Ocean carbon sequestration: Particle fragmentation by copepods as a significant unrecognised factor?

Ocean biology helps regulate global climate by fixing atmospheric CO2 and exporting it to deep waters as sinking detrital particles. New observations demonstrate that particle fragmentation is the principal factor controlling the depth to which these particles penetrate the ocean's interior, and hence how long the constituent carbon is sequestered from the atmosphere. The underlying cause is, however, poorly understood. We speculate that small, particle‐associated copepods, which intercept and inadvertently break up sinking particles as they search for attached protistan prey, are the principle agents of fragmentation in the ocean. We explore this idea using a new marine ecosystem model. Results indicate that explicitly representing particle fragmentation by copepods in biogeochemical models offers a step change in our ability to understand the future evolution of biologically‐mediated ocean carbon storage. Our findings highlight the need for improved understanding of the distribution, abundance, ecology and physiology of particle‐associated copepods

Properties of continuous Fourier extension of the discrete cosine transform and its multidimensional generalization

A versatile method is described for the practical computation of the discrete Fourier transforms (DFT) of a continuous function $g(t)$ given by its values $g_{j}$ at the points of a uniform grid $F_{N}$ generated by conjugacy classes of elements of finite adjoint order $N$ in the fundamental region $F$ of compact semisimple Lie groups. The present implementation of the method is for the groups SU(2), when $F$ is reduced to a one-dimensional segment, and for $SU(2)\times ... \times SU(2)$ in multidimensional cases. This simplest case turns out to result in a transform known as discrete cosine transform (DCT), which is often considered to be simply a specific type of the standard DFT. Here we show that the DCT is very different from the standard DFT when the properties of the continuous extensions of these two discrete transforms from the discrete grid points $t_j; j=0,1, ... N$ to all points $t \in F$ are considered. (A) Unlike the continuous extension of the DFT, the continuous extension of (the inverse) DCT, called CEDCT, closely approximates $g(t)$ between the grid points $t_j$. (B) For increasing $N$, the derivative of CEDCT converges to the derivative of $g(t)$. And (C), for CEDCT the principle of locality is valid. Finally, we use the continuous extension of 2-dimensional DCT to illustrate its potential for interpolation, as well as for the data compression of 2D images.Comment: submitted to JMP on April 3, 2003; still waiting for the referee's Repor

Quality Assessment and Data Analysis for microRNA Expression Arrays

MicroRNAs are small (∼22 nt) RNAs that regulate gene expression and play important roles in both normal and disease physiology. The use of microarrays for global characterization of microRNA expression is becoming increasingly popular and has the potential to be a widely used and valuable research tool. However, microarray profiling of microRNA expression raises a number of data analytic challenges that must be addressed in order to obtain reliable results. We introduce here a universal reference microRNA reagent set as well as a series of nonhuman spiked-in synthetic microRNA controls, and demonstrate their use for quality control and between-array normalization of microRNA expression data. We also introduce diagnostic plots designed to assess and compare various normalization methods. We anticipate that the reagents and analytic approach presented here will be useful for improving the reliability of microRNA microarray experiments

Geometric stoichiometry: unifying concepts of animal nutrition to understand how protein-rich diets can be “too much of a good thing”

Understanding the factors that control the growth of heterotrophic organisms is central to predicting food web interactions and biogeochemical cycling within ecosystems. We present a new framework, Geometric Stoichiometry (GS), that unifies the disciplines of Nutritional Geometry (NG) and Ecological Stoichiometry (ES) by extending the equations of ES to incorporate core NG concepts, including macromolecules as currencies and the ability of animals to select foods that balance deficits and excesses of nutrients. The resulting model is used to investigate regulation of consumer growth by dietary protein:carbohydrate ratio. Growth on protein-poor diets is limited by nitrogen. Likewise, we show that growth is also diminished on protein-rich diets and that this can be mechanistically explained by means of a metabolic penalty that arises when animals use protein for energy generation. These penalties, which are incurred when dealing with the costs of producing and excreting toxic nitrogenous waste, have not hitherto been represented in standard ES theory. In order to incorporate GS within ecosystem and biogeochemical models, a new generation of integrated theoretical and experimental studies based on unified concepts of NG and ES is needed, including measurements of food selection, biomass, growth and associated physiology, and involving metabolic penalties

Using Markov chain Monte Carlo methods for estimating parameters with gravitational radiation data

We present a Bayesian approach to the problem of determining parameters for coalescing binary systems observed with laser interferometric detectors. By applying a Markov Chain Monte Carlo (MCMC) algorithm, specifically the Gibbs sampler, we demonstrate the potential that MCMC techniques may hold for the computation of posterior distributions of parameters of the binary system that created the gravity radiation signal. We describe the use of the Gibbs sampler method, and present examples whereby signals are detected and analyzed from within noisy data.Comment: 21 pages, 10 figure

Annotare—a tool for annotating high-throughput biomedical investigations and resulting data

Summary: Computational methods in molecular biology will increasingly depend on standards-based annotations that describe biological experiments in an unambiguous manner. Annotare is a software tool that enables biologists to easily annotate their high-throughput experiments, biomaterials and data in a standards-compliant way that facilitates meaningful search and analysis

Graphs in molecular biology

Graph theoretical concepts are useful for the description and analysis of interactions and relationships in biological systems. We give a brief introduction into some of the concepts and their areas of application in molecular biology. We discuss software that is available through the Bioconductor project and present a simple example application to the integration of a protein-protein interaction and a co-expression network

Quantifying the roles of food intake and stored lipid for growth and development throughout the life cycle of a high-latitude copepod, and consequences for ocean carbon sequestration

Copepods are a critical component of ocean ecosystems, providing an important link between phytoplankton and higher trophic levels as well as regulating biogeochemical cycles of carbon (C) and nutrients. Lipid-rich animals overwinter in deep waters where their respiration may sequester a similar quantity of C as that due to sinking detritus. This ‘seasonal lipid pump’ nevertheless remains absent from global biogeochemical models that are used to project future ocean-climate interactions. Here, we make an important step to resolving this omission by investigating the biogeochemical cycling of C and nitrogen (N) by high-latitude copepods using a new individual-based stoichiometric model that includes explicit representation of lipid reserves. Simulations are presented for Calanus finmarchicus throughout its life cycle at Station Mike (66°N, 2°E) in the Norwegian Sea, although the model is applicable to any suitable location and species with a similar life history. Results indicate that growth, development and egg production in surface waters are driven primarily by food intake (quantity) which provides a good stoichiometric match to metabolic requirements. In contrast, the main function of stored lipid is to support overwintering respiration and gonad development with these two processes respectively accounting for 19 and 55% of the lipid accumulated during the previous spring/summer. The animals also catabolise 41% of body protein in order to provide N for the maintenance of structural biomass. In total, each individual copepod sequesters 9.6 μmol C in deep water. If the areal density of animals is 15,000–40,000 m-2, these losses correspond to a sequestration of 1.7–4.6 g C m-2 yr-1. Lipids contribute only 1% of the C used in egg production in the following year. Accumulating extra lipid in spring would potentially increase egg production but our analysis suggests that any such benefit is outweighed by a higher risk of predator mortality. Our work indicates that the seasonal lipid pump may be of similar magnitude to C sequestration via sinking particles in the North Atlantic and highlights the need for improved physiological understanding of lipid use by high-latitude copepods in order to better constrain C fluxes in ocean food-webs and biogeochemical models

Prognosis of the individual course of disease - steps in developing a decision support tool for Multiple Sclerosis

<p>Abstract</p> <p>Background</p> <p>Multiple sclerosis is a chronic disease of uncertain aetiology. Variations in its disease course make it difficult to impossible to accurately determine the prognosis of individual patients. The Sylvia Lawry Centre for Multiple Sclerosis Research (SLCMSR) developed an "online analytical processing (OLAP)" tool that takes advantage of extant clinical trials data and allows one to model the near term future course of this chronic disease for an individual patient.</p> <p>Results</p> <p>For a given patient the most similar patients of the SLCMSR database are intelligently selected by a model-based matching algorithm integrated into an OLAP-tool to enable real time, web-based statistical analyses. The underlying database (last update April 2005) contains 1,059 patients derived from 30 placebo arms of controlled clinical trials. Demographic information on the entire database and the portion selected for comparison are displayed. The result of the statistical comparison is provided as a display of the course of Expanded Disability Status Scale (EDSS) for individuals in the database with regions of probable progression over time, along with their mean relapse rate. Kaplan-Meier curves for time to sustained progression in the EDSS and time to requirement of constant assistance to walk (EDSS 6) are also displayed. The software-application OLAP anticipates the input MS patient's course on the basis of baseline values and the known course of disease for similar patients who have been followed in clinical trials.</p> <p>Conclusion</p> <p>This simulation could be useful for physicians, researchers and other professionals who counsel patients on therapeutic options. The application can be modified for studying the natural history of other chronic diseases, if and when similar datasets on which the OLAP operates exist.</p