bluuebunny/crossref_metadata_2025 huggingface dataset:
A modeling tool to evaluate regional coral reef responses to changes in climate and ocean chemistry
Authors: Buddemeier Robert W. , Jokiel Paul L. , Zimmerman Kirby M. , Lane Diana R. , Carey Julie M. , Bohling Geoffrey C. , Martinich Jeremy A.
Published: April 2011

We developed a spreadsheet‐based model for the use of managers, conservationists, and biologists for projecting the effects of climate change on coral reefs at local‐to‐regional scales. The COMBO (Coral Mortality and Bleaching Output) model calculates the impacts to coral reefs from changes in average SST and CO2 concentrations, and from high temperature mortality (bleaching) events. The model uses a probabilistic assessment of the frequency of high temperature events under a future climate to address scientific uncertainties about potential adverse effects. COMBO offers data libraries and default factors for three selected regions (Hawai'i, Great Barrier Reef, and Caribbean), but it is structured with user‐selectable parameter values and data input options, making possible modifications to reflect local conditions or to incorporate local expertise. Preliminary results from sensitivity analyses and simulation examples for Hawai'i demonstrate the relative importance of high temperature events, increased average temperature, and increased CO2 concentration on the future status of coral reefs; illustrate significant interactions among variables; and allow comparisons of past environmental history with future predictions.
Artifacts in measurements of chlorophyll fluorescence transients, with specific application to fast repetition rate fluorometry
Authors: Laney Samuel R. , Letelier Ricardo M.
Published: April 2011

A theoretical framework was developed to describe how instrument and sample artifacts affect measurements of variable fluorescence transients in phytoplankton. This framework identified the proper procedure for correcting for common artifacts in the transients measured with a widely used instrument, the Fasttracka fast repetition rate fluorometer. The impulse response of this fluorometer can be substantial, requiring correction for a dynamic instrument artifact in addition to the static artifacts that can be assessed using traditional “blanks.” In a low‐biomass region of the North Pacific, approximately one‐third of the fluorescence transient measured with this instrument represented such artifacts. Correcting for these using filtered seawater blanks only, and not accounting for the instrument's own response, failed to remove errors as high as 22% in estimates in the photochemical yield and as much as −16% to +22% in estimates of the functional cross section of Photosystem II. This analytical framework and the corrective procedure are generalized and can be used to determine how a wide range of artifacts affect measured variable fluorescence transients, including those characteristic of fluorometers other than the Fasttracka or those more relevant in meso‐ or eutrophic regions of the ocean.
Isolation of microsatellites from unknown genomes using known genomes as enrichment templates
Authors: Leese Florian , Mayer Christoph , Held Christoph
Published: April 2011

This study analyzes the performance of a method to isolate microsatellites from largely unknown target genomes. This reporter genome protocol (RGP) utilizes naturally occurring repeat motifs in genomes of distantly related organisms as hybridization probes. The RGP proved very successful in all 13 enrichment reactions from eight marine target species (comprising a dinoflagellate, a diatom, and six arthropod species), yielding on average 85.5% positive colonies. The RGP naturally screens for all repeat types occurring in the reporter genomes and is therefore less biased than standard protocols that typically test few, short motifs only. Using the genomes of Mus musculus, Drosophila melanogaster, and Homo sapiens as reporter genomes in this study, 133 different di‐ to hexanucleotide repeat types were obtained. Success of the RGP did not depend on overall microsatellite density in the reporter genome but increased with genetic distance between target and reporter genomes because hybridization to conserved nonrepeat regions is less frequent. Relative abundance of repeat types in the reporter genome had a significant effect on repeat type frequencies in the target library. Altogether, the RGP greatly simplifies the isolation of microsatellites from unknown genomes and makes microsatellite markers more attractive for a wide range of studies.
The use of denaturing gradient gel electrophoresis with fully degenerate pufM primers to monitor aerobic anoxygenic phototrophic assemblages
Authors: Yutin Natalya , Béjà Oded , Suzuki Marcelino T.
Published: April 2011

Aerobic Anoxygenic Photosynthetic bacteria (AAnP) were recently proposed to be significant contributors to the global ocean carbon and energy cycles, but relatively little is known about the spatial and temporal distribution of AAnP populations. Here, we report on the development of denaturing gradient gel electrophoresis (DGGE) analyses to monitor naturally occurring marine AAnP populations using the pufM gene. We developed an approach using fully degenerate universal pufM primers, and tested the effect of different primers and PCR conditions on DGGE band resolution and migration. PufM‐DGGE analyses of eastern Mediterranean environmental DNA samples show that AAnP composition was coherent among stations and seasons. Furthermore, samples from different depths of stratified water columns resulted in clearly different DGGE patterns, while very similar DGGE patterns at varying depths were observed under well‐mixed conditions. These results demonstrate the potential use of DGGE with fully degenerate primers as a tool for rapid analyses of natural marine AAnP communities.
High‐frequency, accurate measurement of dimethylsulfide in surface marine environments using a microporous membrane contactor
Authors: Park Ki‐Tae , Lee Kitack
Published: April 2011

An automated sampling and analysis system for the shipboard measurement of dissolved dimethylsulfide (DMS) in surface marine waters is described. The system includes DMS extraction and trapping devices, a gas chromatograph (GC) equipped with a flame photometric detector (FPD), and a data acquisition system based on Visual Basic 6.0/C 6.0. The DMS is continuously and rapidly extracted from a seawater stream flowing at 100 mL min−1 across the hydrophobic wall pores of a membrane contactor. The stripping gas stream containing DMS flows at a rate of 300 mL min−1 for 1 min through an 8 cm Tenax‐TA‐filled glass tube controlled at −10°C by a thermoelectric cooler, within which DMS is selectively trapped. The trapped DMS is released by heating the trap to 160°C and is quantified by the GC‐FPD. The detection limit of the proposed automated system is 0.2 nM of S (DMS), and the analytical precision is better than 3%. A complete analytical cycle takes 7 min from the extraction of DMS from the seawater stream to measurement of the DMS peak area, which is 3–4 times shorter than has been achieved using sparge‐trap analytical setups. In field operations, the system runs on a daily cycle during which three DMS standards are measured at the beginning of the cycle and DMS derived from the seawater stream is subsequently analyzed throughout the day. The successful application of this analysis system to coastal waters suggests that the proposed DMS detection method will greatly facilitate data collection in future biogeochemical studies of the marine environment.
Hydrodynamic characterization and performance of an autonomous benthic chamber for use in coastal systems
Authors: Ferrón Sara , Alonso‐Pérez Fernando , Castro Carmen G. , Ortega Teodora , Pérez Fiz F. , Ríos Aída F. , Gómez‐Parra Abelardo , Forja Jesús M.
Published: April 2011

A benthic chamber (covering 5030 cm2 of seafloor) with real‐time control of sampling and sensor data transmission has been developed for studying benthic fluxes in coastal sediments. Enclosed water is stirred by three submersible centrifugal pumps, which are connected to power circuits that regulate their input voltage, and thus, the current velocity inside the chamber. The complete mixing of the incubated water is achieved within 4 min. The 3‐D velocity field and the distribution of the diffusive boundary layer (DBL) inside the chamber were characterized at different pump rates in a laboratory tank with a bottom layer of sediment or a false bottom supporting alabaster dissolution plates. Two different outlet devices from the pumps were tested. For the one finally selected, averaged tangential velocities at 5 cm above the bottom ranged from 2.0 cm s−1 to 4.8 cm s−1, depending on the voltage applied to the pumps, providing averaged DBL thicknesses that ranged from 125 µm to 279 µm. Average tangential velocity and average DBL thickness were found to correlate according to: VH = 615 × [DBL]−1.02 (R2 = 0.97). Successful field chamber measurements were performed in two shallow coastal systems: Ría de Vigo (NW Spain) and Bay of Cádiz (SW Spain).
Advanced laser fluorometry of natural aquatic environments
Authors: Chekalyuk Alexander , Hafez Mark
Published: April 2011

The Advanced Laser Fluorometer (ALF) provides spectral deconvolution (SDC) analysis of the laser‐stimulated emission (LSE) excited at 405 or 532 nm for assessment of chlorophyll a, phycoerythrin, and chromophoric dissolved organic matter. Three spectral types of phycoerythrin are discriminated for characterization of cyanobacteria and cryptophytes in mixed phototrophic populations. The SDC analysis is integrated with measurements of variable fluorescence, Fv/Fm, corrected for the SDC‐retrieved background fluorescence, BNC, for improved photophysiological assessments of phytoplankton. The ALF deployments in the Atlantic and Pacific Oceans, and Chesapeake, Delaware, and Monterey Bays revealed significant spectral complexity of LSE. Considerable variability in chlorophyll a fluorescence peak, 673‐685 nm, was detected. High correlation (R2 = 0.93) was observed in diverse water types between chlorophyll a concentration and fluorescence normalized to water Raman scattering. Three unidentified red bands, peaking at 625, 644, and 662 nm, were detected in the LSE excited at 405 nm. Significant variability in the BNC/chlorophyll a ratio was observed in diverse waters. Examples of the ALF spectral correction of Fv/Fm, underway shipboard measurements of horizontal variability, and vertical distributions compiled from the discrete samples analyses are presented. The field deployments have demonstrated the utility of the ALF technique as an integrated tool for research and observations.
Field applications of the second‐generation Environmental Sample Processor (ESP) for remote detection of harmful algae: 2006‐2007
Authors: Greenfield Dianne I. , Marin Roman , Doucette Gregory J. , Mikulski Christina , Jones Kelly , Jensen Scott , Roman Brent , Alvarado Nilo , Feldman Jason , Scholin Chris
Published: April 2011

We assess the application of the second‐generation Environmental Sample Processor (ESP) for the detection of harmful algal bloom (HAB) species in field and laboratory settings using two molecular probe techniques: a sandwich hybridization assay (SHA) and fluorescent in situ hybridization (FISH). During spring 2006, the first time this new instrument was deployed, the ESP successfully automated application of DNA probe arrays for various HAB species and other planktonic taxa, but non‐specific background binding on the SHA probe array support made results interpretation problematic. Following 2006, the DNA array support membrane that we were using was replaced with a different membrane, and the SHA chemistry was adjusted. The sensitivity and dynamic range of these modifications were assessed using 96‐well plate and ESP array SHA formats for several HAB species found commonly in Monterey Bay over a range of concentrations; responses were significantly correlated (p < 0.01). Modified arrays were deployed in 2007. Compared to 2006, probe arrays showed improved signal:noise, and remote detection of various HAB species was demonstrated. We confirmed that the ESP and affiliated assays can detect HAB populations at levels below those posing human health concerns, and results can be related to prevailing environmental conditions in near real‐time.
A nonparametric method for the measurement of size diversity with emphasis on data standardization
Authors: Quintana Xavier D. , Brucet Sandra , Boix Dani , López‐Flores Rocío , Gascón Stéphanie , Badosa Anna , Sala Jordi , Moreno‐Amich Ramon , Egozcue Juan J.
Published: April 2011

The most suitable method for estimation of size diversity is investigated. Size diversity is computed on the basis of the Shannon diversity expression adapted for continuous variables, such as size. It takes the form of an integral involving the probability density function (pdf) of the size of the individuals. Different approaches for the estimation of pdf are compared: parametric methods, assuming that data come from a determinate family of pdfs, and nonparametric methods, where pdf is estimated using some kind of local evaluation. Exponential, generalized Pareto, normal, and log‐normal distributions have been used to generate simulated samples using estimated parameters from real samples. Nonparametric methods include discrete computation of data histograms based on size intervals and continuous kernel estimation of pdf. Kernel approach gives accurate estimation of size diversity, whilst parametric methods are only useful when the reference distribution have similar shape to the real one. Special attention is given for data standardization. The division of data by the sample geometric mean is proposed as the most suitable standardization method, which shows additional advantages: the same size diversity value is obtained when using original size or log‐transformed data, and size measurements with different dimensionality (longitudes, areas, volumes or biomasses) may be immediately compared with the simple addition of ln k where k is the dimensionality (1, 2, or 3, respectively). Thus, the kernel estimation, after data standardization by division of sample geometric mean, arises as the most reliable and generalizable method of size diversity evaluation.
A submersible three‐dimensional particle tracking velocimetry system for flow visualization in the coastal ocean
Authors: Smith W.A.M. Nimmo
Published: April 2011

A submersible three‐dimensional particle tracking velocimetry (3D‐PTV) system has been developed to investigate the form and dynamics of coherent vortical structures within the bottom boundary layer of the coastal ocean. The system consists of four high‐resolution digital cameras operating simultaneously to record the tracks of naturally occurring suspended particles within a 20 × 20 × 20 cm sample volume. The system has been deployed close to the seabed in Plymouth Sound, UK, and data recorded at 25 Hz in 20 min duration bursts. On average, about 150 particles can be tracked within the sample volume for durations in excess of 2.4 s (60 frames). Instantaneous three‐dimensional velocity fields show that moderate flows within the tidal bottom boundary layer are mostly quiescent and interspersed by coherent vortices, consistent with previous observations using other techniques.
Quantifying fluxes and characterizing compositional changes of dissolved organic matter in aquatic systems in situ using combined acoustic and optical measurements
Authors: Downing Bryan D. , Boss Emmanuel , Bergamaschi Brian A. , Fleck Jacob A. , Lionberger Megan A. , Ganju Neil K. , Schoellhamer David H. , Fujii Roger
Published: April 2011

Studying the dynamics and geochemical behavior of dissolved and particulate organic material is difficult because concentration and composition may rapidly change in response to aperiodic as well as periodic physical and biological forcing. Here we describe a method useful for quantifying fluxes and analyzing dissolved organic matter (DOM) dynamics. The method uses coupled optical and acoustic measurements that provide robust quantitative estimates of concentrations and constituent characteristics needed to investigate processes and calculate fluxes of DOM in tidal and other lotic environments. Data were collected several times per hour for 2 weeks or more, with the frequency and duration limited only by power consumption and data storage capacity. We assessed the capabilities and limitations of the method using data from a winter deployment in a natural tidal wetland of the San Francisco Bay estuary. We used statistical correlation of in situ optical data with traditional laboratory analyses of discrete water samples to calibrate optical properties suited as proxies for DOM concentrations and characterizations. Coupled with measurements of flow velocity, we calculated long‐term residual horizontal fluxes of DOC into and out from a tidal wetland. Subsampling the dataset provides an estimate for the maximum sampling interval beyond which the error in flux estimate is significantly increased.
Improved algorithm for the computation of nitrate concentrations in seawater using an in situ ultraviolet spectrophotometer
Authors: Sakamoto Carole M. , Johnson Kenneth S. , Coletti Luke J.
Published: April 2011

Improvements in the data processing algorithm and calibration procedures have greatly increased the accuracy of nitrate measurements using an in situ ultraviolet spectrophotometer (ISUS). Two major changes in the algorithm involve application of a temperature‐dependent correction to the bromide spectrum and then using the observed temperature and salinity to subtract the bromide component before fitting nitrate. By reducing the degrees of freedom in calculating nitrate concentrations, the accuracy of the ISUS instrument is substantially improved. The new algorithm was tested in environments ranging from the Southern Ocean to oligotrophic eastern Pacific seawater and found to be applicable at all temperatures and depths. The standard error of the estimate for regression between ISUS nitrate values and discrete samples measured by standard wet chemistry methods for the combined data set is reduced by greater than 2‐fold (1.4 down to 0.65 µM) using the new algorithm. This corresponds to a 5‐fold reduction in variance (2.0 down to 0.4 µM2). Although biofouling and calibration drift remain issues for any instrument deployed in situ for long periods of time, using the measured salinity and temperature to correct the ultraviolet spectra before the nitrate calculations will reduce the impacts of these confounding processes.
Cell homogenization and subcellular fractionation in two phytoplanktonic algae: implications for the assessment of metal subcellular distributions
Authors: Lavoie Michel , Bernier Jonathan , Fortin Claude , Campbell Peter G.C.
Published: April 2011

Metal subcellular distribution in phytoplankton is of interest from both ecotoxicologic and trophic transfer perspectives. Differential centrifugation preceded by cell disruption is frequently used to separate metals in different intracellular compartments. Homogenization efficiency varies widely among species, however, and a quantitative assessment of this parameter is necessary. Moreover, fractions isolated by differential centrifugation remain operationally defined, and confirmation of the nature of these fractions is thus needed. In the present study, homogenization efficiencies for two chlorophytes were evaluated for different methods (sonicator, beadbeater, rotor‐stator homogenizer). For the most promising approach (sonication), homogenization efficiency was optimized, using a particle counter, 14C uptake, and growth experiments. The separation efficiency of a subcellular fractionation protocol was also optimized and applied to algae that had been exposed to environmentally relevant concentrations of Cd (0.7 nM Cd2+). The homogenization efficiency could be reliably estimated with the particle counter. Contrasting homogenization efficiencies were obtained for the two test species; virtually all C. reinhardtii cells were easily broken, whereas a large proportion of P. subcapitata cells remained intact (73.2 ± 2.8%). Failure to consider the specific homogenization efficiency for P. subcapitata cells would lead to a greater than threefold underestimate of Cd quotas in the organelle and cytosol fractions.
Evaluation of oscillating grids and orbital shakers as means to generate isotropic and homogeneous small‐scale turbulence in laboratory enclosures commonly used in plankton studies
Authors: Guadayol Òscar , Peters Francesc , Stiansen Jan Erik , Marrasé Cèlia , Lohrmann Atle
Published: April 2011

The effects of turbulent motion on planktonic organisms have mainly been studied in the laboratory with devices capable of generating controlled turbulent conditions. Owing to technical and logistical difficulties, thorough assessments of hydrodynamics in such experiments are not routinely made. In this study, we examined the suitability of two widely used systems to generate isotropic, homogeneous, and stationary turbulence in laboratory containers: oscillating grid devices with large stroke length and relatively low frequencies of oscillation and orbital shaker tables. Turbulent kinetic energy dissipation rates were estimated from velocity measurements made with acoustic Doppler velocimeters. Both systems were shown to generate isotropic conditions in a relatively broad range of dissipation rates. Grid‐stirred tanks produce homogeneous turbulence in both the horizontal and vertical dimensions, as long as stroke length is comparable to the height of the container. Turbulence in orbital shakers is not completely homogeneous, as it depends on the distance to the wall and to the surface. Empirical models are derived as a tool for the calculation of dissipation rates in the two systems within the ranges and conditions examined in this study.
Profiling neutral lipids in individual fish larvae by using short‐column gas chromatography with flame ionization detection
Authors: Hooper Tara , Parrish Christopher C.
Published: April 2011

The triacylglycerol (TAG) to sterol (ST) ratio, which has been used to determine the condition index in marine species, has regularly been measured via thin‐layer chromatography with flame ionization detection (TLC/FID) using the Chromarod‐Iatroscan system. However, this method is labor intensive, requires long analysis times, and has a detection limit of ~50 ng. For the determination of lipids in very small samples such as individual fish larvae, short‐column gas chromatography with flame ionization detection (GC/FID) provides an excellent alternative to Iatroscan TLC/FID, owing to its lower detection limit (~1 ng for high‐molecular‐weight TAG and ~0.1 ng for lower‐molecular‐weight species). As well, GC/FID individually profiles lipids based on their carbon number, whereas TLC/FID groups lipids according to their lipid class. Here we describe a method for the determination of neutral lipids from individual Cyclopterus lumpus (lumpfish) and Myoxocephalus scorpius (short‐horn sculpin) larvae using short‐column GC/FID. By using an internal standard and applying weight correction factors, ST and TAG can be accurately and precisely measured. The results reveal that there were no significant differences between GC/FID and TLC/FID in the quantification of TAG or ST in individual fish larvae (P > 0.05); however, GC/FID is more sensitive, precise, rapid, and cost‐efficient.
Application of cross‐flow ultrafiltration for isolating exopolymeric substances from a marine diatom (Amphora sp.)
Authors: Zhang Saijin , Santschi Peter H.
Published: April 2011

The increasing recognition of the roles that exopolymeric substances (EPS) play in the aquatic environment necessitates obtaining sufficient quantities of purified EPS for exploration of its physical, chemical, and biological properties, as well as for quantitative and structural analysis of its composition. For this purpose, three preconcentration/ purification techniques, i.e., 1) ethanol precipitation, 2) stirred‐cell ultrafiltration, and 3) cross‐flow ultrafiltration, followed by stirred‐cell diafiltration, were compared for their effectiveness to quantitatively isolate EPS from laboratory cultures of Amphora sp. The results showed that the classical ethanol precipitation method was not effective in isolating and concentrating EPS from this seawater culture medium. Stirredcell ultrafiltration appeared best for harvesting EPS from this diatom. However, because of its limitations in terms of time and volume, cross‐flow ultrafiltration needed to be first applied, along with some necessary improvements, followed by a three‐step cartridge soaking and stirred‐cell diafiltration. After cartridge soaking, the yields of the two ultrafiltration methods were comparable. Two different fractions were obtained from EPS of Amphora sp. by anion exchange chromatography and were characterized respectively. Whereas these purified fractions had similar molecular weights of 1000 kDa, their monosaccharide composition was different. In conclusion, cross‐flow ultrafiltration followed by stirred‐cell diafiltration with additional cartridge washing turned out to be the optimal method for EPS separation, based on time, cost, and yield.
Characterization of low molecular weight dissolved organic nitrogen by liquid chromatography‐electrospray ionization‐mass spectrometry
Authors: Curtis‐Jackson Philippa K. , Massé Guillaume , Gledhill Martha , Fitzsimons Mark F.
Published: April 2011

Low molecular weight (LMW; <1 kDa) dissolved organic nitrogen (DON) is the dominant DON fraction in marine systems. However, existing methods for DON characterization exclude this fraction through size exclusion or destruction during sample hydrolysis. In this study, we developed a method for the extraction and analysis of LMW peptides in saline waters. The procedure involves a solid phase extraction (SPE) preconcentration step using a polystyrene‐divinylbenzene sorbent, then elution and detection by liquid chromatographyelectrospray ionization‐mass spectrometry (LC/ESI/MS). The procedure was tested with 1‐L water samples containing peptides (10 ng L−1) ranging from 188.2‐1946.0 Da. The analytes were characterized using “top‐down” sequencing to confirm their structure, and the method was then successfully applied to saline water samples extracted from a mono‐algal culture of Phaeodactylum tricornutum. This enabled a number of unknown analytes to be partially sequenced (complete sequencing should be possible using additional MSn scans and larger sample volumes). The method allows for the detection of peptides at the ng L−1 level and further preconcentration is possible. The SPE step allowed determination of peptides from saline water, a matrix incompatible with direct LC/MS analysis. The method can, therefore, be used in DON characterization studies.
Macro camera temperature logger array for deep‐sea hydrothermal vent and benthic studies
Authors: Rinke Christian , Lee Raymond W.
Published: April 2011

Long‐term observations of faunal communities are essential to identify biological and ecological key phenomena. Observational studies of deep sea habitats such as hydrothermal vents, however, have been restricted by technological limitations. Here we describe our recently developed instrument SMOKE (Submersible Macrophotography Observation Kamera Equipment) that was used for time‐lapse macrophotography synchronized with temperature readings for up to 28 h at 2200 m depth. Lighting was provided by a novel low‐cost white LED array powered by AA or AAA batteries embedded in epoxy within an aluminum case. SMOKE was successfully deployed at the Juan de Fuca ridge in the Northeast Pacific and delivered fine‐resolution pictures as well as centimeter‐scale temperature readings in diffuse vent flow habitats of small motile invertebrates. We found high spatial temperature changes within faunal assemblages and could identify and track specimens down to a size of 2 mm. SMOKE is also characterized by low fabrication and maintenance costs and a straight‐forward, reliable design. Overall, this device proved to be a valuable tool for macrofaunal observations linked with temperature changes over extended time periods.
Effect of chloride on the chemical conversion of nitrate to nitrous oxide for δ15N analysis
Authors: Ryabenko Evgenia , Altabet Mark A. , Wallace Douglas W.R.
Published: April 2011

We investigate the influence of chloride concentration on the performance of the chemical reduction method for measurement of the nitrogen isotopic ratio (δ15N) in NO3− in natural waters (McIlvin and Altabet, 2005). In this method, NO3− is first reduced to NO2− using activated cadmium metal, with further reduction to N2O using sodium azide in an acetic acid buffer. N2O is introduced into an isotope ratio mass spectrometer (IRMS) for isotopic measurement. Previously, it was recognized that the presence of halides was necessary for the speed and efficiency of the second step but not thought to be important for the first step. Whereas quantitative Cd reduction of NO3− to NO2− had been noted for seawater samples, here we report, for freshwater and low‐salinity (S < 30) samples, a variable conversion efficiency (both under‐ and overreduction were observed) and significant variation in δ15N determination. Addition of 5 M NaCl to all samples resulted in rapid (<4 h) and quantitative (>99%) reduction of NO3− to NO2− as well as stable δ15N values that closely matched expected values for standards (within 0.3‰ of standard value). The positive effect of NaCl is likely due to a decrease in free Cd2+ produced over the course of the reaction due to formation of CdCl2.
Eddy correlation measurements of oxygen uptake in deep ocean sediments
Authors: Berg Peter , Glud Ronnie N. , Hume Andrew , Stahl Henrik , Oguri Kazumasa , Meyer Volker , Kitazato Hiroshi
Published: April 2011

We present and compare small sediment‐water fluxes of O2 determined with the eddy correlation technique, with in situ chambers, and from vertical sediment microprofiles at a 1450 m deep‐ocean site in Sagami Bay, Japan. The average O2 uptake for the three approaches, respectively, was 1.62 ± 0.23 (SE, n = 7), 1.65 ± 0.33 (n = 2), and 1.43 ± 0.15 (n = 25) mmol m−2 d−1. The very good agreement between the eddy correlation flux and the chamber flux serves as a new, important validation of the eddy correlation technique. It demonstrates that the eddy correlation instrumentation available today is precise and can resolve accurately even very small benthic O2 fluxes. The correlated fluctuations in vertical velocity and O2 concentration that give the eddy flux had average values of 0.074 cm s−1 and 0.049 µM. The latter represents only 0.08% of the 59 µM mean O2 concentration of the bottom water. Note that these specific fluctuations are average values, and that even smaller variations were recorded and contributed to the eddy flux. Our findings demonstrate that the eddy correlation technique is a highly attractive alternative to traditional flux methods for measuring even very small benthic O2 fluxes.
Group‐specific primary production based on stable‐isotope labeling of phospholipid‐derived fatty acids
Authors: Dijkman Nicole A. , Boschker Henricus T. S. , Middelburg Jack J. , Kromkamp Jacco C.
Published: April 2011

Stable‐isotope labeling of phospholipid‐derived fatty acids (PLFAs) is a potentially powerful technique to study group‐specific primary production of phytoplankton, as many algal groups possess a specific PLFA composition, and it is relatively simple to measure the isotopic composition of a large number of PLFAs. Experiments with cultured algae showed that differences exist in labeling among PLFAs and between PLFAs and particulate organic carbon (POC), most likely owing to differences in biosynthesis pathways causing some components of the cell with short pathways to be labeled faster. These differences were constant, however, during the first few hours of incubation, and correction factors were used to convert PLFA labeling to total carbon uptake. In algal cultures, growth rates based on 13C‐PLFA labeling agreed well with those based on biomass increases in terms of PLFA concentrations and cell numbers. At two contrasting sites in the Scheldt estuary, PLFA synthesis rates were calculated using 2‐h incubations. Group‐specific primary production was estimated from PLFA synthesis rates and PLFA compositional spectra of samples and algal taxa using the matrix factorization program Chemtax. When accompanied with studies or information on system‐relevant phytoplankton, this sensitive method will be applicable to a wide range of pelagic ecosystems and also to benthic systems such as algal mats.
Detection and quantification of marine larvae orientation in the pelagic environment
Authors: Irisson Jean‐Olivier , Guigand Cédric , Paris Claire B.
Published: April 2011

The pelagic larval phase represents a major opportunity for dispersal in benthic organisms, yet behaviors controlling and potentially limiting dispersal are still largely unknown for most larvae. Here, we present a new means of observing the orientation of larvae of all developmental stages in the pelagic environment. A cylindrical frame holding a semi‐open arena in which larvae are filmed is set to drift at a controlled depth within the natural environment. Larval trajectories are extracted from video data and used to quantify orientation behavior. Field tests with late‐stage coral reef fish larvae show that orientation can be detected from individual larval positions in the arena and can be significantly differentiated from random movement or artifactual behavior.
New method for the determination of extracellular production of superoxide by marine phytoplankton using the chemiluminescence probes MCLA and red‐CLA
Authors: Godrant Aurélie , Rose Andrew L. , Sarthou Géraldine , Waite T. David
Published: April 2011

A new rapid and highly sensitive microplate‐based chemiluminescence method for the detection of extracellular production of superoxide by phytoplankton cultures has been developed. Replicates of the sample, blank, and three standards were placed into 96‐well plates and the chemiluminescence was detected with a microplate luminometer. The method was tested on Trichodesmium erythraeum cultures using two superoxide‐specific chemiluminescent probes, MCLA and the closely related compound red‐CLA, which emit light at 460 and 610 nm, respectively, in the presence of superoxide. Calibration of the chemiluminescent signal is performed individually for each sample using the xanthine/xanthine oxidase system by adding a fixed concentration of xanthine (50 µM) and variable concentrations of xanthine oxidase (0.001–0.5 units L−1). The method is selective for superoxide, and the detection limits are as low as 1.41 pmol/s for MCLA and 76 fmol s−1 for red‐CLA, with limits of quantification of 4.70 pmol/s for MCLA and 253 fmol s−1 for red‐CLA. Application of the new method to the determination of extracellular superoxide production by the prolific superoxide‐producing phytoplankton Chattonella marina yielded results comparable to those obtained using an existing flow injection analysis method. The use of microplates offers several advantages over existing methods, including a short analysis time of 10 min for triplicates of blank, sample, and standards; good reliability of signals; and use of small sample volumes.
Comparison of inherent optical properties as a surrogate for particulate matter concentration in coastal waters
Authors: Boss Emmanuel , Taylor Lisa , Gilbert Sherryl , Gundersen Kjell , Hawley Nathan , Janzen Carol , Johengen Tom , Purcell Heidi , Robertson Charles , Schar Daniel W. H. , Smith G. Jason , Tamburri Mario N.
Published: April 2011

Particulate matter concentration (PM, often referred to as total suspended solids [TSS]) is an important parameter in the evaluation of water quality. Several optical measurements used to provide an estimate of water turbidity have also been used to estimate PM, among them light transmission, backscattering, and side‐scattering. Here we analyze such measurements performed by the Alliance for Coastal Technologies (ACT) at various coastal locations to establish whether a given optical method performs better than others for the estimation of PM. All the technologies were found to perform well, predicting PM within less than 55% relative difference for 95% of samples (n = 85, four locations). Backscattering performed best as a predictor of PM, predicting PM with less than 37% relative difference for 95% of samples. The correlation coefficient (R) was between 0.96 and 0.98 for all methods with PM data ranging between 1.2 to 82.4 g m−3. In addition, co‐located measurements of backscattering and attenuation improves PM prediction and provides compositional information about the suspended particles; when their ratio is high, the bulk particulate matter is dominated by inorganic material while when low, dominated by organic material.
Bioinformatics education in an MLIS program: the McGill experience
Authors: Bartlett Joan C
Published: April 2011

Program objective  The objective of this course (GLIS691  Bioinformatics) was to provide formal bioinformatics education within a master of library and information studies (MLIS) program. As bioinformatics becomes increasingly integral to biomedical research, there is a need for librarians to expand their practice into the domain of bioinformatics, supporting the efficient and accurate use of these complex resources. We developed this course, the first such course offered in a Canadian library school, in response to the demand for librarians to be able to support bioinformatics information needs. Setting  The course was offered in the winter term of 2005 in the Graduate School of Library and Information Studies, McGill University. Participants  Course participants were MLIS students. Program  The course took a library and information science perspective to bioinformatics. The goal was to provide students with the skills and knowledge to provide information services in the domain of bioinformatics and to collaborate in the design and development of bioinformatics resources. This included understanding the field of bioinformatics and the range of resources, the needs and requirements of user groups, practical searching skills, the creation of resources, and the role of the librarian. Conclusions  This course represents one approach to providing formal bioinformatics education for librarians. Librarians who are knowledgeable and proficient in bioinformatics will be able to expand the role of the library into this domain; apply their knowledge, skills, and expertise in a complex, chaotic information environment; and develop the essential role of the librarian in the domain of bioinformatics.
Open access for the medical librarian
Authors: Morrison Heather , Waller Andrew
Published: April 2011

In this article open access is defined, and the resources and issues of greatest relevance to the medical librarian are discussed. The economics of open access publishing is examined from the point of view of the university library. Open access resources, both journals and articles in repositories, are already significant and growing rapidly. There are close to 2300 fully open access, peer-reviewed journals listed in the Directory of Open Access Journals (DOAJ) (320 health sciences titles are included). DOAJ is adding new titles at the rate of 1.5 per day. An OAIster search of resources in repositories includes more than 7.6 million items (a rough estimate of the number of articles in repositories, although not all items are full text), and this number will exceed one billion items before the end of 2007. Medical research funders, including the US National Institutes of Health, the Wellcome Trust, the UK Medical Research Council, and the Canadian Institutes of Health Research, either have implemented or are considering open access policies. This will drive greater growth in open access resources, particularly in the area of medicine. There are implications and leadership opportunities for librarians in the open access environment.
Improving access to multilingual health information for newcomers to Canada
Authors: Gallo Stampino Victoria
Published: April 2011

Canada's immigrant and refugee population is a vulnerable group in our health care system with specific information needs. Newcomers to Canada face certain socioeconomic, cultural–linguistic, and systemic barriers to access to health care that government, social agencies, and health care organizations work to overcome. To address some of the communication barriers, many health organizations develop information resources such as online brochures and education handouts. Several organizations offer specifically tailored multilingual publications to meet newcomers' information needs and write them using cross-cultural approaches. However, multilingual health information may be hard to locate and is not readily available through major Canadian consumer Web sites. This article discusses the advantages of sharing multilingual publications online and asks whether a central portal or repository is a possible solution for making publications more widely available across Canada.
Life as a knowledge broker in public health
Authors: Robeson Paula , Dobbins Maureen , DeCorby Kara
Published: April 2011

Program objective – Knowledge brokers (KBs), like clinical librarians (CLs), are information professionals involved in the promotion of evidence-informed decision-making (EIDM). As with CLs, the impact of literature-evaluating KBs on the health sector is sparse, and there is limited consensus on their role. To provide guidance to information professionals and organizations regarding the KB role, this paper describes a typical “day in the life” of a KB in delivering a program to promote EIDM among Canadian public health professionals. Setting – The KB program was implemented in a randomized controlled trial evaluating knowledge transfer and exchange strategies. Participants – Public health managers at various levels within Canadian public health units or regional health authorities. Program – The KB identified decision makers’ (DMs) evidence needs; facilitated access to and use of high-quality evidence; assisted in decision making; and facilitated EIDM skill development. Results – The KB role, activities and related tasks, lessons learned, and challenges are described. Conclusion – Central themes included the importance of relationship development, ongoing support, customized approaches, and individual and organizational capacity development. The novelty of the KB role in public health provided a unique opportunity to assess the need for and reaction to the role and its associated activities.
Biological effects of non-ionizing electromagnetic energy: A critical review of the reports by the US National Research Council and the US National Institute of Environmental Health Sciences as they relate to the broad realm of EMF bioeffects
Authors: Havas M
Published: April 2011

Our dependence on electricity and our growing dependence on wireless telecommunication technology is causing this planet to be inundated with electromagnetic energy ranging in frequency from less than 60 Hz to greater than 2 GHz. Concerns expressed by the public, who live near power lines, cell phone antennas, or television and radio broadcast towers, have prompted two major reviews: one by the US National Research Council (NRC) and the other by the US National Institute of Environmental Health Science (NIEHS). Both of these documents deal with the biological and health effects primarily in a residential setting of extremely low frequency (ELF) or power frequency (50 and 60 Hz) fields. This paper critically evaluates the NRC and NIEHS documents. This evaluation includes both the content and the process leading to the final reports. It summarizes the information available on human exposure to electric and magnetic fields and identifies key biological markers and potential mechanisms that have been linked to electromagnetic exposure. It examines the conclusions of both documents in terms of the slightly broader realm associated with occupational exposure, non-power frequency fields, EMF hypersensitivity, and response of species other than humans. It presents some of the scientific controversy surrounding the question "Are low frequency electric and magnetic fields harmful?'' and examines the concepts of bias and consistency in data interpretation. This paper also attempts to place the discussions about technologically generated fields (technofields) into a much broader perspective, a perspective that includes naturally occurring geofields and biofields. Key words: leukemia, breast cancer, melatonin, calcium flux, extremely low frequency electromagnetic fields, radio frequency radiation.
Stable lead isotope characteristics of lead ore deposits of environmental significance
Authors: Sangster D F , Outridge P M , Davis W J
Published: April 2011

Stable Pb isotopes are increasingly used in environmental science as tracers of natural and anthropogenic Pb sources. This review provides a summary of the recent geological literature concerning Pb isotopes in global Pb ore deposits. The isotopic characteristics of 151 Pb deposits, including 78 20th-century producing mines, have been summarized using the 204Pb-based ratios common to geological science and the 206Pb- and 207Pb-based ratios (i.e., excluding 204Pb) more often employed in environmental studies. A number of current mines, including those exploiting several Australian, Scandinavian, and U.S.A. deposits, have extreme isotopic compositions that provide unique signatures. However, a majority of mines (and unproductive deposits) fall within a relatively narrow range:206Pb/207Pb of 1.15-1.22 and 208Pb/207Pb of 2.42-2.50. In some contexts, unequivocal identification of a source exhibiting one of these common signatures would be difficult, especially with the relatively low precision (ca. 0.2-0.5% RSD) of quadrupole inductively coupled plasma - mass spectrometry (ICP-MS) which has been the most common instrument for environmental Pb isotope measurements. In settings with disparate industrial and natural Pb signatures (i.e., sources withisotopic ratios differing by about 2% or more), ICP-MS precision is adequate for source discrimination. Statistical analyses suggested that while 204Pb is critical for identifying a small proportion of environmental Pb sources, about 86% of the source discrimination power is due to the 206Pb, 207Pb, and 208Pb isotopes. Thus, the requisite analytical precision, rather than a lack of 204Pb data, is the most critical issue with respect to unequivocal identification of Pb sources in most cases. Several factors, especially the increasing dominance of recycling in global Pb production and the international transportation of ore concentrate and refined Pb, may cause unpredictable changes in the isotopic signatures of industrial sources,with a long-term trend towards homogenization. More frequent,comprehensive, and high-precision isotopic characterization of possible point and non-point Pb emitters such as gasoline, smelters, and battery-recycling plants, together with increased efforts to document the origin of constituent leads in industrial sources, would help to address these concerns.Key words: lead isotopes; lead pollution; source identification; lead ore deposits.
The value of paleoecology as an aid to monitoring ecosystems and landscapes, chiefly with reference to North America
Authors: Gorham Eville , Brush Grace S , Graumlich Lisa J , Rosenzweig Michael L , Johnson Arthur H
Published: April 2011

Paleoecological indicators are examined as to their accuracy in reconstructing past biotic communities and environmental conditions, their utility in answering important questions about such communities and conditions, and the temporal and spatial scales over which they are effective. Next, environmental problems susceptible of paleoecological analysis are considered, as are the ecosystem and landscape properties that can be inferred from such an analysis. The usefulness of paleoecology in anticipating ecological ``surprises'' is then discussed. Finally, a set of conclusions and recommendations is presented.Key words: ecosystem properties, environmental problems, surprise factor.