA regulation of bovine monocyte inflammatory and metabolic networks in an in vivo infection model.

peer-reviewedBovine mastitis is an inflammation-driven disease of the bovine mammary gland that costs the global dairy industry several billion dollars per annum. Because disease susceptibility is a multi-factorial complex phenotype, an integrative biology approach is required to dissect the molecular networks involved. Here, we report such an approach, using next generation sequencing combined with advanced network and pathway biology methods to simultaneously profile mRNA and miRNA expression at multiple time-points (0, 12, 24, 36 and 48h) in both milk and blood FACS-isolated CD14+ monocytes from animals infected in vivo with Streptococcus uberis. More than 3,700 differentially expressed (DE) genes were identified in milk-isolated monocytes (MIMs), a key immune cell recruited to the site of infection during mastitis. Up-regulated genes were significantly enriched for inflammatory pathways, while down-regulated genes were enriched for non-glycolytic metabolic pathways. Monocyte transcriptional changes in the blood, however, were more subtle but highlighted the impact of this infection systemically. Genes up-regulated in blood-isolated-monocytes (BIMs) showed a significant association with interferon and chemokine signalling. Furthermore, twenty-six miRNAs were differentially expressed in MIMs and three in BIMs. Pathway analysis revealed that predicted targets of down-regulated miRNAs were highly enriched for roles in innate immunity (FDR < 3.4E-8) in particular TLR signalling, while up-regulated miRNAs preferentially targeted genes involved in metabolism. We conclude that during S. uberis infection miRNAs are key amplifiers of monocyte inflammatory response networks and repressors of several metabolic pathways.This study was funded in part by Teagasc RMIS 6018 and United States Department of Agriculture ARS funding 3625-32000-102-00. NL is supported by a Teagasc Walsh Fellowship

A computationally engineered RAS rheostat reveals RAS-ERK signaling dynamics.

Synthetic protein switches controlled with user-defined inputs are powerful tools for studying and controlling dynamic cellular processes. To date, these approaches have relied primarily on intermolecular regulation. Here we report a computationally guided framework for engineering intramolecular regulation of protein function. We utilize this framework to develop chemically inducible activator of RAS (CIAR), a single-component RAS rheostat that directly activates endogenous RAS in response to a small molecule. Using CIAR, we show that direct RAS activation elicits markedly different RAS-ERK signaling dynamics from growth factor stimulation, and that these dynamics differ among cell types. We also found that the clinically approved RAF inhibitor vemurafenib potently primes cells to respond to direct wild-type RAS activation. These results demonstrate the utility of CIAR for quantitatively interrogating RAS signaling. Finally, we demonstrate the general utility of our approach in design of intramolecularly regulated protein tools by applying it to the Rho family of guanine nucleotide exchange factors