Atlantic mackerel and horse mackerel egg survey: Dutch participation May and June 2010

Every three years an international Atlantic survey is carried out by different European institutes to monitor the spatial and seasonal distribution of Atlantic mackerel and horse mackerel. During this survey mackerel and horse mackerel eggs are sampled using a plankton torpedo or bongo nets. The survey covers the whole spawning area and season. It starts along the Portuguese coast in February and continues until July when the waters west of Scotland are sampled. The mackerel and horse mackerel egg survey is coordinated by the ICES working group for mackerel and horse mackerel egg surveys (WGMEGS). England and France started the egg survey in the western area in 1977. The Netherlands participates since 1983. Nowadays participating countries and sampling area have expanded. In 2010 the following countries participated in this survey: Faeröer Islands, Germany, Iceland, Ireland, Norway, Portugal, Scotland, Spain and The Netherlands

Cluster analysis of flow cytometric list mode data on a personal computer

A cluster analysis algorithm, dedicated to analysis of flow cytometric data is described. The algorithm is written in Pascal and implemented on an MS-DOS personal computer. It uses k-means, initialized with a large number of seed points, followed by a modified nearest neighbor technique to reduce the large number of subclusters. Thus we combine the advantage of the k-means (speed) with that of the nearest neighbor technique (accuracy). In order to achieve a rapid analysis, no complex data transformations such as principal components analysis were used. \ud Results of the cluster analysis on both real and artificial flow cytometric data are presented and discussed. The results show that it is possible to get very good cluster analysis partitions, which compare favorably with manually gated analysis in both time and in reliability, using a personal computer

A new principle of cell sorting by using selective electroporation in a modified flow cytometer

When a strong electric field pulse of a few microseconds is applied to biological cells, small pores are formed in the cell membranes; this process is called electroporation. At high field strengths and/or long pulse durations the membranes will be damaged permanently. This eventually leads to cell kill. \ud We have developed a modified flow cytometer in which one can electroporate individual cells selected by optical analysis. The first experiments with this flow cytometer were designed to use it as a damaging sorter; we used electric pulses of 10 s and resulting field strengths of 2.0 and 3.2 X 106 V/m to kill K562 cells and lymphocytes respectively. The hydrodynamically focused cells are first optically analyzed in the usual way in a square flow channel. At the end of this channel the cells are forced to flow through a small Coulter orifice, into a wider region. If optical analysis indicates that a cell is unwanted, the cell is killed by applying a strong electric field across the Coulter orifice. The wanted living cells can be subsequently separated from the dead cells and cell fragments by a method suitable for the particular application (e.g., centrifugation, cell growth, density gradient, etc.). \ud The results of these first experiments demonstrate that by using very simple equipment, sorting by selective killing with electric fields is possible at rates of 1,000 cells/s with a purity of the sorted fraction of 99.9%

Global surface-ocean pCO2 and sea–air CO2 flux variability from an observation-driven ocean mixed-layer scheme

A temporally and spatially resolved estimate of the global surface-ocean CO₂ partial pressure field and the sea–air CO₂ flux is presented, obtained by fitting a simple data-driven diagnostic model of ocean mixed-layer biogeochemistry to surface-ocean CO₂ partial pressure data from the SOCAT v1.5 database. Results include seasonal, interannual, and short-term (daily) variations. In most regions, estimated seasonality is well constrained from the data, and compares well to the widely used monthly climatology by Takahashi et al. (2009). Comparison to independent data tentatively supports the slightly higher seasonal variations in our estimates in some areas. We also fitted the diagnostic model to atmospheric CO₂ data. The results of this are less robust, but in those areas where atmospheric signals are not strongly influenced by land flux variability, their seasonality is nevertheless consistent with the results based on surface-ocean data. From a comparison with an independent seasonal climatology of surface-ocean nutrient concentration, the diagnostic model is shown to capture relevant surface-ocean biogeochemical processes reasonably well. Estimated interannual variations will be presented and discussed in a companion paper

Global Carbon Budget: Ocean carbon sink.

CO2 emissions from human activities, the main contributor to global climate change, are set to rise again in 2014 reaching 40 billion tonnes CO2 The natural carbon ‘sinks’ on land and in the ocean absorb on average 55% of the total CO2 emissions, thus slowing the rate of global climate change Increasing CO2 in the oceans is causing ocean acidificatio

Differential geometry tools for multidisciplinary design optimization, Part I: Theory

Analysis within the field of Multidisciplinary Design Optimization (MDO) generally falls under the headings of architecture proofs and sensitivity information manipulation. We propose a differential geometry (DG) framework for further analyzing MDO systems, and here, we outline the theory undergirding that framework: general DG, Riemannian geometry for use in MDO, and the translation of MDO into the language of DG. Calculating the necessary quantities requires only basic sensitivity information (typically from the state equations) and the use of the implicit function theorem. The presence of extra or non-differentiable constraints may limit the use of the framework, however. Ultimately, the language and concepts of DG give us new tools for understanding, evaluating, and developing MDO methods; in Part I, we discuss the use of these tools and in Part II, we provide a specific application.This research is supported by the Natural Sciences and Engineering Research Council of Canada (NSERC) and the Cambridge Commonwealth Trust and Cambridge Overseas Trust (CCT/COT).This is the author accepted manuscript. The final version is available from Springer via http://dx.doi.org/10.1007/s00158-014-1186-

Variability and nature of the binary in the Red Rectangle Nebula

We present new observations of the central binary inside the Red Rectangle nebula. The detection of zinc in the optical spectrum confirms that the peculiar photospheric abundances are due to accretion of circumstellar gas. Grey brightness variations with the orbital period are observed. They are interpreted as being due to the variation of the scattering angle with orbital phase. The small orbital separation of the system is not compatible with previous normal evolution of the primary on the AGB. We point out the similarity of the orbital history of this and other similar systems with those of some close Barium stars and suggest that the nonzero eccentricity of the orbit is the result of tidal interaction with the circumbinary disk.Comment: 4 pages, 3 figures, A&A Letters accepte

Differential geometry tools for multidisciplinary design optimization, part II: application to QSD

Having previously developed a differential geometry framework for analyzing and conceptualizing Multidisciplinary Design Optimization (MDO) problems and methods, we now apply that framework to consider the Quasi-Separable Decomposition (QSD) architecture. Based on our theoretical investigations, we predict that QSD will fail to return feasible designs for MDO problems. In the same vein, we analyze the Individual Discipline Feasible (IDF) architecture, predict that IDF will converge to feasible designs, and propose a modified version of QSD which we believe will also output feasible design points. To test these predictions, we run all three architectures on a well-known analytical MDO problem. Our predictions regarding feasibility prove to be accurate: QSD does not return any feasible points, whereas all of the final design points from IDF and the modified QSD are feasible. Now that convergence to feasibility has been established, the next step is to investigate the optimization performance of various QSD modificationsThis research is supported by the Natural Sci- ences and Engineering Research Council of Canada (NSERC) and the Cambridge Commonwealth Trust and Cambridge Overseas Trust (CCT/COT).This is the author's accepted manuscript. The final version is available from Springer at http://link.springer.com/article/10.1007/s00158-014-1170-3

Lineage specific recombination rates and microevolution in Listeria monocytogenes

Background: The bacterium Listeria monocytogenes is a saprotroph as well as an opportunistic human foodborne pathogen, which has previously been shown to consist of at least two widespread lineages (termed lineages I and II) and an uncommon lineage (lineage III). While some L. monocytogenes strains show evidence for considerable diversification by homologous recombination, our understanding of the contribution of recombination to L. monocytogenes evolution is still limited. We therefore used STRUCTURE and ClonalFrame, two programs that model the effect of recombination, to make inferences about the population structure and different aspects of the recombination process in L. monocytogenes. Analyses were performed using sequences for seven loci (including the house-keeping genes gap, prs, purM and ribC, the stress response gene sigB, and the virulence genes actA and inlA) for 195 L. monocytogenes isolates. Results: Sequence analyses with ClonalFrame and the Sawyer's test showed that recombination is more prevalent in lineage II than lineage I and is most frequent in two house-keeping genes (ribC and purM) and the two virulence genes (actA and inlA). The relative occurrence of recombination versus point mutation is about six times higher in lineage II than in lineage I, which causes a higher genetic variability in lineage II. Unlike lineage I, lineage II represents a genetically heterogeneous population with a relatively high proportion (30% average) of genetic material imported from external sources. Phylograms, constructed with correcting for recombination, as well as Tajima's D data suggest that both lineages I and II have suffered a population bottleneck. Conclusion: Our study shows that evolutionary lineages within a single bacterial species can differ considerably in the relative contributions of recombination to genetic diversification. Accounting for recombination in phylogenetic studies is critical, and new evolutionary models that account for the possibility of changes in the rate of recombination would be required. While previous studies suggested that only L. monocytogenes lineage I has experienced a recent bottleneck, our analyses clearly show that lineage II experienced a bottleneck at about the same time, which was subsequently obscured by abundant homologous recombination after the lineage II bottleneck. While lineage I and lineage II should be considered separate species from an evolutionary viewpoint, maintaining single species name may be warranted since both lineages cause the same type of human disease