| 1. |
- 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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| 2. |
- Bylesjö, Max, et al.
(författare)
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MASQOT : a method for cDNA microarray spot quality control.
- 2005
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Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 6, s. 250-
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundcDNA microarray technology has emerged as a major player in the parallel detection of biomolecules, but still suffers from fundamental technical problems. Identifying and removing unreliable data is crucial to prevent the risk of receiving illusive analysis results. Visual assessment of spot quality is still a common procedure, despite the time-consuming work of manually inspecting spots in the range of hundreds of thousands or more.ResultsA novel methodology for cDNA microarray spot quality control is outlined. Multivariate discriminant analysis was used to assess spot quality based on existing and novel descriptors. The presented methodology displays high reproducibility and was found superior in identifying unreliable data compared to other evaluated methodologies.ConclusionThe proposed methodology for cDNA microarray spot quality control generates non-discrete values of spot quality which can be utilized as weights in subsequent analysis procedures as well as to discard spots of undesired quality using the suggested threshold values. The MASQOT approach provides a consistent assessment of spot quality and can be considered an alternative to the labor-intensive manual quality assessment process.
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| 3. |
- Hanberg, Annika, et al.
(författare)
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Phthalates and their metabolites in human breast milk, blood and urine as measures for monitoring exposure in human risk groups
- 2005
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- För att undersöka halter av ftalater i svenskar och vilken matris som bäst lämpar sig för hälsorelaterad miljöövervakning har ftalater och ftalatmetaboliter analyserats i en grupp kvinnor som nyligen fött barn. I samband med förlossning på Universitetssjukhuset i Lund tillfrågades förstföderskor om medverkan och 42 kvinnor kom att ingå i studien. När barnet var 2-3 veckor gammalt pumpade mamman ut 50 mL bröstmjölk. Blod- och urinprov togs en vecka senare. Omfattande förändringar av standardmetoder för provtagning av mjölk och blod gjordes för att minimera risken för kontaminering av proverna. För mjölkprovtagningen användes en specialkonstruerad manuell pump av polykarbonat med ftalatfri packning. Blodprov togs med hjälp av endast kanyl och provrör (eftersom propparna i vaccutainrör innehåller ftalater). Proverna förvarades i värmebehandlade glasbehållare och fosforsyra tillsattes för att motverka metabolism av ftalater i mjölk- och blodprover. Analyserna av bröstmjölk visade värden nära eller under detektionsgränsen (LOD) för flertalet ftalater eller deras metaboliter. Även i blod och serum var nivåerna vanligtvis nära eller under LOD. I urin analyserades endast metaboliter och dessa kunde kvantifieras i 53-100 % av proverna. Nivåerna av ftalatmetaboliter i urin hos de svenska kvinnorna var i paritet med nivåerna hos en allmänbefolkning i USA och Tyskland. Några klara korrelationer mellan nivåer i t ex urin och bröstmjölk respektive blod påvisades inte. Resultaten av studien anger att för närvarande är analys av ftalatmetaboliter i urin den mest framkomliga vägen för skattning av ftalatexponering hos människa. Provtagning och analys av mjölk och blod innebar betydligt större svårigheter. Framför allt framstår risken för kontaminering vid provtagning som betydande och en stor del av ftalaterna och dess metaboliter uppvisade låga halter, vid eller under LOD. Dessutom kan ftalater brytas ned i blod och mjölk. I flertalet internationella publicerade studier av ftalatexponering används urinmetabolit-analyser som ett mått på exponering för ftalater. I en nyligen publicerad amerikansk studie av ett 80-tal nyfödda pojkar sågs ett samband mellan kort ano-genitalt avstånd och nivåer av ftalatmetaboliter i urin hos deras mammor under graviditeten. Den amerikanska studien behöver bekräftas, men metaboliterna var desamma som i vår studie och en jämförelse visar att mediannivåerna var lägre för vissa men högre för andra metaboliter. Vår studie indikerar att svenska kvinnor i fertil ålder inte sällan exponeras för ftalater i nivåer som satts i samband med fosterpåverkan.
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| 4. |
- Hellsten, Johan, et al.
(författare)
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Electroconvulsive seizures induce angiogenesis in adult rat hippocampus
- 2005
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Ingår i: Biological Psychiatry. - : Elsevier BV. - 0006-3223. ; 58:11, s. 871-878
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Tidskriftsartikel (refereegranskat)abstract
- Background: Electroconvulsive seizure (ECS)-treatment, a model for electroconvulsive therapy (ECT) has been shown to induce proliferation of endothelial cells in the dentate gyrus (DG) of adult rats. Here we quantified the net angiogenic response after hypoxia a known inducer of aniogenesis. Therefore we also examined the effect of oxygenation on ECS-induced proliferation of endothelial cells. Methods: Total endothelial cell numbers and vessel length were estimated utilizing design based stereological analysis methods. Endothelial cell proliferation in the DG after ECS with or withouy oxygenation was assessed using bromodeoxyuridine. Results: The total number of endothelial cell numbers and vessels lenght was increased. Oxygenation did not abolish the ECS-induced proliferation of endothelial cells in the DG. Conclusions: ECS-treatment induces a dramatic increase in endothelial cell proliferation leading to a 30% increase in the total numberof endothelial cells. The increase in cell number resulted i na 16% increase in vessel length. These findings raise the possibility that similar vascular growth is induced by clinically administered ECT.
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| 5. |
- Jansson, Johan, 1978, et al.
(författare)
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Computational modeling of dynamical systems
- 2005
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Ingår i: Mathematical Models and Methods in Applied Sciences. - 0218-2025. ; 15:3, s. 471-481
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Tidskriftsartikel (refereegranskat)abstract
- In this short note, we discuss the basic approach to computational modeling of dynamical systems. If a dynamical system contains multiple time scales, ranging from very fast to slow, computational solution of the dynamical system can be very costly. By resolving the fast time scales in a short time simulation, a model for the effect of the small time scale variation on large time scales can be determined, making solution possible on a long time interval. This process of computational modeling can be completely automated. Two examples are presented, including a simple model problem oscillating at a time scale of 10-9 computed over the time interval [0, 100], and a lattice consisting of large and small point masses. © World Scientific Publishing Company.
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| 6. |
- Jansson, Johan, 1974-
(författare)
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Internetbranschen i Stockholms innerstad : En studie av agglomerationsfördelar, sociala nätverksrelationer och informationsflöden
- 2005
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis deals with questions concerning spatial agglomeration of economic activities. The object of study is the Internet industry in central Stockholm. Through the use of statistical data and an interview study the Internet industry is described, measured, and analyzed through theories concerning agglomerations, social network relations, and knowledge and information flows. These theories are interpreted through five agglomeration themes related to the role of customers, subcontractors and partners, competitors, financing, and labour market, respec-tively.The research has recognized the importance of proximity to create and maintain social networks, and to spread information and knowledge, especially tacit knowledge. The thesis also shows how social networks, and information and knowledge flows have an essential role in all the five agglomeration themes that are analyzed. The results of this analysis show that the proximity to customers is the most important factor for the location of the Internet indus-try. Also, the local labour market and access to suppliers and partners are important factors. Competitors and rivals have a role to play when it comes to the diffusion of knowledge and information, although its importance as a location factor is hard to estimate. The analysis of the firms’ financing demonstrate that this factor hardly has been of crucial importance for the location of the Internet industry, but access to (venture) capital might have been of indirect importance for the location and the pace of the development of the Internet industry.
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| 7. |
- Nilsson, Christer, 1951-, et al.
(författare)
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Forecasting environmental responses to restoration of rivers used as log floatways : an interdisciplinary challenge
- 2005
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Ingår i: Ecosystems (New York. Print). - : Springer Science and Business Media LLC. - 1432-9840 .- 1435-0629. ; 8:7, s. 779-800
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Tidskriftsartikel (refereegranskat)abstract
- Log floating in the 19th to mid 20th centuries has profoundly changed the environmental conditions in many northern river systems of the world. Regulation of flow by dams, straightening and narrowing of channels by various piers and wing dams, and homogenization of bed structure are some of the major impacts. As a result, the conditions for many riverine organisms have been altered. Removing physical constructions and returning boulders to the channels can potentially restore conditions for these organisms. Here we describe the history of log driving, review its impact on physical and biological conditions and processes, and predict the responses to restoration. Reviewing the literature on comparable restoration efforts and building upon this knowledge, using boreal Swedish rivers as an example, we address the last point. We hypothesize that restoration measures will make rivers wider and more sinuous, and provide rougher bottoms, thus improving land-water interactions and increasing the retention capacity of water, sediment, organic matter and nutrients. The geomorphic and hydraulic/hydrologic alterations are supposed to favor production, diversity, migration and reproduction of riparian and aquatic organisms. The response rates are likely to vary according to the types of processes and organisms. Some habitat components, such as beds of very large boulders and bedrock outcrops, and availability of sediment and large woody debris are believed to be extremely difficult to restore. Monitoring and evaluation at several scales are needed to test our predictions.
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| 8. |
- Woldegiorgis, A., et al.
(författare)
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Fabrication of silica nano wires on the internal perimeter of narrow bore fused silicia tubing by non-isothermal etching
- 2005
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Ingår i: Journal of Materials Science. - : Springer Science and Business Media LLC. - 0022-2461 .- 1573-4803. ; 40:3, s. 583-589
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Tidskriftsartikel (refereegranskat)abstract
- An method for fabrication of long silica nano wires is presented. The nano structured material is an integral part of the inner surface of narrow bore fused silica capillary tubing. The wire preparation method is based on a hydrothermal action and decomposition of 2-chloro-1,1,2-trifluoroethyl methyl ether at elevated temperature. In our previous work, reproducible nano wire outgrowth could only be accomplished in capillaries with an inner diameter less than 10 mum [1], and the centre of the capillary lumen remained free of wires. In the present article we report on nano wire outgrowth in capillaries with larger inner diameters. These wires are entangled via carbon nucleating particles and stretch across the entire lumen of the capillary. The long nano wire outgrowth was induced by a time dependent, non isothermal etching of the capillaries. Suggested mechanisms for the growth process are discussed.
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