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- Andersson, Anders, et al.
(författare)
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A transcriptional timetable of autumn senescence
- 2004
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 5:4, s. R24-
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Tidskriftsartikel (refereegranskat)abstract
- Background We have developed genomic tools to allow the genus Populus (aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag (EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence. Results On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree (Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates. Conclusions We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.
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| 2. |
- Andersson, C., et al.
(författare)
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Improved systems for hydrophobic tagging of recombinant immunogens for efficient iscom incorporation
- 2000
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Ingår i: JIM - Journal of Immunological Methods. - 0022-1759 .- 1872-7905. ; 238:02-jan, s. 181-193
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Tidskriftsartikel (refereegranskat)abstract
- We have previously reported a strategy for production in Escherichia coli of recombinant immunogens fused to a hydrophobic tag to improve their capacity to associate with an adjuvant formulation [Andersson et al., J. Immunol. Methods 222 (1999) 171]. Here, we describe a further development of the previous strategy and present significant improvements. In the novel system, the target immunogen is produced with an N-terminal affinity tag suitable for affinity purification, and a C-terminal hydrophobic tag, which should enable association through hydrophobic interactions of the immunogen with an adjuvant system, here being immunostimulating complexes (iscoms). Two different hydrophobic tags were evaluated: (i) a tag denoted M, derived from the membrane-spanning region of Staphylococcus aureus protein A (SpA), and (ii) a tag denoted MI consisting of the transmembrane region of hemagglutinin from influenza A virus. Furthermore, two alternative affinity tags were evaluated; the serum albumin-binding protein ABP, derived from streptococcal protein G, and the divalent IgG-binding ZZ-domains derived from SpA. A malaria peptide M5, derived from the central repeat region of the Plasmodium falciparum blood-stage antigen Pf155/RESA, served as model immunogen in this study. Four different fusion proteins, ABP-MS-M, ABP-MS-MI, ZZ-MS-M and ZZ-MS-MI, were thus produced, affinity purified and evaluated in iscom-incorporation experiments. All of the fusion proteins were found in the iscom fractions in analytical ultracentrifugation, indicating iscom incorporation. This was further supported by electron microscopy analysis showing that iscoms were formed. In addition, these iscom preparations were demonstrated to induce MS-specific antibody responses upon immunisation of mice, confirming the successful incorporation into iscoms. The novel system for hydrophobic tagging of immunogens, with optional affinity and hydrophobic tags, gave expression levels that were increased ten to fifty-fold, as compared to the earlier reported system. We believe that the presented strategy would be a convenient way to achieve efficient adjuvant association for recombinant immunogens.
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| 5. |
- Björklund, Henrik, et al.
(författare)
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A Discrete Subexponential Algorithm for Parity Games
- 2002
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- We suggest a new randomized algorithm for solving Parity Games with the worst case time complexity roughlymin(O( n3 · ( n/k+1 )k), 2O(sqrt(nlog n))),where n is the number of vertices and k the number of colors of the game. Comparable with the previously known algorithms, which are efficient when the number of colors is small, it is subexponential when the number of colors is large, k = Omega (n1/2 + varepsilon).
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| 6. |
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| 7. |
- Björklund, Henrik, et al.
(författare)
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Algorithms for Combinatorial Optimization and Games Adapted from Linear Programming
- 2003
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The problem of maximizing functions from the boolean hypercube to real numbers arises naturally in a wide range of applications. This paper studies an even more general setting, in which the function to maximize is defined on what we call a hyperstructure. A hyperstructure is the Cartesian product of finite sets with possibly more than two elements. We also relax the codomain to any partially ordered set. Well-behaved such functions arise in game theoretic contexts, in particular from parity games (equivalent to the modal mu-calculus model checking) and simple stochastic games (Björklund, Sandberg, Vorobyov 2003). We show how several subexponential algorithms for linear programming (Kalai 1992, Matousek, Sharir, Welzl 1992) can be adapted to hyperstructures and give a reduction to the abstract optimization problems introduced in (Gärtner1995).
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| 8. |
- Björklund, Henrik, et al.
(författare)
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An Experimental Study of Algorithms for Completely Unimodal Optimization
- 2002
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The paper presents an account of the experimental study of five different algorithms for the Completely Unimodal Pseudoboolean Function (CUPBF) Optimization. CUPBFs satisfy the Hirsch's conjecture, but are not known (although conjectured) to be polynomial. We summarize known and new upper and lower bounds, describe methods of random CUPBFs generation, and use them to compare the algorithms.
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| 9. |
- Björklund, Henrik, et al.
(författare)
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An Improved Subexponential Algorithm for Parity Games
- 2003
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- We suggest a new algorithm for deciding parity games, a fundamental problem of unknown complexity (in NPcapcoNP, not known to belong to P) in game, automata, complexity theories, combinatorial optimization, temporal logic of programs, computer-aided verification. The novelty of the algorithm consists in exploiting a special form of parity games with retreats, where optimal retreat edges define absorbing facets (with better values than their neighbors on complementary facets) in the strategy space. A superset of such absorbing facets can be found by standard random iterative improvement algorithms in expected polynomial time. Additional dual techniques are used to minimize this superset. As a result, the dimension of the problem shrinks, to which we finally apply the Kalai-Matousek-Sharir-Welzl-Ludwig-style randomization techniques we recently adapted for games [Bjorklund, Sandberg, Vorobyov, STACS'2003 and TR-2003-002]
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