Bathyraja panthera, a new species of skate (Rajidae: Arhynchobatinae) from the western Aleutian Islands, and resurrection of the subgenus Arctoraja Ishiyama

We provide morphological and molecular evidence to recognize a new species of skate from the North Pacific, Bathyraja panthera. We also resurrect the skate subgenus Arctoraja Ishiyama, confirming its monophyly and the validity of the subgenus. Arctoraja was previously recognized as a distinct subgenus of Breviraja and later synonymized with Bathyraja (family Rajidae). Although the nominal species of Arctoraja have all been considered synonyms of Bathyraja parmifera by various authors, on the basis of morphometric, meristic, chondrological, and molecular data we recognize four species, including the new species. Species of Arctoraja are distributed across the North Pacific Ocean and adjacent seas from southern Japan to British Columbia. Bathyraja parmifera is abundant in the eastern Bering Sea, Aleutian Islands, and northern Gulf of Alaska; B. smirnovi is a western Pacific species found in the Sea of Okhotsk and Sea of Japan; B. simoterus is restricted to waters around the northern and eastern coasts of Hokkaido, Japan; and the new species B. panthera is restricted to the western Aleutian Islands. Bathyraja panthera is diagnosed by its color pattern of light yellow blotches with black spotting on a greenish brown background, high thorn and vertebral counts, chondrological characters of the neurocranium and clasper, and a unique nucleotide sequence within the mitochondrial cytochrome oxidase gene. Furthermore, the species presently recognized as Bathyraja parmifera exhibits two haplotypes among specimens from Alaska, suggesting the possibility of a second, cryptic species.

Chemical contamination in southwest Puerto Rico: a survey of contaminants in the coral Porites astreoides

Coral ( Porites astreoides ) from eight sites in southwest Puerto Rico were analyzed for approximately 150 chemical contaminants, to provide a preliminary characterization of environmental contamination in the corals, and assess the relationships between chemical contamination in corals and adjacent sediments. Overall, the concentration of PAHs (polycyclic aromatic hydrocarbons) and PCBs (polychlorinated biphenyls) detected in the limited number of coral samples collected were comparable to concentrations found in sediments. However, the concentration of a chemical contaminant (e.g., PAHs) in the corals at a site was often different from what was found in adjacent sediments. The level of PCBs and DDT (dichlorodiphenyltrichloroethane) in the corals appeared higher just outside of Guanica Bay, and there was some evidence of a downstream concentration gradient for these two contaminant classes. The trace elements copper and zinc were frequently detected in Porites astreoides , and the concentrations were usually comparable to those found in adjacent sediments. Chromium was an exception in that it was not detected in any of the coral samples analyzed, although it was detected in all of the sediment samples.

Chemical contaminants in the coral Porites astreoides from southwest Puerto Rico

This report presents an initial characterization of chemical contamination in coral tissues (Porites astreoides) from southwest Puerto Rico. It is the second technical report from a project to characterize chemical contaminants and assess linkages between contamination and coral condition. The first report quantified chemical contaminants in sediments from southwest Puerto Rico. This document summarizes the analysis of nearly 150 chemical contaminants in coral tissues. Although only eight coral samples were collected, some observations can be made on the correlations between observed tissue and sediment contaminant concentrations. The concentrations of polycyclic aromatic hydrocarbons (PAHs), typically associated with petroleum spills and the combustion of fossil fuels, and polychlorinated biphenyls (PCBs) in the coral tissues were comparable to concentrations found in adjacent sediments. However, the concentration of a chemical contaminant (e.g., PAHs) in the coral tissues at a particular site was not a good predictor of what was in the adjacent sediments. In addition, the types of PAHs found in the coral tissues were somewhat different (higher ratios of alkylated PAHs) than in sediments. The levels of PCBs and DDT in coral tissues appeared higher just outside of Guanica Bay, and there was evidence of a downstream concentration gradient for these two contaminant classes. The trace elements copper, zinc and nickel were frequently detected in coral tissues, and the concentration in the corals was usually comparable to that found in adjacent sediments. Chromium was an exception in that it was not detected in any of the coral tissues analyzed. Additional work is needed to assess how spatial patterns in chemical contamination affect coral condition, abundance and distribution.

Characterizing Jobos Bay, Puerto Rico: a watershed modeling analysis and monitoring plan

Land-based pollution is commonly identified as a major contributor to the observed deterioration of shallow-water coral reef ecosystem health. Human activity on the coastal landscape often induces nutrient enrichment, hypoxia, harmful algal blooms, toxic contamination and other stressors that have degraded the quality of coastal waters. Coral reef ecosystems throughout Puerto Rico, including Jobos Bay, are under threat from coastal land uses such as urban development, industry and agriculture. The objectives of this report were two-fold: 1. To identify potentially harmful land use activities to the benthic habitats of Jobos Bay, and 2. To describe a monitoring plan for Jobos Bay designed to assess the impacts of conservation practices implemented on the watershed. This characterization is a component of the partnership between the U.S. Department of Agriculture (USDA) and the National Oceanic and Atmospheric Administration (NOAA) established by the Conservation Effects Assessment Project (CEAP) in Jobos Bay. CEAP is a multi-agency effort to quantify the environmental benefits of conservation practices used by private landowners participating in USDA programs. The Jobos Bay watershed, located in southeastern Puerto Rico, was selected as the first tropical CEAP Special Emphasis Watershed (SEW). Both USDA and NOAA use their respective expertise in terrestrial and marine environments to model and monitor Jobos Bay resources. This report documents NOAA activities conducted in the first year of the three-year CEAP effort in Jobos Bay. Chapter 1 provides a brief overview of the project and background information on Jobos Bay and its watershed. Chapter 2 implements NOAA’s Summit to Sea approach to summarize the existing resource conditions on the watershed and in the estuary. Summit to Sea uses a GIS-based procedure that links patterns of land use in coastal watersheds to sediment and pollutant loading predictions at the interface between terrestrial and marine environments. The outcome of Summit to Sea analysis is an inventory of coastal land use and predicted pollution threats, consisting of spatial data and descriptive statistics, which allows for better management of coral reef ecosystems. Chapters 3 and 4 describe the monitoring plan to assess the ecological response to conservation practices established by USDA on the watershed. Jobos Bay is the second largest estuary in Puerto Rico, but has more than three times the shoreline of any other estuarine area on the island. It is a natural harbor protected from offshore wind and waves by a series of mangrove islands and the Punta Pozuelo peninsula. The Jobos Bay marine ecosystem includes 48 km² of mangrove, seagrass, coral reef and other habitat types that span both intertidal and subtidal areas. Mapping of Jobos Bay revealed 10 different benthic habitats of varying prevalence, and a large area of unknown bottom type covering 38% of the entire bay. Of the known benthic habitats, submerged aquatic vegetation, primarily seagrass, is the most common bottom type, covering slightly less than 30% of the bay. Mangroves are the dominant shoreline feature, while coral reefs comprise only 4% of the total benthic habitat. However, coral reefs are some of the most productive habitats found in Jobos Bay, and provide important habitat and nursery grounds for fish and invertebrates of commercial and recreational value.

A habitat-use model to determine essential fish habitat for juvenile brown shrimp (Farfantepenaeus aztecus) in Galveston Bay, Texas

A density prediction model for juvenile brown shrimp (Farfantepenaeus aztecus) was developed by using three bottom types, five salinity zones, and four seasons to quantify patterns of habitat use in Galveston Bay, Texas. Sixteen years of quantitative density data were used. Bottom types were vegetated marsh edge, submerged aquatic vegetation, and shallow nonvegetated bottom. Multiple regression was used to develop density estimates, and the resultant formula was then coupled with a geographical information system (GIS) to provide a spatial mosaic (map) of predicted habitat use. Results indicated that juvenile brown shrimp (<100 mm) selected vegetated habitats in salinities of 15−25 ppt and that seagrasses were selected over marsh edge where they co-occurred. Our results provide a spatially resolved estimate of high-density areas that will help designate essential fish habitat (EFH) in Galveston Bay. In addition, using this modeling technique, we were able to provide an estimate of the overall population of juvenile brown shrimp (<100 mm) in shallow water habitats within the bay of approximately 1.3 billion. Furthermore, the geographic range of the model was assessed by plotting observed (actual) versus expected (model) brown shrimp densities in three other Texas bays. Similar habitat-use patterns were observed in all three bays—each having a coefficient of determination >0.50. These results indicate that this model may have a broader geographic application and is a plausible approach in refining current EFH designations for all Gulf of Mexico estuaries with similar geomorphological and hydrological characteristics.

The sequence and de novo assembly of the giant panda genome

Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.

A QUANTITATIVE ASSESSMENT OF SOURCE CONTRIBUTIONS TO INHALABLE PARTICULATE MATTER POLLUTION IN METROPOLITAN BOSTON

In this paper, source apportionment techniques are employed to identify and quantify the major particle pollution source classes affecting a monitoring site in metropolitan Boston, MA. A Principal Component Analysis (PCA) of paniculate elemental data allows the estimation of mass contributions for five fine mass panicle source classes (soil, motor vehicle, coal related, oil and salt aerosols), and six coarse panicle source classes (soil, motor vehicle, refuse incineration, residual oil, salt and sulfate aerosols). Also derived are the elemental characteristics of those source aerosols and their contributions to the total recorded elemental concentrations (i.e. an elemental mass balance). These are estimated by applying a new approach to apportioning mass among various PCA source components: the calculation of Absolute Principal Component Scores, and the subsequent regression of daily mass and elemental concentrations on these scores.

Yangtze- and Taiwan-derived sediments on the inner shelf of East China Sea

X-ray diffraction (XRD) mineralogical and grain-size analyses indicate that inner continental shelf sediments in the East China Sea (ECS) represent a unique mixing of clays derived from the Yangtze River and silts/sands from small western Taiwanese rivers. Taiwanese (e g., Choshui) clays (< 2 mu m) display no smectite but the best illite crystallinity and are only distributed along southeastern Taiwan Strait. Both Yangtze and Taiwanese river clays are illite-dominated, but the poor illite crystallinity and the presence of smectite and kaolinite indicate that Taiwan Strait clays are mainly Yangtze-dominated. In contrast, medium silts (20-35 mu m) and very fine sands (63-90 mu m) in the Taiwan Strait are characterized by low feldspar/quartz, low K-feldspar/plagioclase and high kaolinite/quartz, indicating their provenance from Taiwanese rivers. Taiwanese silts and sands are introduced primarily by the way of typhoon-derived floods and transported northward by the Taiwan Warm Current during summer-fall months. Yangtze clays, in contrast, are widely dispersed southward about 1000 km to the western Taiwan Strait, transported by the China Coastal Current during winter-spring months Since most Taiwan Strait samples were collected in May 2006, clay results in this paper might only represent the winter-spring pattern of the dispersal of Yangtze sediments. (C) 2009 Elsevier Ltd. All rights reserved.

Colliding and Moving Bose-Einstein Condensates: Studies of superfluidity and optical tweezers for condensate transport

In this thesis, two different sets of experiments are described. The first is an exploration of the microscopic superfluidity of dilute gaseous Bose- Einstein condensates. The second set of experiments were performed using transported condensates in a new BEC apparatus. Superfluidity was probed by moving impurities through a trapped condensate. The impurities were created using an optical Raman transition, which transferred a small fraction of the atoms into an untrapped hyperfine state. A dramatic reduction in the collisions between the moving impurities and the condensate was observed when the velocity of the impurities was close to the speed of sound of the condensate. This reduction was attributed to the superfluid properties of a BEC. In addition, we observed an increase in the collisional density as the number of impurity atoms increased. This enhancement is an indication of bosonic stimulation by the occupied final states. This stimulation was observed both at small and large velocities relative to the speed of sound. A theoretical calculation of the effect of finite temperature indicated that collision rate should be enhanced at small velocities due to thermal excitations. However, in the current experiments we were insensitive to this effect. Finally, the factor of two between the collisional rate between indistinguishable and distinguishable atoms was confirmed. A new BEC apparatus that can transport condensates using optical tweezers was constructed. Condensates containing 10-15 million sodium atoms were produced in 20 s using conventional BEC production techniques. These condensates were then transferred into an optical trap that was translated from the ‘production chamber’ into a separate vacuum chamber: the ‘science chamber’. Typically, we transferred 2-3 million condensed atoms in less than 2 s. This transport technique avoids optical and mechanical constrainsts of conventional condensate experiments and allows for the possibility of novel experiments. In the first experiments using transported BEC, we loaded condensed atoms from the optical tweezers into both macroscopic and miniaturized magnetic traps. Using microfabricated wires on a silicon chip, we observed excitation-less propagation of a BEC in a magnetic waveguide. The condensates fragmented when brought very close to the wire surface indicating that imperfections in the fabrication process might limit future experiments. Finally, we generated a continuous BEC source by periodically replenishing a condensate held in an optical reservoir trap using fresh condensates delivered using optical tweezers. More than a million condensed atoms were always present in the continuous source, raising the possibility of realizing a truly continuous atom lase.

Taxi! Urban economies and the social and transport Impacts of the taxicab.

The taxicab provides a significant contribution to the accessibility of a city and provides a wide range of services across many social groups. Considering the role of the taxi this books examines the impacts that the mode currently has, and how it may continue to develop in the provision of access within the city.

The operation of multiquantum-well barriers

The multiquantum barrier (MQB), proposed by Iga et al in 1986, has been shown by several researchers to be an effective structure for improving the operating characteristics of laser diodes. These improvements include a reduction in the laser threshold current and increased characteristic temperatures. The operation of the MQB has been described as providing an increased barrier to electron overflow by reflecting high energy electrons trying to escape from the active region of the laser.This is achieved in a manner analogous to a Bragg reflector in optics. This thesis presents an investigation of the effectiveness of the MQB as an electron reflector. Numerical models have been developed for calculating the electron reflection due to MQB. Novel optical and electrical characterisation techniques have been used to try to measure an increase in barrier height due to the MQB in AlGaInP.It has been shown that the inclusion of MQB structures in bulk double heterostructure visible laser diodes can halve the threshold current above room temperature and the characteristic temperature of these lasers can be increased by up to 20K.These improvements are shown to occur in visible laser diodes even with the inclusion of theoretically ineffective MQB structures, hence the observed improvement in the characteristics of the laser diodes described above cannot be uniquely attributed to an increased barrier height due to enhance electron reflection. It is proposed here that the MQB improves the performance of laser diodes by proventing the diffusion of zinc into the active region of the laser. It is also proposed that the trapped zinc in the MQB region of the laser diode locally increases the p-type doping bringing the quasi-Fermi level for holes closer to the valence band edge thus increasing the barrier to electron overflow in the conduction band.

Synthesis of iminophosphine and phosphinoiminol cyclometallated Pt (II) and Pt (IV) chloro complexes and studies into their biological and photophysical properties

This thesis focuses on the synthesis and analysis of novel chloride based platinum complexes derived from iminophosphine and phosphinoamide ligands, along with studies on their reactivity towards substitution and oxidation reactions. Also explored here are the potential applications of these complexes for biological and luminescent purposes. Chapter one provides an extensive overview of platinum coordination chemistry with examples of various mixed donor ligands along with the history of platinum anticancer therapy. It also looks at metals in medicine, both for biological functions as well as for therapeutic purposes and gives a background to some other applications for platinum complexes. Chapter two outlines the design and synthetic strategies employed for the development of novel platinum (II) chloride complexes from iminophosphine and phosphinoamide ligands. Also reported is the cyclometallation of these complexes to form stable tridentate mixed donor platinum (II) compounds. In Chapter three the development of a direct method for displacing a chloride from a platinum metal centre with a desired phosphine is reported. Numerous methods for successful oxidation of the platinum (II) complexes will also be explored, leading to novel platinum (IV) complexes being reported here also. The importance of stabilisation of the displaced anion, chloride, by the solvent system will also be discussed in this chapter. Chapter four investigates the reactivity of the platinum (II) complexes towards two different biomolecules to form novel platinum bio-adducts. The potential application of the platinum (II) cyclometallates as chemotherapeutics will also be explored here using in-vitro cancer cell testing. Finally, luminescence studies are also reported here for the ligands and platinum complexes reported in chapter two and three to investigate potential applications in this field also. Chapter five provides a final conclusion and an overall summary of the entire project as well as identifying key areas for future work.