On the time value of Parisian ruin in (dual) renewal risk processes with exponential jumps

This paper studies the Parisian ruin problem first proposed by Dassios and Wu (2008a,b), where the Parisian ruin time is defined to be the first time when the surplus process has stayed below zero continuously for a pre-specified time length $d$. Both the insurance risk process and the dual model will be considered under exponential distributional assumption on the jump sizes while keeping the inter-arrival times arbitrary. In these two models, the Laplace transform of the Parisian ruin time is derived by extending the excursion techniques in Dassios and Wu (2008a) and taking advantage of the memoryless property exponential distributions. Our results are represented in integral forms, which are expressed in terms of the (joint) densities of various ruin-related quantities that are available in the literature or obtainable using the Lagrange's expansion theorem. As a by-product, we also provide the joint distribution of the numbers of periods of negative surplus that are of duration more than $d$ and less than $d$, which can be obtained using some of our intermediate results. The case where the Parisian delay period $d$ is replaced by a random time is also discussed, and it is applied to find the Laplace transform of the occupation time when the surplus is negative. Numerical illustrations concerning an Erlang(2) insurance risk model are given at the end.postprin

A constructive approach for discovering new drug leads: Using a kernel methodology for the inverse-QSAR problem

<p>Abstract</p> <p>Background</p> <p>The inverse-QSAR problem seeks to find a new molecular descriptor from which one can recover the structure of a molecule that possess a desired activity or property. Surprisingly, there are very few papers providing solutions to this problem. It is a difficult problem because the molecular descriptors involved with the inverse-QSAR algorithm must adequately address the forward QSAR problem for a given biological activity if the subsequent recovery phase is to be meaningful. In addition, one should be able to construct a feasible molecule from such a descriptor. The difficulty of recovering the molecule from its descriptor is the major limitation of most inverse-QSAR methods.</p> <p>Results</p> <p>In this paper, we describe the reversibility of our previously reported descriptor, the vector space model molecular descriptor (VSMMD) based on a vector space model that is suitable for kernel studies in QSAR modeling. Our inverse-QSAR approach can be described using five steps: (1) generate the VSMMD for the compounds in the training set; (2) map the VSMMD in the input space to the kernel feature space using an appropriate kernel function; (3) design or generate a new point in the kernel feature space using a kernel feature space algorithm; (4) map the feature space point back to the input space of descriptors using a pre-image approximation algorithm; (5) build the molecular structure template using our VSMMD molecule recovery algorithm.</p> <p>Conclusion</p> <p>The empirical results reported in this paper show that our strategy of using kernel methodology for an inverse-Quantitative Structure-Activity Relationship is sufficiently powerful to find a meaningful solution for practical problems.</p

Comparative Genomic and Transcriptomic Characterization of the Toxigenic Marine Dinoflagellate Alexandrium ostenfeldii

Many dinoflagellate species are notorious for the toxins they produce and ecological and human health consequences associated with harmful algal blooms (HABs). Dinoflagellates are particularly refractory to genomic analysis due to the enormous genome size, lack of knowledge about their DNA composition and structure, and peculiarities of gene regulation, such as spliced leader (SL) trans-splicing and mRNA transposition mechanisms. Alexandrium ostenfeldii is known to produce macrocyclic imine toxins, described as spirolides. We characterized the genome of A. ostenfeldii using a combination of transcriptomic data and random genomic clones for comparison with other dinoflagellates, particularly Alexandrium species. Examination of SL sequences revealed similar features as in other dinoflagellates, including Alexandrium species. SL sequences in decay indicate frequent retro-transposition of mRNA species. This probably contributes to overall genome complexity by generating additional gene copies. Sequencing of several thousand fosmid and bacterial artificial chromosome (BAC) ends yielded a wealth of simple repeats and tandemly repeated longer sequence stretches which we estimated to comprise more than half of the whole genome. Surprisingly, the repeats comprise a very limited set of 79–97 bp sequences; in part the genome is thus a relatively uniform sequence space interrupted by coding sequences. Our genomic sequence survey (GSS) represents the largest genomic data set of a dinoflagellate to date. Alexandrium ostenfeldii is a typical dinoflagellate with respect to its transcriptome and mRNA transposition but demonstrates Alexandrium-like stop codon usage. The large portion of repetitive sequences and the organization within the genome is in agreement with several other studies on dinoflagellates using different approaches. It remains to be determined whether this unusual composition is directly correlated to the exceptionally genome organization of dinoflagellates with a low amount of histones and histone-like proteins

Systematic and Evolutionary Insights Derived from mtDNA COI Barcode Diversity in the Decapoda (Crustacea: Malacostraca)

Background: Decapods are the most recognizable of all crustaceans and comprise a dominant group of benthic invertebrates of the continental shelf and slope, including many species of economic importance. Of the 17635 morphologically described Decapoda species, only 5.4% are represented by COI barcode region sequences. It therefore remains a challenge to compile regional databases that identify and analyse the extent and patterns of decapod diversity throughout the world. Methodology/Principal Findings: We contributed 101 decapod species from the North East Atlantic, the Gulf of Cadiz and the Mediterranean Sea, of which 81 species represent novel COI records. Within the newly-generated dataset, 3.6% of the species barcodes conflicted with the assigned morphological taxonomic identification, highlighting both the apparent taxonomic ambiguity among certain groups, and the need for an accelerated and independent taxonomic approach. Using the combined COI barcode projects from the Barcode of Life Database, we provide the most comprehensive COI data set so far examined for the Order (1572 sequences of 528 species, 213 genera, and 67 families). Patterns within families show a general predicted molecular hierarchy, but the scale of divergence at each taxonomic level appears to vary extensively between families. The range values of mean K2P distance observed were: within species 0.285% to 1.375%, within genus 6.376% to 20.924% and within family 11.392% to 25.617%. Nucleotide composition varied greatly across decapods, ranging from 30.8 % to 49.4 % GC content. Conclusions/Significance: Decapod biological diversity was quantified by identifying putative cryptic species allowing a rapid assessment of taxon diversity in groups that have until now received limited morphological and systematic examination. We highlight taxonomic groups or species with unusual nucleotide composition or evolutionary rates. Such data are relevant to strategies for conservation of existing decapod biodiversity, as well as elucidating the mechanisms and constraints shaping the patterns observed.FCT - SFRH/BD/25568/ 2006EC FP6 - GOCE-CT-2005-511234 HERMESFCT - PTDC/MAR/69892/2006 LusomarBo

Protozoan cell cycle control

Many genes belonging to the cyclin-dependent kinase (cdk) family have been isolated from protozoans. While their role in cell cycle has yet to be proven unequivocally, at least one cdk can complement the cdc2(ts)/cdc28(ts) mutants in yeasts. Among the interesting questions relating to cdks in protozoa are: whether one cdk acts throughout the whole cell cycle and whether cyclin partnership is absolutely required. In protozoa, cell cycle control is closely associated with developmental control, Many life cycle differentiation phases can only occur during a specific window in the cell cycle. Because of different DNA biosynthetic pathways, some protozoa among the earliest eukaryotic lineages are unresponsive to common inhibitors of DNA synthesis like hydroxyurea. However, many protozoa do have different checkpoint controls in relation to their response to cell cycle inhibitors

LARVAL DEVELOPMENT OF THE PALAEMONID PRAWN, MACROBRACHIUM-LANCHESTERI (DEMAN) REARED IN THE LABORATORY (DECAPODA, CARIDEA)

The larval development of the palaemonid prawn, Macrobrachium lanchesteri (De Man) was observed under laboratory conditions. Metamorphosis to post-larva was first observed 30 days after hatching at a temperature of 26-degrees-28-degrees-C and in freshwater. Nine larval stages (Zoea I to Zoea IX) were observed and described. The pattern of development is considered in relation to other Macrobrachium species with similar number of larval stages. In relation to larval developmental mode, M. lanchesteri is most similar to M. niloticum from northern Africa. These are the only species in the genus with the fifth pereiopod appearing as a rudimentary bud in the first larval stage and fully formed by the second or the third stage. The size of the fifth pereiopod is also considerably larger than in other species of the genus at the same stage of development

Lipid biosynthesis and its coordination with cell cycle progression

The activation of cell cycle regulators at the G(1)/S boundary has been linked to the cellular protein synthesis rate. It is conceivable that regulatory mechanisms are required to allow cells to coordinate the synthesis of other macromolecules with cell cycle progression. The availability of highly synchronized cells and flow cytometric methods facilitates investigation of the dynamics of lipid synthesis in the entire cell cycle of the heterotrophic dinoflagellate Crypthecodinium cohnii. Flow cytograms of Nile red-stained cells revealed a stepwise increase in the polar lipid content and a continuous increase in neutral lipid content in the dinoflagellate cell cycle. A cell cycle delay at early G but not G(2)/M, was observed upon inhibition of lipid synthesis. However, lipid synthesis continued during cell cycle arrest at the G(1)/S transition. A cell cycle delay was not observed when inhibitors of cellulose synthesis and fatty acid synthesis were added after the late G, phase of the cell cycle. This implicates a commitment point that monitors the synthesis of fatty acids at the late G, phase of the dinoflagellate cell cycle. Reduction of the glucose concentration in the medium down-regulated the G, cell size with a concomitant forward shift of the commitment point. Inhibition of lipid synthesis up-regulated cellulose synthesis and resulted in an increase in cellulosic contents, while an inhibition of cellulose synthesis had no effects on lipid synthesis. Fatty acid synthesis,and cellulose synthesis are apparently coupled to the cell cycle via independent pathways

PCNA-like proteins in dinoflagellates

Dinoflagellate chromosomes are permanently condensed and lack nucleosomes, These features suggest that dinoflagellate chromosomes must have an altered structural arrangement when compared to other eukaryotes and some modified DNA replication machinery to accommodate it. To investigate this possibility, proliferating cell nuclear antigen (PCNA), an essential component of the DNA replication machinery, was chosen for closer examination. A protein in the dinoflagellate Crypthecodinium cohnii Biecheler was found to react specifically with two monoclonal. antibodies raised against PCNA, The observed band had a size of 55 kDa, which is far in excess of what has been described previously. Another dinoflagellate, Gymnodinium catenatum Brave, also displayed a band of this size; however, a third species Amphidinium carterae Hulburt, had a band of lower molecular weight. The putative PCNA homolog in C. cohnii showed a nonconstitutive expression pattern. A time-course western blot using cells from a synchronized G(1) population showed that protein levels peak during S phase of the cell cycle, Both C. cohnii and A. carterae displayed a strong nuclear localization as determined by immunofluorescence microscopy, The signal was present in a subpopulation of cells, supporting cell-cycle-specific expression pattern. It is possible that the larger size of this protein ia some dinoflagellates reflects the unusual cell cycle and DNA arrangement of this group

Fluorescence activated cell-sorting of haemocytes in Penaeid prawns

Prawn haemocytes can usually be divided into three subtypes by their cell sizes and the degree of granularity. The hyaline cells are generally smaller, while the semi-granulocytes and the granulocytes have increasing amount of granules inside their cells. Both relative cell sizes and granularity can conveniently be measured by the forward scatter (FSC) and side scatter (SSC), respectively, in most cytometers. In this paper, we demonstrated the use of these two parameters to distinguish Penaeid haemocytes into distinct subpopulations. The hyaline cells had the smallest values of FSC, while the semi-granulocytes and granulocytes had increasing values of SSC. This pattern is significantly different from a previous report on flow cytometric analysis of Penaeus japonicus. We were also able to use the same parameters to sort the morphologically distinct haemocyte types from P. penicillatus, A monodon and P. japonicus. (C) 2002 Elsevier Science B.V. All rights reserved

Cyclins in a dinoflagellate cell cycle

The dinoflagellates are distinct among eukaryotes in having an extranuclear spindle and permanently condensed chromosomes. These cytologic features implicate special adaptations to the molecular mechanisms of cell cycle control. We have demonstrated the presence of cyclin-box-containing polypeptides in dinoflagellates by using peptide-generated antibodies. We identified four major cyclin-box-containing polypeptides. The cell cycle dynamics of these polypeptides were also investigated in synchronized populations, using a newly developed method. Of the four major cyclin-box-containing polypeptides detected, a tripler with apparent molecular weight of 75 kDa did not change appreciably during the cell cycle. For two other cyclin-box-containing polypeptides with apparent molecular weights of 50 and 65 kDa, we observed an early expression in the cell cycle, with the level accumulating and eventually being degraded on the exit of mitosis. At least one cyclin-box-containing polypeptide (50 kDa) was also observed in a protein complex bound to p13(suc1) beads. The bound complex had associated histone kinase activity. Variation of this activity corresponded well with the periodic expression of the 50-kDa cyclin-box-containing polypeptide during the cell cycle of Crypthecodinium cohnii. This demonstrates the presence of cyclins and cyclin-dependent kinases in dinoflagellates