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At least 109 records · Page 6Linked to original sources
PubMed2002

Macroecological patterns of phytoplankton in the northwestern North Atlantic Ocean.

Many issues in biological oceanography are regional or global in scope; however, there are not many data sets of extensive areal coverage for marine plankton. In microbial ecology, a fruitful approach to large-scale questions is comparative analysis wherein statistical data patterns are sought from different ecosystems, frequently assembled from unrelated studies. A more recent approach termed macroecology characterizes phenomena emerging from large numbers of biological units by emphasizing the shapes and boundaries of statistical distributions, because these reflect the constraints on variation. Here, I use a set of flow cytometric measurements to provide macroecological perspectives on North Atlantic phytoplankton communities. Distinct trends of abundance in picophytoplankton and both small and large nanophytoplankton underlaid two patterns. First, total abundance of the three groups was related to assemblage mean-cell size according to the 3/4 power law of allometric scaling in biology. Second, cytometric diversity (an ataxonomic measure of assemblage entropy) was maximal at intermediate levels of water column stratification. Here, intermediate disturbance shapes diversity through an equitable distribution of cells in size classes, from which arises a high overall biomass. By subsuming local fluctuations, macroecology reveals meaningful patterns of phytoplankton at large scales.

Animals↗
PubMed2005

Polar ocean ecosystems in a changing world.

Polar organisms have adapted their seasonal cycles to the dynamic interface between ice and water. This interface ranges from the micrometre-sized brine channels within sea ice to the planetary-scale advance and retreat of sea ice. Polar marine ecosystems are particularly sensitive to climate change because small temperature differences can have large effects on the extent and thickness of sea ice. Little is known about the interactions between large, long-lived organisms and their planktonic food supply. Disentangling the effects of human exploitation of upper trophic levels from basin-wide, decade-scale climate cycles to identify long-term, global trends is a daunting challenge facing polar bio-oceanography.

Animals↗
PubMed2006

Deciphering the evolution and metabolism of an anammox bacterium from a community genome.

Anaerobic ammonium oxidation (anammox) has become a main focus in oceanography and wastewater treatment. It is also the nitrogen cycle's major remaining biochemical enigma. Among its features, the occurrence of hydrazine as a free intermediate of catabolism, the biosynthesis of ladderane lipids and the role of cytoplasm differentiation are unique in biology. Here we use environmental genomics--the reconstruction of genomic data directly from the environment--to assemble the genome of the uncultured anammox bacterium Kuenenia stuttgartiensis from a complex bioreactor community. The genome data illuminate the evolutionary history of the Planctomycetes and allow us to expose the genetic blueprint of the organism's special properties. Most significantly, we identified candidate genes responsible for ladderane biosynthesis and biological hydrazine metabolism, and discovered unexpected metabolic versatility.

Anaerobiosis↗
PubMed2002

Carbon sequestration in Synechococcus Sp.: from molecular machines to hierarchical modeling.

The U.S. Department of Energy recently announced the first five grants for the Genomes to Life (GTL) Program. The goal of this program is to "achieve the most far-reaching of all biological goals: a fundamental, comprehensive, and systematic understanding of life." While more information about the program can be found at the GTL website (www.doegenomestolife.org), this paper provides an overview of one of the five GTL projects funded, "Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling." This project is a combined experimental and computational effort emphasizing developing, prototyping, and applying new computational tools and methods to elucidate the biochemical mechanisms of the carbon sequestration of Synechococcus Sp., an abundant marine cyanobacteria known to play an important role in the global carbon cycle. Understanding, predicting, and perhaps manipulating carbon fixation in the oceans has long been a major focus of biological oceanography and has more recently been of interest to a broader audience of scientists and policy makers. It is clear that the oceanic sinks and sources of CO(2) are important terms in the global environmental response to anthropogenic atmospheric inputs of CO(2) and that oceanic microorganisms play a key role in this response. However, the relationship between this global phenomenon and the biochemical mechanisms of carbon fixation in these microorganisms is poorly understood. The project includes five subprojects: an experimental investigation, three computational biology efforts, and a fifth which deals with addressing computational infrastructure challenges of relevance to this project and the Genomes to Life program as a whole. Our experimental effort is designed to provide biology and data to drive the computational efforts and includes significant investment in developing new experimental methods for uncovering protein partners, characterizing protein complexes, identifying new binding domains. We will also develop and apply new data measurement and statistical methods for analyzing microarray experiments. Our computational efforts include coupling molecular simulation methods with knowledge discovery from diverse biological data sets for high-throughput discovery and characterization of protein-protein complexes and developing a set of novel capabilities for inference of regulatory pathways in microbial genomes across multiple sources of information through the integration of computational and experimental technologies. These capabilities will be applied to Synechococcus regulatory pathways to characterize their interaction map and identify component proteins in these pathways. We will also investigate methods for combining experimental and computational results with visualization and natural language tools to accelerate discovery of regulatory pathways. Furthermore, given that the ultimate goal of this effort is to develop a systems-level of understanding of how the Synechococcus genome affects carbon fixation at the global scale, we will develop and apply a set of tools for capturing the carbon fixation behavior of complex of Synechococcus at different levels of resolution. Finally, because the explosion of data being produced by high-throughput experiments requires data analysis and models which are more computationally complex, more heterogeneous, and require coupling to ever increasing amounts of experimentally obtained data in varying formats, we have also established a companion computational infrastructure to support this effort as well as the Genomes to Life program as a whole.

Algorithms↗
PubMed2006

Coherent assembly of phytoplankton communities in diverse temperate ocean ecosystems.

The annual cycle of phytoplankton cell abundance is coherent across diverse ecosystems in the temperate North Atlantic Ocean. In Bedford Basin, on the Scotian Shelf and in the Labrador Sea, the numerical abundance of phytoplankton is low in spring and high in autumn, thus in phase with the temperature cycle. Temperature aligns abundance on a common basis, effectively adjusting apparent cell discrepancies in waters that are colder or warmer than the regional norm. As an example of holistic simplicity arising from underlying complexity, the variance in a community variable (total abundance) is explained by a single predictor (temperature) to the extent of 75% in the marginal seas. In the estuarine basin, weekly averages of phytoplankton and temperature computed from a 13 year time-series yield a predictive relationship with 91% explained variance. Temperature-directed assembly of individual phytoplankton cells to form communities is statistically robust, consistent with observed biomass changes, amenable to theoretical analysis, and a sentinel for long-term change. Since cell abundance is a community property in the same units for all marine microbes at any trophic level and at any phylogenetic position, it promises to integrate biological oceanography into general ecology and evolution.

Atlantic Ocean↗
PubMed2000

Universal geometric condition for the transverse instability of solitary waves

Transverse instabilities correspond to a class of perturbations traveling in a direction transverse to the direction of the basic solitary wave. Solitary waves traveling in one space direction generally come in one-parameter families. We embed them in a two-parameter family and deduce a new geometric condition for transverse instability of solitary waves. This condition is universal in the sense that it does not require explicit properties of the solitary wave-or the governing equation. In this paper the basic idea is presented and applied to the Zakharov-Kuznetsov equation for illustration. An indication of how the theory applies to a large class of equations in physics and oceanography is also discussed.

Journal Article↗
PubMed2005

Multifractal method for the instantaneous evaluation of the stream function in geophysical flows.

Multifractal or multiaffine analysis is a promising new branch of methods in nonlinear physics for the study of turbulent flows and turbulentlike systems. In this Letter we present a new method based on the multifractal singularity extraction technique, the maximum singular stream-function method (MSSM), which provides a first order approximation to the stream function from experimental data in 2D turbulent systems. The essence of MSSM relies in relating statistical properties associated with the energy cascade in flows with geometrical properties. MSSM is a valuable tool to process sparse collections of data and to obtain instant estimates of the velocity field. We show an application of MSSM to oceanography as a way to obtain the current field from sea surface temperature satellite images; we validate the result with independent dynamical information obtained from sea level measurements.

Journal Article↗
PubMed2006

Determining scale and sea state from water video.

In most image processing and computer vision applications, real-world scale can only be determined when calibration information is available. Dynamic scenes further complicate most situations. However, some types of dynamic scenes provide useful information that can be used to recover real-world scale. In this paper, we focus on ocean scenes and propose a method for finding sizes in real-world units and the sea state from an uncalibrated camera. Fourier transforms in the space and time dimensions yield spatial and temporal frequency spectra. For water waves, the dispersion relation defines a square relationship between the wavelength and period of a wave. Our method applies this dispersion relation to recover the real-world scale of an ocean sequence. The sea state--including the peak wavelength and period, the wind speed that generated the waves, and the wave heights--is also determined from the frequency spectrum of the sequence combined with stochastic oceanography models. The process is demonstrated on synthetic and real sequences, validating the results with known scene geometry. This has wide applications in port monitoring and coastal surveillance.

Algorithms↗
PubMedDate not supplied

A trajectory-preserving synchronization method for collaborative visualization.

In the past decade, a lot of research work has been conducted to support collaborative visualization among remote users over the networks, allowing them to visualize and manipulate shared data for problem solving. There are many applications of collaborative visualization, such as oceanography, meteorology and medical science. To facilitate user interaction, a critical system requirement for collaborative visualization is to ensure that remote users will perceive a synchronized view of the shared data. Failing this requirement, the user's ability in performing the desirable collaborative tasks will be affected. In this paper, we propose a synchronization method to support collaborative visualization. It considers how interaction with dynamic objects is perceived by application participants under the existence of network latency, and remedies the motion trajectory of the dynamic objects. It also handles the false positive and false negative collision detection problems. The new method is particularly well designed for handling content changes due to unpredictable user interventions or object collisions. We demonstrate the effectiveness of our method through a number of experiments.

Journal Article↗
PubMed2003

Patterns of larval dispersal and their effect on the maintenance of a blue mussel hybrid zone in southwestern England.

The blue mussels Mytilus edulis and M. galloprovincialis hybridize in southwestern England. Within this hybrid zone environmentally based directional selection favors individuals with alleles specific to M. galloprovincialis. What forces are countering this directional selection and allowing for the maintenance of a stable hybrid population are unknown. We used both the genetics of recently settled larvae and a fine-scale model of the physical oceanography of the region to determine the patterns of larval dispersal throughout the hybrid zone and the bordering parental populations. Evidence from both the model and the genetics suggests that the hybrid zone lies between two barriers to dispersal. Start Point separates the M. edulis population from the hybrid zone and allows minimal dispersal from the hybrid zone into the M. edulis population, but none in the other direction. Likewise, the M. galloprovincialis populations along the northern coast of Cornwall regularly receive immigrating larvae from the hybrid zone, but larvae from the M. galloprovincialis population do not enter the hybrid zone. However, larvae settling at hybrid zone sites have high frequencies of alleles specific to M. edulis, suggesting that reproductive barriers, selection in the larval stage, or gene flow from an undetermined source is effectively balancing the directional selection observed in the adults.

Animals↗
PubMed2004

Phylogeography of the Patelloida profunda group (Gastropoda: Lottidae): diversification in a dispersal-driven marine system.

In the last decade, greater than expected levels of genetic structure have been reported for many marine taxa with high dispersal capabilities. Although little-studied to date, it is predicted that taxa with poor dispersal abilities would exhibit even more genetic differentiation than high dispersal taxa. These systems may track biogeographical processes better than more dispersive taxa and, more critically, function as the 'lowest common denominators' in MPA design initiatives. We investigate phylogeographical patterns in the poorly dispersing, yet widely distributed Patelloida profunda group and related congeners across the Indo-west Pacific region. One hundred and twenty-five individuals were sequenced for COI mtDNA [593 base pairs (bp)] and 44 individuals were sequenced for 16S mtDNA (539 bp). Identified P. profunda group lineages are highly geographically structured, with 12 reciprocally monophyletic lineages reported from 13 localities. Divergences within Indian and Pacific basins range from d = 0.013 to 0.127 and between basins from d = 0.147 to 0.197. The latter split is ancient (> 15 Myr) and cannot be related to Plio-Pleistocene sea-level fluctuations, characteristic of previously reported divergences in the same region. Juxtaposed against this structure is genetic connectivity between two widely separated P. profunda populations that share a common haplotype (phiST = 0.001). This finding contrasts with previous work in the same geographical region and cautions strongly against single taxon indicators for designing conservation priorities or marine protected areas (MPAs). Historical and/or biological factors may play more significant roles than oceanography alone in determining the genetic structuring of taxa. In light of these findings, we discuss the difficulty in deriving biogeographical process or directionality from phylogenetic trees in dispersal-driven systems. Even with a well-resolved, highly supported topology, many equally parsimonious scenarios are possible.

Animals↗
PubMed2007

Pleistocene isolation and recent gene flow in Haliotis asinina, an Indo-Pacific vetigastropod with limited dispersal capacity.

Haliotis asinina is a broadcast-spawning mollusc that inhabits Indo-Pacific coral reefs. This tropical abalone develops through a nonfeeding larval stage that is competent to settle on specific species of coralline algae after 3-4 days in the plankton. Failure to contact an inductive algae within 10 days of hatching usually results in death. These life cycle characteristics suggest a limited capacity for dispersal and thus gene flow. This makes H. asinina particularly suitable for elucidating phylogeographical structure throughout the Indo-Malay Archipelagoes, and eastern Indian and western Pacific Oceans, all regions of biogeographical complexity and high conservation value. We assayed 482 bp of the mitochondrial cytochrome oxidase II gene in 206 abalone collected from 16 geographically discrete sites across the Indian and Pacific Oceans and Indo-Malay Archipelagoes. DNA sequence variation was analysed via population genetics and phylogenetics, and by nested clade analyses (NCA). Our data resolved clear phylogeographical breaks among major biogeographical regions, with sequence divergences ranging from a high of 3.7% and 3.0% between Indian and Pacific sites and Pacific and Indo-Malay sites, respectively, to a low of 1.1% between Indian and Indo-Malay sites. Despite the apparent limited dispersal capacity of H. asinina, no finer scale phylogeographical structure was resolved within the respective biogeographical regions. However, amova and NCA identified several significant associations between haplotypes and geographical distribution, most notably higher gene flow among geographical populations associated with major ocean currents. Our study provides further evidence that larval dispersal capacity alone is not a good predictor of population genetic structure in marine invertebrates. We infer instead that a combination of historical events (long-term barriers followed by range expansion associated with Pleistocene sea level changes) and contemporary processes (gene flow restricted by life history and oceanography) have shaped observed patterns of H. asinina phylogeography.

Animals↗
PubMed2000

A software model to estimate zones of impact on marine mammals around anthropogenic noise.

Anthropogenic noise impacts marine mammals in a variety of ways. In order to estimate over which ranges this happens, we first need to understand the propagation of noise through the ocean away from the noise source, and, second, understand the relationship between received noise levels and impact thresholds. A software package combining both aspects is presented. (1) A sound propagation model based on ray theory was developed to calculate received noise levels as a function of range, depth, and frequency. (2) Current knowledge of noise impact thresholds for marine mammals was gathered and included in software routines predicting zones of impact on marine mammals around industrial underwater noise sources. As input parameters, this software package requires the source level and spectrum of the noise of interest; physical oceanography data about the local ocean environment such as bathymetry, bottom and surface loss data, and sound speed profiles; and bioacoustical information about the target species in the form of an audiogram, critical auditory bandwidths, spectra of typical animal vocalizations, reported sound levels of disturbance, and criteria for hearing damage. As output, the software produces data files and plots of the zones of audibility, masking, disturbance, and potential hearing damage around a noise source.

Animals↗
PubMed2003

Absolute measurements of total target strength from reverberation in a cavity.

A new method was developed to acoustically measure the density and total scattering cross-section (sigma(t)) or total target strength [TTS = 10log10(sigma(t)/4pi)] of objects in motion in a highly reflective cavity [J. De Rosny and P. Roux, J. Acoust. Soc. Am. 109, 2587-2597 (2001)]. From an ensemble of pulse-echo recordings, the average contribution of the scatterer(s) to the reverberation within the cavity provides a measurement of the scattering mean free path. The latter was shown through theory and experiment to be proportional to the volume of the cavity and inversely proportional the product of the mean sigma(t) and number of scatterers. Here, the TTS measurement uncertainty is characterized using standard metal spheres as references. Theoretical TTS was calculated for multiple copper and tungsten carbide standard spheres (Cu: 60.0 30.05 and 23 mm and WC: 38.1 and 33.4 mm diameters, respectively), using well-described theory for scattering from elastic spheres and the optical theorem. Measurements of TTS were made over a wide bandwidth (30-120 kHz) and compared to their theoretical values. Measurements were made in a corrugated, cylindrical, galvanized-steel tank with 25 or 50 l of fresh water at a temperature of 21 +/- 1 degrees C. The results indicate the method can provide TTS measurements that are accurate to at least 0.4 dB with an average precision of +/-0.7 dB (95% confidence interval). Discussed are the requisite cavity volumes and signal-to-noise ratios for quality measurements of TTS, tank volume, and/or numerical abundance of mobile targets. Also discussed are multiple potential applications of this technique in bioacoustical oceanography.

Journal Article↗
PubMed1997

Acoustic effects of the ATOC signal (75 Hz, 195 dB) on dolphins and whales.

The Acoustic Thermometry of Ocean Climate (ATOC) program of Scripps Institution of Oceanography and the Applied Physics Laboratory, University of Washington, will broadcast a low-frequency 75-Hz phase modulated acoustic signal over ocean basins in order to study ocean temperatures on a global scale and examine the effects of global warming. One of the major concerns is the possible effect of the ATOC signal on marine life, especially on dolphins and whales. In order to address this issue, the hearing sensitivity of a false killer whale (Pseudorca crassidens) and a Risso's dolphin (Grampus griseus) to the ATOC sound was measured behaviorally. A staircase procedure with the signal levels being changed in 1-dB steps was used to measure the animals' threshold to the actual ATOC coded signal. The results indicate that small odontocetes such as the Pseudorca and Grampus swimming directly above the ATOC source will not hear the signal unless they dive to a depth of approximately 400 m. A sound propagation analysis suggests that the sound-pressure level at ranges greater than 0.5 km will be less than 130 dB for depths down to about 500 m. Several species of baleen whales produce sounds much greater than 170-180 dB. With the ATOC source on the axis of the deep sound channel (greater than 800 m), the ATOC signal will probably have minimal physical and physiological effects on cetaceans.

Acoustics↗
PubMed2000

Acoustic normal mode fluctuation statistics in the 1995 SWARM internal wave scattering experiment

In order to understand the fluctuations imposed upon low frequency (50 to 500 Hz) acoustic signals due to coastal internal waves, a large multilaboratory, multidisciplinary experiment was performed in the Mid-Atlantic Bight in the summer of 1995. This experiment featured the most complete set of environmental measurements (especially physical oceanography and geology) made to date in support of a coastal acoustics study. This support enabled the correlation of acoustic fluctuations to clearly observed ocean processes, especially those associated with the internal wave field. More specifically, a 16 element WHOI vertical line array (WVLA) was moored in 70 m of water off the New Jersey coast. Tomography sources of 224 Hz and 400 Hz were moored 32 km directly shoreward of this array, such that an acoustic path was constructed that was anti-parallel to the primary, onshore propagation direction for shelf generated internal wave solitons. These nonlinear internal waves, produced in packets as the tide shifts from ebb to flood, produce strong semidiurnal effects on the acoustic signals at our measurement location. Specifically, the internal waves in the acoustic waveguide cause significant coupling of energy between the propagating acoustic modes, resulting in broadband fluctuations in modal intensity, travel-time, and temporal coherence. The strong correlations between the environmental parameters and the internal wave field include an interesting sensitivity of the spread of an acoustic pulse to solitons near the receiver.

Journal Article↗
PubMed1998

Major bacterial contribution to marine dissolved organic nitrogen

Next to N2 gas, the largest pool of reduced nitrogen in the ocean resides in the enormous reservoir of dissolved organic nitrogen (DON). The chemical identity of most of this material, and the mechanisms by which it is cycled, remain fundamental questions in contemporary oceanography. Amino acid enantiomeric ratios in the high molecular weight fraction of DON from surface and deep water in three ocean basins show substantial enrichment in D enantiomers of four amino acids. The magnitude and pattern of these D/L enrichments indicate that peptidoglycan remnants derived from bacterial cell walls constitute a major source of DON throughout the sea. These observations suggest that structural properties of specific bacterial biopolymers, and the mechanisms for their accumulation, are among the central controls on long-term cycling of dissolved organic nitrogen in the sea.

Journal Article↗
PubMed1964

EFFECT OF CHELATING AGENTS ON THE GROWTH OF ESCHERICHIA COLI IN SEAWATER.

Jones, Galen E. (Scripps Institution of Oceanography, University of California, La Jolla). Effect of chelating agents on the growth of Escherichia coli in seawater. J. Bacteriol. 87:483-499. 1964.-Escherichia coli did not grow at 37 C, or grew only after a prolonged lag phase in filter-sterilized basal seawater medium (synthetic or natural seawater supplemented with glucose, NH(4)Cl, and K(2)HPO(4)). When this basal medium was enriched with 0.01% or less organic matter, such as casein hydrolysate, peptone, or yeast extract, growth always occurred after a short lag phase. Adding 10(-5)m cysteine or autoclaving the seawater gave a similar effect. A variety of organic chelating agents (histidine, glycine, methionine, glycylglycine, 8-hydroxyquinoline, thioglycolic acid, o-phenanthroline, disodium ethylenediaminetetraacetic acid, etc.) reversed the toxicity of filter-sterilized basal seawater medium in concentrations predictable from stability constants. Even metal-complexing agents such as Na(2)S(2)O(3), Na(2)S, and NaCN in appropriate concentrations reversed toxicity. The quality of the distilled water and the treatment of glassware had a significant effect on the growth of E. coli in basal seawater medium. It was concluded that iodate is probably not the toxic substance for E. coli in seawater, since relatively high concentrations were stimulatory. The inhibition resulting from the individual salts of synthetic seawater was proportional to their concentration; NaCl was most inhibitory. This toxicity is believed to be derived from trace impurities in the reagent-grade chemicals used to prepare synthetic seawater. Evidence was also found for the toxicity of heavy metals in natural seawater. Heavy metals in seawater appear to inhibit growth but not respiration.

Chelating Agents↗