Analysis of medaka cytochrome P450 3A homotropic and heterotropic cooperativity

We have previously demonstrated that medaka CYP3A is associated with metabolism of several endobiotics including steroids and bile acids. In this study, we demonstrate that medaka CYP3A catalysis exhibits unusual kinetic behaviors consistent with allosteric interaction which cannot be described by hyperbolic kinetic models. Using 7-benzyloxy-4-(trifluoromethyl)-coumarin (BFC) and nonylphenol as CYP3A substrates, we describe both homotropic and heterotropic cooperative interactions. Given the role of CYP3A in maintaining the homeostatic balance for numerous endobiotics, enzymatic activation/inhibition by endocrine disruptors (EDCs) represents a putative (non-genomic) mechanism for endocrine disruption.     

Robust Range-Only Beacon Localization

In this paper, we present a system capable of simultaneously estimating the position of an autonomous underwater vehicle (AUV) and the positions of stationary range-only beacons. Notably, our system does not require beacon positions a priori, and our system performs well even when range measurements are severely degraded by noise and outliers. We present a powerful outlier rejection method that can identify groups of range measurements that are consistent with each other, and a method for initializing beacon positions in an extended Kalman filter (EKF). We have successfully applied our algorithms to real-world data and have demonstrated a simultaneous localization and mapping (SLAM) system whose navigation performance is comparable to that of systems that assume known beacon locations     

Mantle plumes: heat-flow near Iceland

In the first of four pieces arising from Gill Foulger's challenge to the mantle plume hypothesis (last issue), Carol Stein and Seth Stein join the debate with some data and comment on heat-flow around Iceland.     

A requiem for the IFQ in US fisheries?

Despite their apparent economic benefits to harvesters, individual fishing quotas (IFQs) have only been adopted in three US fisheries: Mid-Atlantic surf clam and ocean quahog; South Atlantic wreckfish; and, North Pacific halibut and sablefish. During the 1996 reauthorization of the Magnuson-Stevens Fishery Conservation and Management Act, Congress temporarily blocked implementation of additional IFQ programs in US fisheries. In this paper, we argue that because of the emergence of an alternative, the cooperative, it is unlikely that new IFQs will be adopted in federally managed US fisheries. From an economic perspective, cooperatives offer the advantage of eliminating production externalities that may remain under an IFQ program with relatively large owner classes. More significantly, development of IFQ programs appears to be increasingly overwhelmed by the proliferation of both equity concerns and seemingly interminable rent-seeking behavior — both issues that can effectively block adoption of IFQs. Ironically (and paradoxically?), by reducing the scope of the equity issues acknowledged, the cooperative alternative narrows the pool of claimants and modifies the behavior of the remainder, making implementation more likely. A further irony exists in that IFQs are widely thought to be best designed at the local/regional level while part of the appeal of the cooperative model is that it appears to shortcut the often protracted nature of the local/regional political process by relying on direct intervention from Washington, DC, in the form of actions by Congress or the Justice Department.     

A multi-proxy record of the Last Glacial Maximum and last 14,500?years of paleoenvironmental change at Lone Spruce Pond, southwestern Alaska

Sediment cores from Lone Spruce Pond (60.007°N, 159.143°W), southwestern Alaska, record paleoenvironmental changes during the global Last Glacial Maximum (LGM), and during the last 14,500 calendar years BP (14.5?cal?ka). We analyzed the abundance of organic matter, biogenic silica, carbon, and nitrogen, and the isotope ratios of C and N, magnetic susceptibility, and grain-size distribution of bulk sediment, abundance of alder shrub (Alnus) pollen, and midge (Chironomidae and Chaoboridae) assemblages in a 4.7-m-long sediment sequence from the depocenter at 22?m water depth. The basal unit contains macrofossils dating to 25?C21?cal?ka (the global LGM), and is interpreted as glacial-lacustrine sediment. The open water requires that the outlet of the Ahklun Mountain ice cap had retreated to within 6?km of the range crest. In addition to cladocerans and diatoms, the glacial-lacustrine mud contains chironomids consistent with deep, oligotrophic conditions; several taxa associated with relatively warm conditions are present, suggestive of relative warmth during the global LGM. The glacial-lacustrine unit is separated from the overlying non-glacial lake sediment by a possible disconformity, which might record a readvance of glacier ice. Non-glacial sediment began accumulating around 14.5?cal?ka, with high flux of mineral matter and fluctuating physical and biological properties through the global deglacial period, including a reversal in biogenic-silica (BSi) content during the Younger Dryas (YD). During the global deglacial interval, the ??¹³C values of lake sediment were higher relative to other periods, consistent with low C:N ratios (8), and suggesting a dominant atmospheric CO₂ source of C for phytoplankton. Concentrations of aquatic faunal remains (chironomids and Cladocera) were low throughout the deglacial interval, diversity was low and warm-indicator taxa were absent. Higher production and air temperatures are inferred following the YD, when bulk organic-matter (OM) content (LOI 550?°C) increased substantially and permanently, from 10 to 30?%, a trend paralleled by an increase in C and N abundance, an increase in C:N ratio (to about 12), and a decrease in ??¹³C of sediment. Post-YD warming is marked by a rapid shift in the midge assemblage. Between 8.9 and 8.5?cal?ka, Alnus pollen tripled (25?C75?%), followed by the near-tripling of BSi (7?C19?%) by 8.2?cal?ka, and ??¹⁵N began a steady rise, reflecting the buildup of N and an increase in denitrification in soils. Several chironomid taxa indicative of relatively warm conditions were present throughout the Holocene. Quantitative chironomid-based temperature inferences are complicated by the expansion of Alnus and resulting changes in lake nutrient status and production; these changes were associated with an abrupt increase in cladoceran abundance and persistent shift in the chironomid assemblage. During the last 2,000?years, chironomid-assemblage changes suggest cooler temperatures, and BSi and OM values were generally lower than their maximum Holocene values, with minima during the seventh and eighth centuries, and again during the eighteenth century.     

Deciphering polymetamorphic episodes in high-grade metamorphic orogens: Constraints from PbSL, Sm/Nd and Lu/Hf garnet dating of low- to high-grade metasedimentary rocks from the Kaoko belt (Namibia)

Three dating techniques for metamorphic minerals using the Sm–Nd, Lu–Hf and Pb isotope systems are combined and interpreted in context with detailed petrologic data from crustal segments in NW Namibia. The combination of isochron ages using these different approaches is a valuable tool to testify for the validity of metamorphic mineral dating. Here, PbSL, Lu–Hf and Sm–Nd garnet ages obtained on low- to medium-grade metasedimentary rocks from the Central Kaoko Zone of the Neoproterozoic Kaoko belt (NW Namibia) indicate that these samples were metamorphosed at around 550–560 Ma. On the other hand, granulite facies metasedimentary rocks from the Western Kaoko Zone underwent two phases of high-grade metamorphism, one at ca. 660–625 Ma and another at ca. 550 Ma providing substantial evidence that the 660–625 Ma-event was indeed a major tectonothermal episode in the Kaoko belt. Our age data suggest that interpreting metamorphic ages by applying a single dating method only is not reliable enough when studying complex metamorphic systems. However, a combination of all three dating techniques used here provides a reliable basis for geochronological age interpretation.     

Transport of Crustacean Larvae Between a Low-Inflow Estuary and Coastal Waters

The effectiveness of larval behavior in regulating transport between well-mixed, low-inflow estuaries and coastal waters in seasonally arid climates is poorly known. We determined the flux of an assemblage of benthic crustacean larvae relative to physical conditions between a shallow estuary and coastal waters on the upwelling coast of northern California (38°18′N, 123°03′W) from 29 to 31 March 2006. We detected larval behaviors that regulate transport in adjacent coastal waters and other estuaries for only two taxa in the low-inflow estuary, but they were apparent for taxa outside the estuary. Vertical mixing in the shallow estuary may have overwhelmed larvae of some species, or salinity fluctuations may have been too slight to cue tidal vertical migrations. Nevertheless, all larval stages of species that complete development in nearshore coastal waters were present in the estuary, because they remained low in the water column reducing seaward advection or they were readily exchanged between the estuary and open coast by tidal flows. Weak tidal flows and gravitational circulation at the head of the estuary reduced seaward transport during development for species that completed development nearshore, whereas larval release during nocturnal ebb tides enhanced seaward transport for species that develop offshore. Thus, nonselective tidal processes dominated larval transport for most species back and forth between the low-inflow estuary and open coastal waters, whereas in adjacent open coastal waters, larval behavior in the presence of wind-induced shear was more important in regulating migrations between adult and larval habitats along this upwelling coast.     

GPS for real-time earthquake source determination and tsunami warning systems

We identify the key design aspects of a GPS-based system (and in the future, GNSS-based systems) that could contribute to real-time earthquake source determination and tsunami warning systems. Our approach is based on models of both transient and permanent displacement of GPS stations caused by large earthquakes, while considering the effect of GPS errors on inverted earthquake source parameters. Our main conclusions are that (1) the spatial pattern, magnitude, and timing of permanent displacement of GPS stations can be inverted for the earthquake source and so predict the 3D displacement field of the ocean bottom, thus providing the initial conditions for tsunami models, and (2) there are no inherently limiting factors arising from real-time orbit and positioning errors, provided sufficient near-field GPS stations are deployed. This signal could be readily exploited by GPS networks currently in place, and will be facilitated by the IGS Real-Time Project as it comes to fruition.