| 31. |
- Björk, Glenn, et al.
(författare)
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A conserved modified wobble nucleoside (mcm5s2U) in lysyl-tRNA is required for viability in yeast.
- 2007
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Ingår i: RNA. - : Cold Spring Harbor Laboratory. - 1355-8382 .- 1469-9001. ; 13:8, s. 1245-55
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Tidskriftsartikel (refereegranskat)abstract
- Transfer RNAs specific for Gln, Lys, and Glu from all organisms (except Mycoplasma) and organelles have a 2-thiouridine derivative (xm(5)s(2)U) as wobble nucleoside. These tRNAs read the A- and G-ending codons in the split codon boxes His/Gln, Asn/Lys, and Asp/Glu. In eukaryotic cytoplasmic tRNAs the conserved constituent (xm(5)-) in position 5 of uridine is 5-methoxycarbonylmethyl (mcm(5)). A protein (Tuc1p) from yeast resembling the bacterial protein TtcA, which is required for the synthesis of 2-thiocytidine in position 32 of the tRNA, was shown instead to be required for the synthesis of 2-thiouridine in the wobble position (position 34). Apparently, an ancient member of the TtcA family has evolved to thiolate U34 in tRNAs of organisms from the domains Eukarya and Archaea. Deletion of the TUC1 gene together with a deletion of the ELP3 gene, which results in the lack of the mcm(5) side chain, removes all modifications from the wobble uridine derivatives of the cytoplasmic tRNAs specific for Gln, Lys, and Glu, and is lethal to the cell. Since excess of the unmodified form of these three tRNAs rescued the double mutant elp3 tuc1, the primary function of mcm(5)s(2)U34 seems to be to improve the efficiency to read the cognate codons rather than to prevent mis-sense errors. Surprisingly, overexpression of the mcm(5)s(2)U-lacking tRNA(Lys) alone was sufficient to restore viability of the double mutant.
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| 32. |
- Borg, O. Anders, et al.
(författare)
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A Computational Study on the Lowest Triplet State of Ruthenium Polypyridyl Complexes used in Artificial Photosynthesis
- 2008
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 112:19, s. 4470-4476
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Tidskriftsartikel (refereegranskat)abstract
- The potential energy surfaces of the first excited triplet state of some ruthenium polypyridyl complexes were investigated by means of density functional theory. Focus was placed on the interaction between the geometrical changes accompanying the photoactivity of these complexes when used as antenna complexes in artificial photosynthesis and dye-sensitized solar cells and the accompanying changes in electronic structure. The loss process (3)MLCT --> (3)MC can be understood by means of ligand-field splitting, traced down to the coordination of the central ruthenium atom.
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| 33. |
- Borg, O Anders, et al.
(författare)
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Photochemistry of bromofluorobenzenes.
- 2006
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Ingår i: J Phys Chem A Mol Spectrosc Kinet Environ Gen Theory. - 1089-5639. ; 110, s. 7045-
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Tidskriftsartikel (refereegranskat)
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| 34. |
- Borg, Sixten, et al.
(författare)
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The cost-effectiveness of treatment with erythropoietin compared to red blood cell transfusions for patients with chemotherapy induced anaemia: a Markov model.
- 2008
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Ingår i: Acta oncologica (Stockholm, Sweden). - : Informa UK Limited. - 1651-226X .- 0284-186X. ; 47:6, s. 1009-1017
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Anaemia is a common complication of chemotherapy. As anaemia can lead to e.g. fatigue, depression, social isolation and chest pain it diminishes physical capacity and quality of life. It is generally accepted that symptomatic anaemia should be corrected. Treatment options include red blood cell transfusion (RBCT), erythropoietin (EPO) administration or a combination of both. OBJECTIVE: The objective of this study was to carry out a cost-effectiveness analysis of treatment with EPO (epoetin alfa), compared to treatment with RBCT for patients with chemotherapy-induced anaemia in Sweden from a health care perspective. METHOD: A model was developed for estimating incremental costs and QALY gains associated with EPO treatment compared to treatment with RBCTs, based on a model commissioned by the UK National Institute for Health and Clinical Excellence and adjusted to reflect Swedish treatment practice. Data regarding patient characteristics, response rates, and RBCT was derived from a Swedish observational study of EPO treatment in cancer patients with chemotherapy related anaemia. Swedish guidelines and unit costs were used throughout the study. A systematic review of EPO for treatment of anaemia associated with cancer was used to estimate QALY gains associated with changes in Hb-concentrations in our model. RESULTS: The model's results validate well to real world data from three major hospitals in Sweden. The cost per QALY gained from administration of EPO was estimated at EUR 24,700 in the base case analysis. Practicing an EPO treatment target Hb-level of 12 g/dl yields a cost per QALY about 40% lower than practicing a Hb-target level of 13 g/dl, which is in agreement with updated recommendations of using a 12 g/dl target. CONCLUSION: The estimated cost per QALY falls well within the range acceptable in Sweden when practicing a Hb-target level of 12 g/dl. The incremental cost of elevating Hb-levels above 13 g/dl is very high in relation to the incremental QALY gain achieved.
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| 35. |
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| 36. |
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| 37. |
- Bresel, Anders, et al.
(författare)
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GenomeLKPG : A comprehensive proteome sequencedatabase for taxonomy studies
- 2008
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Tidskriftsartikel (refereegranskat)abstract
- Background: In order to perform taxonomically unbiased analyses of protein relationships, there is a need ofcomplete proteomes rather than databases with bias towards well characterized protein families. However, nocomprehensive resource of completed proteomes is currently available. Instead, the proteomes need to be down-loaded manually from di®erent servers, all using different filename conventions and fasta header formats. Results: We have developed a semi-automatic algorithm that retrieves complete proteomes from multiple FTP-servers and maps the species-speci¯c sequence entries to the NCBI taxonomy. The compiled data is provided ina sequence database named genomeLKPG. Conclusions: The usefulness of genomeLKPG is proven in several published taxonomical studies.
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| 38. |
- Bresell, Anders, et al.
(författare)
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Bioinformatic and enzymatic characterization of the MAPEG superfamily
- 2005
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Ingår i: The FEBS Journal. - : Wiley. - 1742-464X .- 1742-4658. ; 272:7, s. 1688-1703
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Tidskriftsartikel (refereegranskat)abstract
- The membrane associated proteins in eicosanoid and glutathione metabolism (MAPEG) superfamily includes structurally related membrane proteins with diverse functions of widespread origin. A total of 136 proteins belonging to the MAPEG superfamily were found in database and genome screenings. The members were found in prokaryotes and eukaryotes, but not in any archaeal organism. Multiple sequence alignments and calculations of evolutionary trees revealed a clear subdivision of the eukaryotic MAPEG members, corresponding to the six families of microsomal glutathione transferases (MGST) 1, 2 and 3, leukotriene C4 synthase (LTC4), 5-lipoxygenase activating protein (FLAP), and prostaglandin E synthase. Prokaryotes contain at least two distinct potential ancestral subfamilies, of which one is unique, whereas the other most closely resembles enzymes that belong to the MGST2/FLAP/LTC4 synthase families. The insect members are most similar to MGST1/prostaglandin E synthase. With the new data available, we observe that fish enzymes are present in all six families, showing an early origin for MAPEG family differentiation. Thus, the evolutionary origins and relationships of the MAPEG superfamily can be defined, including distinct sequence patterns characteristic for each of the subfamilies. We have further investigated and functionally characterized representative gene products from Escherichia coli, Synechocystis sp., Arabidopsis thaliana and Drosophila melanogaster, and the fish liver enzyme, purified from pike (Esox lucius). Protein overexpression and enzyme activity analysis demonstrated that all proteins catalyzed the conjugation of 1-chloro-2,4-dinitrobenzene with reduced glutathione. The E. coli protein displayed glutathione transferase activity of 0.11 µmol·min−1·mg−1 in the membrane fraction from bacteria overexpressing the protein. Partial purification of the Synechocystis sp. protein yielded an enzyme of the expected molecular mass and an N-terminal amino acid sequence that was at least 50% pure, with a specific activity towards 1-chloro-2,4-dinitrobenzene of 11 µmol·min−1·mg−1. Yeast microsomes expressing the Arabidopsis enzyme showed an activity of 0.02 µmol·min−1·mg−1, whereas the Drosophila enzyme expressed in E. coli was highly active at 3.6 µmol·min−1·mg−1. The purified pike enzyme is the most active MGST described so far with a specific activity of 285 µmol·min−1·mg−1. Drosophila and pike enzymes also displayed glutathione peroxidase activity towards cumene hydroperoxide (0.4 and 2.2 µmol·min−1·mg−1, respectively). Glutathione transferase activity can thus be regarded as a common denominator for a majority of MAPEG members throughout the kingdoms of life whereas glutathione peroxidase activity occurs in representatives from the MGST1, 2 and 3 and PGES subfamilies.
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| 39. |
- Bresell, Anders, et al.
(författare)
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Characterization of oligopeptide patterns in large protein sets
- 2007
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 8:346, s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- Background: Recent sequencing projects and the growth of sequence data banks enable oligopeptide patterns to be characterized on a genome or kingdom level. Several studies have focused on kingdom or habitat classifications based on the abundance of short peptide patterns. There have also been efforts at local structural prediction based on short sequence motifs. Oligopeptide patterns undoubtedly carry valuable information content. Therefore, it is important to characterize these informational peptide patterns to shed light on possible new applications and the pitfalls implicit in neglecting bias in peptide patterns. Results: We have studied four classes of pentapeptide patterns (designated POP, NEP, ORP and URP) in the kingdoms archaea, bacteria and eukaryotes. POP are highly abundant patterns statistically not expected to exist; NEP are patterns that do not exist but are statistically expected to; ORP are patterns unique to a kingdom; and URP are patterns excluded from a kingdom. We used two data sources: the de facto standard of protein knowledge Swiss-Prot, and a set of 386 completely sequenced genomes. For each class of peptides we looked at the 100 most extreme and found both known and unknown sequence features. Most of the known sequence motifs can be explained on the basis of the protein families from which they originate. Conclusion: We find an inherent bias of certain oligopeptide patterns in naturally occurring proteins that cannot be explained solely on the basis of residue distribution in single proteins, kingdoms or databases. We see three predominant categories of patterns: (i) patterns widespread in a kingdom such as those originating from respiratory chain-associated proteins and translation machinery; (ii) proteins with structurally and/or functionally favored patterns, which have not yet been ascribed this role; (iii) multicopy species-specific retrotransposons, only found in the genome set. These categories will affect the accuracy of sequence pattern algorithms that rely mainly on amino acid residue usage. Methods presented in this paper may be used to discover targets for antibiotics, as we identify numerous examples of kingdom-specific antigens among our peptide classes. The methods may also be useful for detecting coding regions of genes.
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| 40. |
- Bresell, Anders, 1978-
(författare)
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Characterization of protein families, sequence patterns, and functional annotations in large data sets
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Bioinformatics involves storing, analyzing and making predictions on massive amounts of protein and nucleotide sequence data. The thesis consists of six papers and is focused on proteins. It describes the utilization of bioinformatics techniques to characterize protein families and to detect patterns in gene expression and in polypeptide occurrences. Two protein families were bioinformatically characterized - the membrane associated proteins in eicosanoid and glutathione metabolism (MAPEG) and the Tripartite motif (TRIM) protein families.In the study of the MAPEG super-family, application of different bioinformatic methods made it possible to characterize many new members leading to a doubling of the family size. Furthermore, the MAPEG members were subdivided into families. Remarkably, in six families with previously predominantly mammalian members, fish representatives were also now detected, which dated the origin of these families back to the Cambrium ”species explosion”, thus earlier than previously anticipated. Sequence comparisons made it possible to define diagnostic sequence patterns that can be used in genome annotations. Upon publication of several MAPEG structures, these patterns were confirmed to be part of the active sites.In the TRIM study, the bioinformatic analyses made it possible to subdivide the proteins into three subtypes and to characterize a large number of members. In addition, the analyses showed crucial structural dependencies between the RING and the B-box domains of the TRIM memberRo52. The linker region between the two domains, denoted RBL, is knownto be disease associated. Now, an amphipathic helix was found to be acharacteristic feature of the RBL region, which also was used to divide the family into three subtypes.The ontology annotation treebrowser (OAT) tool was developed to detect functional similarities or common concepts in long lists of proteins or genes, typically generated from proteomics or microarray experiments. OAT was the first annotation browser to include both Gene Ontology (GO) and Medical Subject Headings (MeSH) into the same framework. The complementarity of these two ontologies was demonstrated. OAT was used in the TRIM study to detect differences in functional annotations between the subtypes.In the oligopeptide study, we investigated pentapeptide patterns that were over- or under-represented in the current de facto standard database of protein knowledge and a set of completed genomes, compared to what could be expected from amino acid compositions. We found three predominant categories of patterns: (i) patterns originating from frequently occurring families, e.g. respiratory chain-associated proteins and translation machinery proteins; (ii) proteins with structurally and/or functionally favored patterns; (iii) multicopy species-specific retrotransposons, only found in the genome set. Such patterns may influence amino acid residue based prediction algorithms. These findings in the oligopeptide study were utilized for development of a new method that detects translated introns in unverified protein predictions, which are available in great numbers due to the many completed and ongoing genome projects.A new comprehensive database of protein sequences from completed genomes was developed, denoted genomeLKPG. This database was of central importance in the MAPEG, TRIM and oligopeptide studies. The new sequence database has also been proven useful in several other studies.
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