A Multilevel Probabilistic Beam Search Algorithm for the Shortest Common Supersequence Problem

The shortest common supersequence problem is a classical problem with many applications in different fields such as planning, Artificial Intelligence and especially in Bioinformatics. Due to its NP-hardness, we can not expect to efficiently solve this problem using conventional exact techniques. This paper presents a heuristic to tackle this problem based on the use at different levels of a probabilistic variant of a classical heuristic known as Beam Search. The proposed algorithm is empirically analysed and compared to current approaches in the literature. Experiments show that it provides better quality solutions in a reasonable time for medium and large instances of the problem. For very large instances, our heuristic also provides better solutions, but required execution times may increase considerably.     

Apoptosis,cytokine and chemokine induction by non-structural 1 (NS1) proteins encoded by different influenza subtypes

Background

Influenza pandemic remains a serious threat to human health. Viruses of avian origin, H5N1, H7N7 and H9N2, have repeatedly crossed the species barrier to infect humans. Recently, a novel strain originated from swine has evolved to a pandemic. This study aims at improving our understanding on the pathogenic mechanism of influenza viruses, in particular the role of non-structural (NS1) protein in inducing pro-inflammatory and apoptotic responses.

Methods

Human lung epithelial cells (NCI-H292) was used as an in-vitro model to study cytokine/chemokine production and apoptosis induced by transfection of NS1 mRNA encoded by seven infleunza subtypes (seasonal and pandemic H1, H2, H3, H5, H7, and H9), respectively.

Results

The results showed that CXCL-10/IP10 was most prominently induced (> 1000 folds) and IL-6 was slightly induced (< 10 folds) by all subtypes. A subtype-dependent pattern was observed for CCL-2/MCP-1, CCL3/MIP-1α, CCL-5/RANTES and CXCL-9/MIG; where induction by H5N1 was much higher than all other subtypes examined. All subtypes induced a similar temporal profile of apoptosis following transfection. The level of apoptosis induced by H5N1 was remarkably higher than all others. The cytokine/chemokine and apoptosis inducing ability of the 2009 pandemic H1N1 was similar to previous seasonal strains.

Conclusions

In conclusion, the NS1 protein encoded by H5N1 carries a remarkably different property as compared to other avian and human subtypes, and is one of the keys to its high pathogenicity. NCI-H292 cells system proves to be a good in-vitro model to delineate the property of NS1 proteins.

     

Pollen-ovule ratio,pollen size,and breeding system in Astragalus (Fabaceae) subgenus Epiglottis: a pollen and seed allocation approach

The correlation between pollen/ovule (P/O) ratio and breeding system has generally been accounted for either on the basis that P/O reflects pollination efficiency, or in terms of the sex allocation theory. The following were assessed for taxa belonging to genus Astragalus subgenus Epiglottis: 1) Degree of correlation between P/O and the breeding system, measured by means of autofertility; 2) The absence or existence of correlation between P/O and pollen grain size; and 3) The ability of various theories to account for the results obtained. Results showed a minimal correlation between P/O and autofertility, and between P/O and pollen grain size in the taxa studied. Analysis of these results in terms of the sex allocation theory enabled this correlation to be explained as a function of the variation existing between taxa with respect to the resources invested in each pollen grain and in each ovule. The predictive capacity of this theory, which has moreover proven valuable in explaining the structural peculiarities of the androecium in these taxa, was also highlighted. The type of self-pollination applicable was also discussed, as was the phenotypic model of selection of self-fertilization considered most plausible for these taxa.     

Causes of shear sensitivity of the toxic dinoflagellate Protoceratium reticulatum

Dinoflagellates have proven extremely difficult to culture because they are inhibited by low‐level shear forces. Specific growth rate of the toxic dinoflagellate Protoceratium reticulatum was greatly decreased compared with static control culture by intermittent exposure to a turbulent hydrodynamic environment with a bulk average shear rate that was as low as 0.3 s^?1. Hydrodynamic forces appeared to induce the production of reactive oxygen species (ROS) within the cells and this caused peroxidation of cellular lipids and ultimately cell damage. Exposure to damaging levels of shear rate correlated with the elevated level of lipoperoxides in the cells, but ROS levels measured directly by flow cytometry did not correlate with shear induced cell damage. This was apparently because the measured level of ROS could not distinguish between the ROS that are normally generated by photosynthesis and the additional ROS produced as a consequence of hydrodynamic shear forces. Continuously subjecting the cells to a bulk average shear rate value of about 0.3 s^?1 for 24‐h caused an elevation in the levels of chlorophyll a, peridinin and dinoxanthin, as the cells apparently attempted to counter the damaging effects of shear fields by producing pigments that are potential antioxidants. In static culture, limitation of carbon dioxide produced a small but measureable increase in ROS. The addition of ascorbic acid (0.1 mM) to the culture medium resulted in a significant protective effect on lipid peroxidation, allowing cells to grow under damaging levels of shear rates. This confirmed the use of antioxidant additives as an efficient strategy to counter the damaging effects of turbulence in photobioreactors where shear sensitive dinoflagellates are cultivated. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Gain of function of mutant p53 by coaggregation with multiple tumor suppressors

Many p53 missense mutations possess dominant-negative activity and oncogenic gain of function. We report that for structurally destabilized p53 mutants, these effects result from mutant-induced coaggregation of wild-type p53 and its paralogs p63 and p73, thereby also inducing a heat-shock response. Aggregation of mutant p53 resulted from self-assembly of a conserved aggregation-nucleating sequence within the hydrophobic core of the DNA-binding domain, which becomes exposed after mutation. Suppressing the aggregation propensity of this sequence by mutagenesis abrogated gain of function and restored activity of wild-type p53 and its paralogs. In the p53 germline mutation database, tumors carrying aggregation-prone p53 mutations have a significantly lower frequency of wild-type allele loss as compared to tumors harboring nonaggregating mutations, suggesting a difference in clonal selection of aggregating mutants. Overall, our study reveals a novel disease mechanism for mutant p53 gain of function and suggests that, at least in some respects, cancer could be considered an aggregation-associated disease.     

Flying lemurs – The 'flying tree shrews'? Molecular cytogenetic evidence for a Scandentia-Dermoptera sister clade

Background  

Flying lemurs or Colugos (order Dermoptera) represent an ancient mammalian lineage that contains only two extant species. Although molecular evidence strongly supports that the orders Dermoptera, Scandentia, Lagomorpha, Rodentia and Primates form a superordinal clade called Supraprimates (or Euarchontoglires), the phylogenetic placement of Dermoptera within Supraprimates remains ambiguous.     

Serial in vivo imaging of the targeted migration of human HSV-TK-transduced antigen-specific lymphocytes

New technologies are needed to characterize the migration, survival, and function of antigen-specific T cells in vivo. Here, we demonstrate that Epstein-Barr virus (EBV)--specific T cells transduced with vectors encoding herpes simplex virus-1 thymidine kinase (HSV-TK) selectively accumulate radiolabeled 2'-fluoro-2'-deoxy-1-beta-D-arabinofuranosyl-5-iodouracil (FIAU). After adoptive transfer, HSV-TK+ T cells labeled in vitro or in vivo with [131I]FIAU or [124I]FIAU can be noninvasively tracked in SCID mice bearing human tumor xenografts by serial images obtained by scintigraphy or positron emission tomography (PET), respectively. These T cells selectively accumulate in EBV+ tumors expressing the T cells' restricting HLA allele but not in EBV- or HLA-mismatched tumors. The concentrations of transduced T cells detected in tumors and tissues are closely correlated with the concentrations of label retained at each site. Radiolabeled transduced T cells retain their capacity to eliminate targeted tumors selectively. This technique for imaging the migration of ex vivo-transduced antigen-specific T cells in vivo is informative, nontoxic, and potentially applicable to humans.     

Filamentous fungi preservation in distilled water.

Some methods for keeping the fungal Culture Collection have been used. However, the choice of either one on the basis that must ensure the cultural genetic stability and its phenotipic characteristics. In this work the preservation method in distilled water recognized in the literature as a single, economic and certain method that guarantie the survival of fungus cultures for long periods was used. 26 strains of generus and species: Aspergillus niger, Aspergillus candidus, Fusarium sp., Fusarium moniliforme, Mucor griseocyanum, Syncephalastrum sp., Trichoderma sp., Trichoderma harzianum and Trichoderma koningii were preserved. Enough inoculum from well developed cultures (mainly spores and hyphae) poured in flasks with sterile distilled water warranted a 100% of survival of those microorganisms for two years. At the same time no apparent changes were observed in respect to morphology and macroscopic features.     

Description of nine South American species of the genus Neralsia cameron, with low scutellar carina (Hymenoptera: Cynipoidea: Figitidae)

In this study a total of nine new species of the genus Neralsia are described for South America: N. desantisi Jiménez & Pujade-Villar n. sp., N. equilatera Jiménez & Pujade-Villar n. sp., N. hermafrodita Jiménez & Pujade-Villar n. sp., N. marioi Jiménez & Pujade-Villar n. sp., N. moisesi Jiménez & Pujade-Villar n. sp., N. obelix Jiménez & Pujade-Villar n. sp., N. parafossulata Jiménez & Pujade-Villar n. sp., N. pseudoneralsia Jiménez & Pujade-Villar n. sp. and N. rauli Jiménez & Pujade-Villar n. sp., all of them have in common the low carina separating the scutellar foveae. Other six known Neralsia species, N. albipennis (Kieffer), N. bogotensis (Kieffer), N. flavidipennis (Kieffer), N. fossulata (Kieffer), N. pilosa (Borgmeier) and N. striaticeps (Kieffer) have the same scutellar character. The morphological characters to differentiate all mentioned species are presented.