Genomic resources for the spotted ragged-tooth shark Carcharias taurus

Genomic data can be a useful tool in the management and conservation of biodiversity. Here, we report the development of genomic resources for the spotted ragged-tooth shark Carcharias taurus using genome-wide DNA data from Illumina next-generation sequencing. We explored two commonly used genetic marker types: microsatellites and mitochondrial DNA. A total of 4 394 putative microsatellites were identified, of which 10 were tested on 24 individuals and found to have ideal properties for population genetic analyses. Additionally, we reconstructed the first complete mitochondrial genome of a South African spotted ragged-tooth shark, and highlight the most informative gene regions to facilitate future primer design. The data reported here may serve as a resource for future studies and can ultimately be applied in the sustainable conservation and fisheries management of this apex predator.     

Preserving Ground Water Samples With Hydrochloric Acid Does Not Result in the Formation of Chloroform

Water samples collected for the determination of volatile organic compounds (VOCs) are often preserved with hydrochloric acid (HCl) to inhibit the biotransformation of the analytes of interest until the chemical analyses can he performed. However, it is theoretically possible that residual free chlorine in the HCl can react with dissolved organic carbon (DOC) to form chloroform via the haloform reaction. Analyses of 1501 ground water samples preserved with HCl from the U.S. Geological Survey's National Water-Quality Assessment Program indicate that chloroform was the most commonly detected VOC among 60 VOCs monitored. The DOC concentrations were not significantly larger in samples with detectable chloroform than in those with no delectable chloroform, nor was there any correlation between the concentrations of chloroform and DOC. Furthermore, chloroform was detected more frequently in shallow ground water in urban areas (28.5% of the wells sampled) than in agricultural areas (1.6% of the wells sampled), which indicates that its detection was more related to urban land-use activities than to sample acidification. These data provide strong evidence that acidification with HCl does not lead to the production of significant amounts of chloroform in ground water samples. To verify these results, an acidification study was designed to measure the concentrations of all trihalomethanes (THMs) that can form as a result of HCl preservation in ground water samples and to determine if ascorbic acid (C₆H₈O₆) could inhibit this reaction if it did occur. This study showed that no THMs were formed as a result of HCl acidification, and that ascorbic acid had no discernible effect on the concentrations of THMs measured.     

Forecast of Tsunamis from the Japan–Kuril–Kamchatka Source Region

This paper describes an investigation of the subfault distribution along the Japan–Kuril–Kamchatka subduction zone for the implementation of a far-field tsunami forecast algorithm. Analyses of seismic data from 1900 to 2000 define the subduction zone, which in turn is divided into 222 subfaults based on the fault characteristics. For unit slip of the subfaults, a linear long-wave model generates a database of mareograms at water-level stations along the subduction zone and at warning points in the North Pacific. When a tsunami occurs, an inverse algorithm determines the slip distribution from near-source water-level records and predicts the waveforms at the warning points using the pre-computed mareograms. A jackknife resampling scheme uses combinations of input water-level records to provide a series of waveform predictions for the computation of the confidence-interval bounds. The inverse algorithm is applied to hindcast two major tsunamis generated from the Japan–Kuril–Kamchatka source and the computed tsunami heights show good agreement with recorded water-level data.     

Chemical remobilization of contaminant metals within floodplain sediments in an incising river system: implications for dating and chemostratigraphy

Metals such as Pb, Zn, Cd and Cu from historical mining activity have been used as stratigraphic markers for dating and provenancing vertically accreted, fine-grained floodplain overbank deposits. This study presents evidence for chemical remobilization of these metals within overbank sediments in the Tyne basin, UK. The evidence includes: breakdown of metal-bearing minerals (sulphides, carbonates, iron and manganese oxyhydroxides); shifts of chemical fractions within zones of relatively low pH towards more soluble and reactive phases; and accumulation of secondary iron and manganese oxyhydroxides at levels related to fluctuating water-table levels or to the breakdown of organic matter. All of this suggests that fine, centimetre-scale, chemostratigraphy using metal concentrations and ratios is unlikely to provide reliable data in river systems that have experienced, or are experiencing, major changes in water-table levels, or pedogenesis. Coarse tens of centimetre- to metre-scale, chemostratigraphy, when applied with caution, may still provide a means of delineating contaminated units. © 1998 John Wiley & Sons, Ltd.     

The dual isotopes of deep nitrate as a constraint on the cycle and budget of oceanic fixed nitrogen

We compare the output of an 18-box geochemical model of the ocean with measurements to investigate the controls on both the mean values and variation of nitrate δ¹⁵N and δ¹⁸O in the ocean interior. The δ¹⁸O of nitrate is our focus because it has been explored less in previous work. Denitrification raises the δ¹⁵N and δ¹⁸O of mean ocean nitrate by equal amounts above their input values for N₂ fixation (for δ¹⁵N) and nitrification (for δ¹⁸O), generating parallel gradients in the δ¹⁵N and δ¹⁸O of deep ocean nitrate. Partial nitrate assimilation in the photic zone also causes equivalent increases in the δ¹⁵N and δ¹⁸O of the residual nitrate that can be transported into the interior. However, the regeneration and nitrification of sinking N can be said to decouple the N and O isotopes of deep ocean nitrate, especially when the sinking N is produced in a low latitude region, where nitrate consumption is effectively complete. The δ¹⁵N of the regenerated nitrate is equivalent to that originally consumed, whereas the regeneration replaces nitrate previously elevated in δ¹⁸O due to denitrification or nitrate assimilation with nitrate having the δ¹⁸O of nitrification. This lowers the δ¹⁸O of mean ocean nitrate and weakens nitrate δ¹⁸O gradients in the interior relative to those in δ¹⁵N. This decoupling is characterized and quantified in the box model, and agreement with data shows its clear importance in the real ocean. At the same time, the model appears to generate overly strong gradients in both δ¹⁸O and δ¹⁵N within the ocean interior and a mean ocean nitrate δ¹⁸O that is higher than measured. This may be due to, in the model, too strong an impact of partial nitrate assimilation in the Southern Ocean on the δ¹⁵N and δ¹⁸O of preformed nitrate and/or too little cycling of intermediate-depth nitrate through the low latitude photic zone.     

The effect of adsorbed lipid on pyrite oxidation under biotic conditions

The chemolithoautotrophic bacterium, Acidithiobacillus ferrooxidans, commonly occurs in acid mine drainage (AMD) environments where it is responsible for catalyzing the oxidation of pyrite and concomitant development of acidic conditions. This investigation reports on the growth of this bacterial species on the pyrite surface and in the aqueous phase at a pH close to 2 as well as the role of adsorbed lipid in preventing pyrite dissolution. Both acid washed pyrite and acid-washed pyrite coated with lipids were used as substrates in the studies. The choice of lipid, 1,2-bis(10,12-tricosadiynoyl)-sn-Glycero-3-Phosphocholine lipid (23:2 Diyne PC), a phosphocholine lipid, was based on earlier work that showed that this lipid inhibits the abiotic oxidation rate of pyrite. Atomic force microscopy showed that under the experimental conditions used in this study, the lipid formed ~4–20 nm layers on the mineral surface. Surface-bound lipid greatly suppresses the oxidation process catalyzed by A. ferrooxidans. This suppression continued for the duration of the experiments (25 days maximum). Analysis of the bacterial population on the pyrite surface and in solution over the course of the experiments suggested that the pyrite oxidation was dependent in large part on the fraction of bacteria bound to the pyrite surface.     

Water quality and sediment geochemistry in lakes of Yunnan Province, southern China

 Yungui Plateau lakes in southwestern China are economically important, although few have been studied previously. Water and sediments of 24 lakes throughout Yunnan Province were sampled in October 1994. We describe the chemical and physical characteristics of Yunnan lakes, and address effects of regional geology and human influences on water quality and sediment type. Water quality differs between deep Yunnan lakes of tectonic origin and shallow solution basins. Shallow lakes generally have higher nutrient concentrations and appear to be more susceptible to riparian disturbance than deeper lakes. Shallow lakes with high macrophyte standing crops, nevertheless, exhibit nutrient-poor waters. Principal ions Ca²⁺, Mg²⁺, and HCO₃ ^– reflect regional carbonate geology, except in Cheng Hai, which is a sodium bicarbonate lake. Specific conductance and δ¹⁸O are positively correlated, indicating that evaporation concentrates both solutes and ¹⁸O. Large, shallow lakes in southeastern Yunnan exhibit ¹⁸O-enriched waters because of substantial evaporation, whereas small, deep lakes are ¹⁸O-depleted. Lake waters are ¹⁸O-depleted in small, shallow basins that receive substantial rainwater input relative to their small volumes. ¹⁸O enrichment in Cheng Hai suggests that a recent 5-m water-level decline in this lake was caused by increased evaporation or diversion of freshwater inflow. Yunnan watersheds have undergone substantial deforestation, agricultural cultivation, soil erosion, and industrialization. Limnetic nutrient concentrations indicate that human activities have affected water quality. Organic matter content is low in sediments because of increased non-carbonate, clastic sediment yield from watersheds. Environmental policies are needed to balance ecological contraints with economic activities that impact water quality. Received: 1 July 1996 / Accepted: 2 October 1996     

UNITED STATES RAILWAY TRAFFIC: AN UPDATE

Recent decades have seen changes in the pattern of rail traffic in the United States. This article describes the development of a United States railroad map depicting current levels of traffic on all rail lines handling over five million gross tons per year. This traffic pattern is compared with the 1929 traffic levels appearing on a similiar map developed by Edward Ullman. Revenue ton-miles have nearly doubled since 1929, with most of the increases concentrated on western and southern lines. Traffic on eastern lines has increased only slightly above 1929 levels.     

A New Late Middle Cambrian Paleomagnetic Pole for the Ellsworth Mountains, Antarctica

A paleomagnetic study of the late Middle to possibly early Late Cambrian Liberty Hills Formation in the Ellsworth Mountains, Antarctica, reveals a stable magnetization with positive fold and reversal tests. The paleopole is based on 16 sites from volcanic and sedimentary rocks and lies at lat 7.3 degrees N and long 326.3 degrees E (A95=6.0&j0;). The new paleomagnetic data support the view that the Ellsworth Mountains are part of a microplate-the Ellsworth-Whitmore Mountains crustal block-that rotated independently of the main Gondwana continental blocks during breakup. The Liberty Hills pole differs from both previous poles recovered from Cambrian rocks in the Ellsworth Mountains and from the available Gondwana reference pole data. Our pole indicates a more northerly prebreakup position for the Ellsworth Mountains than previously suggested, contradicting the overwhelming geologic evidence for a prebreakup position close to southern Africa. The reasons for this are uncertain, but we suggest that problems with the Gondwana apparent polar wander path may be important. More well constrained, early Paleozoic paleomagnetic data are required from the Ellsworth Mountains and the Gondwana continents if the data are to constrain further the Middle-Late Cambrian location of the Ellsworth-Whitmore Mountains block.     

Analytical solution for two-phase flow in a wellbore using the drift-flux model

This paper presents analytical solutions for steady-state, compressible two-phase flow through a wellbore under isothermal conditions using the drift flux conceptual model. Although only applicable to highly idealized systems, the analytical solutions are useful for verifying numerical simulation capabilities that can handle much more complicated systems, and can be used in their own right for gaining insight about two-phase flow processes in wells. The analytical solutions are obtained by solving the mixture momentum equation of steady-state, two-phase flow with an assumption that the two phases are immiscible. These analytical solutions describe the steady-state behavior of two-phase flow in the wellbore, including profiles of phase saturation, phase velocities, and pressure gradients, as affected by the total mass flow rate, phase mass fraction, and drift velocity (i.e., the slip between two phases). Close matching between the analytical solutions and numerical solutions for a hypothetical CO₂ leakage problem as well as to field data from a CO₂ production well indicates that the analytical solution is capable of capturing the major features of steady-state two-phase flow through an open wellbore, and that the related assumptions and simplifications are justified for many actual systems. In addition, we demonstrate the utility of the analytical solution to evaluate how the bottomhole pressure in a well in which CO₂ is leaking upward responds to the mass flow rate of CO₂-water mixture.