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  • 1.
    Bohlin, Christina
    Karlstad University, Faculty of Technology and Science.
    In vitro and in vivo oxidation of diastereomers of lignin models of arylgylcerol b-aryl ether type and heterologous expression of laccase2008Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Enzymic and non-enzymic oxidation of lignin models of the arylglycerol β-aryl ether type was investigated in experiments aimed at providing a better understanding of the initial phase of biological lignin degradation. Product profiles and diasteromer selectivity were determined to gain knowledge of the properties of the oxidants and pave the way for evaluation of the presence of the oxidants in ligninolytic fungal cultures.

    Diastereomers of the non-phenolic lignin model 1-(3,4-dimethoxyphenyl)-2-(2-methoxyphenoxy)-1,3-propanediol (1) were oxidized in vitro with lignin peroxidase (LP), laccase-mediator systems, Fenton's reagent, cerium(IV) ammonium nitrate (CAN) and lead(IV) tetraacetate. The product profiles were found to be distinctive for the different oxidants, except for LP and CAN, which generated the same products in similar proportions. The reactions resulted in preferential degradation of the threo isomer, except for the Fenton's reagent reaction, which showed no stereo-preference, and the laccase reaction mediated by ABTS, which preferentially degraded the erythro isomer. Cultures of the white-rot fungi Trametes versicolor and Phanerochaete chrysosporium preferentially degraded the threo isomer of 1. This is not in agreement with the action of Fenton's reagent, since this oxidant does not exhibit any stereo-preference.

    Laccase from T. versicolor was expressed in Pichia pastoris and Aspergillus niger. Production of catalytically active T. versicolor laccase was achieved in both P. pastoris and A. niger using glyceraldehyde-3-phosphate dehydrogenase promoters. The level of laccase activity obtained with P. pastoris was significantly lower than that obtained with A. niger, but speed and convenience make the P. pastoris system attractive for screening purposes. A. niger produced high yields of heterologous laccase with properties similar to those of the native enzyme. A method was devised to purify laccase from cultures of A. niger. The method gave a 250-fold purification and a yield of >50%.

  • 2.
    Broman, Natasja
    Karlstad University, Faculty of Health, Science and Technology (starting 2013).
    Attempt to purify and identify an unknown cytochrome c in Ideonella dechloratans2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Oxochlorates are compounds consisting of chlorine and oxygen and are in high concentrations toxic to mammals and the environment. They exist and can be formed naturally but most of the oxochlorates in the environment are a result of human activities, for example the paper industry. Bacteria capable of growth anaerobically with (per)chlorate as terminal electron acceptor in its respiratory chain are utilized to purify the waste water. One of those bacteria is Ideonella dechloratans, which uses chlorate reductase to reduce chlorate into chlorite and then chlorite dismutase to decompose chlorite into chlorine and molecular oxygen.

    Present work deals with detection and purification of c cytochromes in I. dechloratans that could have a role in electron transport during chlorate reduction. Earlier work has demonstrated the presence of two major periplasmic c cytochromes with apparent molecular weights around 6 and 13 kDa. These have been purified and characterized. The "6 kDa protein" was shown to be capable of donating electrons to chlorate reductase and terminal oxidase in vitro. The molecular weight as determined by mass spectrometry analysis was shown to be 9.4 kDa. The "13 kDa protein" was shown to be unable to act as an electron donor directly to chlorate reductase in vitro. Attempts with mass spectrometry analysis has yet been unsuccessful.

    In this study, attempts were made to purify this 13 kDa cytochrome c from anaerobically cultivated I. dechloratans to investigate its properties with 2D electrophoresis and if possible, cut out a spot and analyze it with mass spectrometry.

    Some purification was achieved with cationic exchange chromatography, where about 10 other proteins were eluted at the same time as the 13 kDa cytochrome c. Further purification attempts had difficulties with the detection of the cytochrome c on SDS-PAGE. It is less likely, but still possible, that this was due to protein degradation or loss of the heme group. Fractions containing the 13 kDa cytochrome c were analyzed with 2D electrophoresis but the protein could not be detected on the gel. This is probably due to the protein having difficulties entering the IPG strip during the rehydration in the first dimension or difficulties transferring from the strip into the gel in the second dimension. Different changes, such as a low voltage applied over the strip during rehydration and increased carrier ampholyte concentration, were made to the protocol but did not help. Attempts to verify if the problem is in the first or second dimension were made but did not show anything.

  • 3.
    Forssén, Patrik
    et al.
    Karlstad University, Faculty of Health, Science and Technology (starting 2013), Department of Engineering and Chemical Sciences (from 2013).
    Multia, Evgen
    University of Helsinki, Finland.
    Samuelsson, Jörgen
    Karlstad University, Faculty of Health, Science and Technology (starting 2013), Department of Engineering and Chemical Sciences (from 2013).
    Andersson, Marie
    Karlstad University, Faculty of Health, Science and Technology (starting 2013), Department of Engineering and Chemical Sciences (from 2013).
    Aastrup, Teodor
    Attana AB, Sweden.
    Altun, Samuel
    Attana AB, Sweden.
    Wallinder, Daniel
    Attana AB, Sweden.
    Wallbing, Linus
    Attana AB, Sweden.
    Liangsupree, Thanaporn
    University of Helsinki, Finland.
    Riekkola, Marja-Liisa
    University of Helsinki, Finland.
    Fornstedt, Torgny
    Karlstad University, Faculty of Health, Science and Technology (starting 2013), Department of Engineering and Chemical Sciences (from 2013).
    Reliable Strategy for Analysis of Complex Biosensor Data2018In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 90, no 8, p. 5366-5374Article in journal (Refereed)
    Abstract [en]

    When using biosensors, analyte biomolecules of several different concentrations are percolated over a chip with immobilized ligand molecules that form complexes with analytes. However, in many cases of biological interest, e.g., in antibody interactions, complex formation steady-state is not reached. The data measured are so-called sensorgram, one for each analyte concentration, with total complex concentration vs time. Here we present a new four-step strategy for more reliable processing of this complex kinetic binding data and compare it with the standard global fitting procedure. In our strategy, we first calculate a dissociation graph to reveal if there are any heterogeneous interactions. Thereafter, a new numerical algorithm, AIDA, is used to get the number of different complex formation reactions for each analyte concentration level. This information is then used to estimate the corresponding complex formation rate constants by fitting to the measured sensorgram one by one. Finally, all estimated rate constants are plotted and clustered, where each cluster represents a complex formation. Synthetic and experimental data obtained from three different QCM biosensor experimental systems having fast (close to steady-state), moderate, and slow kinetics (far from steady-state) were evaluated using the four-step strategy and standard global fitting. The new strategy allowed us to more reliably estimate the number of different complex formations, especially for cases of complex and slow dissociation kinetics. Moreover, the new strategy proved to be more robust as it enables one to handle system drift, i.e., data from biosensor chips that deteriorate over time.

  • 4.
    Goetelen, Thijs
    Karlstad University, Faculty of Health, Science and Technology (starting 2013). University College Leuven Limburg.
    Ideonella dechloratans: Investigation of the chlorite dismutase promoter2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Chlorate and perchlorate pollutions have become a problem in the environment in the last decades. Studies have shown that some bacteria can degrade these substances into unharmful substances such as chloride and molecular oxygen. One of these chlorate degrading bacteria is Ideonella dechloratans that uses chlorate reductase and chlorite dismutase to process chlorate. In the promoter gene sequence of chlorite dismutase there might be regulator sequences such as fumarate and nitrate reductase regulator (FNR) and aerobic respiration control protein (ArcA) that might control the transcription of this enzyme. This promoter sequence was placed in a pBBR1MCS-4-LacZ reporter vector and the possible regulatory sequences were changed through site-directed mutagenesis and tested on activity through beta-galactosidase assays. The changes in the FNR binding sequence gave beta-galactosidase activity that was close to a negative control which might give conclusions that either FNR has an important role or an important part of the promoter was hit. The changes in the ArcA regulator binding sequence did not give such big differences and no certainty can be given if this made important changes to the promoter.

  • 5.
    Hellberg Lindqvist, Miriam
    et al.
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    Nilsson, Thomas
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    Rova, Maria
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    Expression of chlorate reductase and chlorite dismutase in the chlorate-respiring bacterium Ideonella dechloratans2012Conference paper (Other academic)
  • 6.
    Hellberg Lindqvist, Miriam
    et al.
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    Nilsson, Thomas
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    Rova, Maria
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    Expression of the gene cluster for chlorate metabolism in the chlorate-respiring bacterium Ideonella dechloratans2012In: Biochimica et Biophysica Acta Bioenergetics, Volume 1817, Supplement, October 2012: EBEC Abstract Book / [ed] Friedrich T., Einsle O., Gräber P., Frankfurt, 2012, p. S157-S158Conference paper (Other academic)
    Abstract [en]

    Ideonella dechloratans is a facultative anaerobe able to use chlorate as a terminal electron acceptor under anaerobic conditions. Two enzymes are necessary for the decomposition of chlorate to chloride and molecular oxygen; chlorate reductase (Clr) and chlorite dismutase (Cld).  The genes for these two enzymes are close to each other in the genome and form, together with a cytochrome c and a mob B gene, a gene cluster for chlorate metabolism. The localization of the cyt c gene suggests a function in electron transport during chlorate reduction but the corresponding protein has not been found. We have addressed the questions of how the expression of Cld and Clr is regulated during the aerob/anaerob switch and if the cyt c gene is expressed in I. dechloratans. The enzyme activities of Cld and Clr were measured in extracts from cells grown at different conditions; aerobically or anaerobically [1]. Both enzymes were found to be active in all samples and the activity increased upon transfer of the cells from aerobic to anaerobic conditions, by five times for Cld and more than 200 times for Clr. Relative mRNA levels of Cld and Clr were determined by qRT-PCR in RNA preparations from cells grown under the same conditions as for the enzyme activity measurements. mRNA from both genes was detected in all preparations but with ten times higher levels in samples from anaerobic conditions. This increase in mRNA level is on the same scale as the increase in enzyme activity for Cld but accounts for less than a tenth of the activity enhancement seen for Clr.  A possible effect of chlorate was tested by the addition of chlorate under aerobic conditions but this resulted in neither increased enzyme activities nor increased mRNA levels. qRT-PCR was performed with primers specific for the cyt c gene and this gene was also found to be expressed at both aerobic and anaerobic conditions. In summary, the results show that chlorate respiration is activated by anaero­biosis but not by chlorate in I. dechloratans and that this activation occurs at the tran­scriptional level. Due to the much larger increase in enzyme activity compared to the increase in mRNA level, the activity of Clr also seems to be effected by other mechanisms. Detection of cyt c mRNA suggests that its gene product can be found and the function investigated.

    [1] Hellberg Lindqvist M, Johansson N, Nilsson T, Rova M (2012) Appl. Environ. Microbiol. 78: 4380-4385

  • 7.
    Hellberg, Miriam
    et al.
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    Nilsson, Thomas
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    Rova, Maria
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    Johansson, Nicklas
    Regulation of the genes for chlorate reductase (Clr) and chlorite dismutase (Cld) in the chlorate-respiring bacterium Ideonella dechloratans2010In: FEBS Journal 277(2010) Supplement 1. Poster presentations, Wiley-Blackwell , 2010, p. B4.62.-Conference paper (Other academic)
    Abstract [en]

    Enzyme activities and mRNA levels of chlorate reductase and chlorite dismutase was investigated in whole cell extracts of Ideonella dechloratans grown under different growth conditions. This bacterium grows well both at aerobic and anaerobic conditions, using oxygen and chlorate, respectively, as a terminal electron acceptor. It was found that preparations from cells grown in the absence of chlorate under aerobic conditions showed activity of both chlorate reductase, measured as chlorate dependent reduction of methyl viologen, and chlorite dismutase, measured as chlorite dependent oxygen production. At aerobic growth conditions, the addition of chlorate resulted in an increased activity of chlorate reductase. The highest activity of chlorate reductase was found in preparations from cells grown anaerobically in the presence of chlorate. No increase in enzyme activity could be detected for chlorite dismutase during anaerobic or aerobic growth in the presence of chlorate, compared to aerobic growth in the absence of chlorate. The mRNA levels for Clr and Cld, measured by real-time quantitative PCR using 16SrRNA as an intern standard, was found to be equal in preparations from cells grown anaerobically in the presence of chlorate compared to cells grown under aerobic conditions in the absence of chlorate. The results suggest that, in I. dechloratans, the activity of chlorate reductase is up-regulated by at least two factors, anaerobiosis and the presence of chlorate. Interestingly, the results also indicate that the studied regulation occurs at post-transcriptional level, while most examples of oxygen regulation in bacteria are reported to occur at transcriptional level.  

  • 8. Magnusson, Ann
    et al.
    Rova, Maria
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    Mamedov, Fikret
    Fredriksson, Per-Olof
    Styring, Stenbjörn
    The role of cytochrome b559 and tyrosineD in protection against photoinhibition during in vivo photoactivation of Photosystem II1999In: Biochimica et Biophysica Acta, Vol. 1411, p. 180-191Article in journal (Refereed)
  • 9.
    Mikladal, Bartal
    Karlstad University, Faculty of Health, Science and Technology (starting 2013).
    Kloning och expression av arsR från Ideonella dechloratans2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Chlorate as a waste product from the paper industry has caused environmental problems due its toxic effect on plants and algae and is also a concern for human health where chlorate has contaminated the tap water supplies. To address this issue, a great deal of research has been carried out on naturally occurring bacteria that can anaerobically reduce chlorate to oxygen and chloride ions. With additional knowledge of how this chlorate-reducing process is regulated, these bacteria may one day provide an effective purification process of wastewater from paper mills. Ideonella dechloratans is such a bacterium that has a gene cluster which encodes the chlorate-reducing enzymes. Downstream of this cluster is an arsR-sequence believed to encode a transcription factor, which could aid in the understanding of the gene expression for the chlorate-reducing operon. The goal of this research is to transform expression cells with the ability to express the arsR-sequence so that future trials can be made to identify any potential binding sites for the ArsR-protein. The arsR-sequence was amplified with primers specific to the ends of the arsR-sequence. The sequence was then ligated into a pET-21a(+) vector from Novagen and transformed with BL21 (DE3) expression cells. By IPTG inducing these transformants it was possible to observe a significant expression of insoluble ArsR. Complications with the outcome and future approaches are discussed.

  • 10.
    Nilsson, Thomas
    et al.
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    Rova, Maria
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    Smedja Bäcklund, Anna
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    Microbial metabolism of oxochlorates: A bioenergetic perspective2013In: Biochimica et Biophysica Acta - Bioenergetics, ISSN 0005-2728, E-ISSN 1879-2650, ISSN 0005-2728, Vol. 1827, no 2, p. 189-197Article, review/survey (Refereed)
    Abstract [en]

    The microbial metabolism of oxochlorates is part of the biogeochemical cycle of chlorine. Organisms capable of growth using perchlorate or chlorate as respiratory electron acceptors are also interesting for applications in biotreatment of oxochlorate-containing effluents or bioremediation of contaminated areas. In this review, we discuss the reactions of oxochlorate respiration, the corresponding enzymes, and the relation to respiratory electron transport that can contribute to a proton gradient across the cell membrane. Enzymes specific for oxochlorate respiration are oxochlorate reductases and chlorite dismutase. The former belong to DMSO reductase family of molybdenum-containing enzymes. The heme protein chlorite dismutase, which decomposes chlorite into chloride and molecular oxygen, is only distantly related to other proteins with known functions. Pathways for electron transport may be different in perchlorate and chlorate reducers, but appear in both cases to be similar to pathways found in other respiratory systems.

  • 11.
    Palm, Eva-Lotta
    Karlstad University, Faculty of Technology and Science.
    c-cytokromer hos den (per)kloratreducerande bakterien GR-1: samt en jämförande studie av c-cytokromer från GR-1, Ideonella dechloratans och Dechloromonas aromatica2007Independent thesis Basic level (professional degree), 20 points / 30 hpStudent thesis
    Abstract [en]

    This work describes an analysis of membrane-anchored and periplasmic c-type cytochromes of perchlorate grown GR-1, and a comparison with the c-type cytochrome content of Ideonella dechloratans, other known c-type cytochromes and the genome of Dechloromonas aromatica. The aim of the comparison was to investigate a hypothesis that the bacteria use different routes for electron transfer to the periplasmic enzyme (per)chlorate reductase. Cell membrane from GR-1 was prepared through ultracentrifugation and periplasm was prepared through osmotic chock. The fractions were separated by SDS-PAGE and peptides containing covalently bound heme (c-type cytochromes) were detected by a specific staining reaction. In an attempt to probe a gene coding for a NapC/NirT-like protein Touchdown PCR was performed on isolated DNA from GR-1, using degenerate primers. Finally, reduced membranes were treated with carbon monoxide to investigate the presence of cbb3-type oxidase.

    Separation and detection resulted in seven periplasmic peptides and eight membrane anchored peptides, all with molecular weights in a range of 8-60 kDa. Nothing has been revealed during this work that opposes the hypothesis of GR-1 and D. aromatica using a NapC/NirT-like protein as an electron carrier to their periplasmic (per)chlorate reductase. The PCR resulted in a product that most likely is a sequence from a gene coding for a NapC/NirT-like protein and two, maybe three, candidates for a NapC/NirT-like protein were also found in the membrane of GR-1. Analysis also revealed that GR-1 most likely makes use of a cbb3-type oxidase for reduction of oxygen during microaerofilic conditions.

    Concerning I. dechloratans, nothing has been revealed during this work that opposes the hypothesis of this bacterium using a soluble cytochrome c as an electron carrier to its chlorate reductase. Three candidates for a soluble cytochrome c protein were found. The theory is also supported by the negative result from earlier attempts to probe a gene coding for a NapC/NirT-like protein in this bacterium.

  • 12.
    Roepstorff, P.
    et al.
    Department of Molecular Biology, Odense University, Denmark.
    Højrup, P.
    Department of Molecular Biology, Odense University, Denmark.
    Sundqvist, B.U.R.
    Tandem Accelerator Laboratory, Uppsala University.
    Jonsson, Gunnar
    Tandem Accelerator Laboratory, Uppsala University.
    Håkansson, P.
    Tandem Accelerator Laboratory, Uppsala University.
    Andersson, S. O.
    Institute for Biological Chemistry A, University of Copenhagen, Denmark.
    Johansson, K. E.
    Mycoplasma Laboratory, The National Veterinary Institute, Uppsala.
    Application of Plasma Desorption Mass Spectrometry to Molecular Weight Determination of Structural Protein from Insect Cuticle1986In: Journal of Mass Spectrometry, ISSN 1076-5174, E-ISSN 1096-9888, Vol. 13, no 12, p. 689-691Article in journal (Refereed)
    Abstract [en]

    During sequence determination of a structural protein from the cuticle of the migratory locust, Locusta migratoria, a discrepancy was found between the molecular weight calculated from the sequence data (15 323) and that estimated by SDS-gel electrophoresis (21 600). The protein contains several repeated sequences, and the discrepancy might indicate that part of the sequence was missing or that the protein contained a large prosthetic group. The molecular weight of the protein was determined by 127I-plasma desorption mass spectrometry to be 15 329±50 which confirms the sequence data and shows the molecular weight determination based on SDS-electrophoresis to be too high.

  • 13.
    Rova, Maria
    et al.
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    Franzén, Lars-Gunnar
    Fredriksson, Per-Olof
    Styring, Stenbjörn
    Photosystem II in a mutant of Chlamydomonas reinhardtii lacking the 23kDa psbP protein shows increased sensitivity to photoinhibition in the absence of chloride1994In: Photosynthesis Research, ISSN 0166-8595, E-ISSN 1573-5079, Vol. 39, p. 75-83Article in journal (Refereed)
  • 14.
    Rova, Maria
    et al.
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    Mamedov, Fikret
    Magnusson, Ann
    Fredriksson, Per-Olof
    Styring, Stenbjörn
    Coupled Activation of the Donor and the Acceptor Side of Photosystem II during Photoactivation of the Oxygen Evolving Cluster1998In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 37, p. 11039-11045Article in journal (Refereed)
  • 15.
    Rova, Maria
    et al.
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    Mc Ewen, Birgitta
    Karlstad University, Division for Environmental Sciences.
    Fredriksson, Per-Olof
    Styring, Stenbjörn
    Photoactivation and Photoinhibition Are Competing in a Mutant of Chlamydomonas reinhardtii Lacking the 23-kDa Extrinsic Subunit of Photosystem II1996In: The Journal of Biological Chemistry, Vol. 271, no 46, p. 28918-28924Article in journal (Refereed)
  • 16.
    Rundgren, Carl-Johan
    et al.
    Stockholm Univ, Dept Math & Sci Educ MND, S-10691 Stockholm, Sweden..
    Hirsch, Richard
    Linkoping Univ, Dept Culture & Commun, S-58183 Linkoping, Sweden..
    Rundgren, Shu-Nu Chang
    Karlstad University, Faculty of Health, Science and Technology (starting 2013), Department of Engineering and Chemical Sciences. Karlstad Univ, Ctr Sci Math & Engn Educ Res SMEER, S-65188 Karlstad, Sweden.;Karlstad Univ, Dept Chem & Biomed Sci, S-65188 Karlstad, Sweden..
    Tibell, Lena A. E.
    Linkoping Univ, ITN, Dept Sci & Technol, S-60174 Norrkoping, Sweden..
    Students' Communicative Resources in Relation to Their Conceptual Understanding: The Role of Non-Conventionalized Expressions in Making Sense of Visualizations of Protein Function2012In: Research in science education, ISSN 0157-244X, E-ISSN 1573-1898, Vol. 42, no 5, p. 891-913Article in journal (Refereed)
    Abstract [en]

    This study examines how students explain their conceptual understanding of protein function using visualizations. Thirteen upper secondary students, four tertiary students (studying chemical biology), and two experts were interviewed in semi-structured interviews. The interviews were structured around 2D illustrations of proteins and an animated representation of water transport through a channel in the cell membrane. In the analysis of the transcripts, a score, based on the SOLO-taxonomy, was given to each student to indicate the conceptual depth achieved in their explanations. The use of scientific terms and non-conventionalized expressions in the students' explanations were investigated based upon a semiotic approach. The results indicated that there was a positive relationship between use of scientific terms and level of education. However, there was no correlation between students' use of scientific terms and conceptual depth. In the interviews, we found that non-conventionalized expressions were used by several participants to express conceptual understanding and played a role in making sense of the visualizations of protein function. Interestingly, also the experts made use of non-conventionalized expressions. The results of our study imply that more attention should be drawn to students' use of scientific and non-conventionalized terms in relation to their conceptual understanding.

  • 17.
    Samuelsson, Jörgen
    et al.
    Karlstad University, Faculty of Health, Science and Technology (starting 2013), Department of Engineering and Chemical Sciences (from 2013).
    Leśko, Marek
    Enmark, Martin
    Karlstad University, Faculty of Health, Science and Technology (starting 2013), Department of Engineering and Chemical Sciences (from 2013).
    Högblom, Joakim
    Karlsson, Anders
    Kaczmarski, Krzysztof
    Optimizing Column Length and Particle Size in Preparative Batch Chromatography Using Enantiomeric Separations of Omeprazole and Etiracetam as Models: Feasibility of Taguchi Empirical Optimization2018In: Chromatographia, Vol. 81, no 6, p. 851-860Article in journal (Refereed)
    Abstract [en]

    The overreaching purpose of this study is to evaluate new approaches for determining the optimal operational and column conditions in chromatography laboratories, i.e., how best to select a packing material of proper particle size and how to determine the proper length of the column bed after selecting particle size. As model compounds, we chose two chiral drugs for preparative separation: omeprazole and etiracetam. In each case, two maximum allowed pressure drops were assumed: 80 and 200 bar. The processes were numerically optimized (mechanistic modeling) with a general rate model using a global optimization method. The numerical predictions were experimentally verified at both analytical and pilot scales. The lower allowed pressure drop represents the use of standard equipment, while the higher allowed drop represents more modern equipment. For both compounds, maximum productivity was achieved using short columns packed with small-particle size packing materials. Increasing the allowed backpressure in the separation leads to an increased productivity and reduced solvent consumption. As advanced numerical calculations might not be available in the laboratory, we also investigated a statistically based approach, i.e., the Taguchi method (empirical modeling), for finding the optimal decision variables and compared it with advanced mechanistic modeling. The Taguchi method predicted that shorter columns packed with smaller particles would be preferred over longer columns packed with larger particles. We conclude that the simpler optimization tool, i.e., the Taguchi method, can be used to obtain “good enough” preparative separations, though for accurate processes, optimization, and to determine optimal operational conditions, classical numerical optimization is still necessary

  • 18.
    Smedja Bäcklund, Anna
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    c Cytochromes as Electron Carriers in Microbial Chlorate Respiration2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Microbial respiration of oxochlorates is important for the biotreatment of effluents from industries where oxochlorates are produced or handled. Several bacterial species are capable to use perchlorate and/or chlorate as an alternative electron acceptor in absence of oxygen. The present study deals with the electron transport from the membrane-bound components to the periplasmic chlorate reductase, in the gram-negative bacterium Ideonella dechloratans. Both chlorate reductase and the terminal oxidase of I. dechloratans were found to utilize soluble c cytochromes as electron donors. For further investigation, two major heme-containing components were purified and characterized. The most abundant was a 9 kDa c-type cytochrome (class I), denoted cytochrome c-Id1. This protein was shown to serve as electron donor for both chlorate reductase, and for a terminal oxidase. The other major component was a 55 kDa homotetrameric cytochrome c', (class II). A function for this cytochrome could not be demonstrated but it does not appear to serve as electron donor to chlorate reductase. A gene predicted to encode a soluble c cytochrome was found in close proximity to the gene cluster for chlorate reduction. The predicted sequence did not match any of the cytochromes discussed above. The gene was cloned and expressed heterologously, and the resulting protein was investigated as a candidate electron donor for chlorate reductase. Electron transfer from this protein could not be demonstrated, suggesting that the gene product does not serve as immediate electron donor for chlorate reductase.

  • 19.
    Smedja Bäcklund, Anna
    et al.
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    Bohlin, Jan
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    Gustavsson, Niklas
    Department of Biochemistry, Lund University.
    Nilsson, Thomas
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    Periplasmic c Cytochromes and Chlorate Reduction in Ideonella dechloratans2009In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 75, p. 2439-2445Article in journal (Refereed)
  • 20. Vera, C. M.
    et al.
    Samuelsson, Jörgen
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences. Karlstad University, Faculty of Health, Science and Technology (starting 2013), Department of Engineering and Chemical Sciences (from 2013).
    Fornstedt, Torgny
    Karlstad University, Faculty of Health, Science and Technology (starting 2013), Department of Engineering and Chemical Sciences (from 2013). Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    Dennis, G. R.
    Shalliker, R. A.
    Protocol for the visualisation of axial temperature gradients in ultra high performance liquid chromatography using infrared cameras2018In: Microchemical journal (Print), ISSN 0026-265X, E-ISSN 1095-9149, Vol. 141, p. 141-147Article in journal (Refereed)
    Abstract [en]

    A protocol was developed for the visualisation of axial temperature gradients on a Kinetex column (1.3 μm C18 100 Å 50 × 2.1 mm) operated at near maximum pressure of the system (Pmax) using an infrared camera. Real time viscous frictional heating effects across the entire column length was observed, and showed that with increasing flow rate there was an increase in the maximum temperature of the column, and the difference between the inlet and outlet temperatures. Temperature profile data over the entire length of the column revealed the dynamics of heat exchange processes along different parts of the column, and raises the question on potential heating effects on eluents. The axial temperature gradients of eluents such as pure methanol, isopropyl alcohol and acetonitrile near Pmax were compared; finding that acetonitrile which had the highest flow velocity at Pmax gave the highest overall temperature increase for these eluents.

  • 21.
    Wahlberg, Sara
    et al.
    Karlstad University, Faculty of Health, Science and Technology (starting 2013), Department of Engineering and Chemical Sciences (from 2013).
    Gericke, Niklas
    Karlstad University, Faculty of Health, Science and Technology (starting 2013), Department of Environmental and Life Sciences (from 2013).
    Conceptual Demography in Upper Secondary Chemistry and Biology Textbooks' Descriptions of Protein Synthesis: A Matter of Context?2018In: CBE - Life Sciences Education, ISSN 1931-7913, E-ISSN 1931-7913, Vol. 17, no 3Article in journal (Refereed)
    Abstract [en]

    This study investigates how the domain-specific language of molecular life science is mediated by the comparative contexts of chemistry and biology education. We study upper secondary chemistry and biology textbook sections on protein synthesis to reveal the conceptual demography of concepts central to the communication of this subject. The term "conceptual demography" refers to the frequency, distribution, and internal relationships between technical terms mediating a potential conceptual meaning of a phenomenon. Data were collected through a content analysis approach inspired by text summarization and text mining techniques. Chemistry textbooks were found to present protein synthesis using a mechanistic approach, whereas biology textbooks use a conceptual approach. The chemistry texts make no clear distinction between core terms and peripheral terms but use them equally frequently and give equal attention to all relationships, whereas biology textbooks focus on core terms and mention and relate them to each other more frequently than peripheral terms. Moreover, chemistry textbooks typically segment the text, focusing on a couple of technical terms at a time, whereas biology textbooks focus on overarching structures of the protein synthesis. We argue that it might be fruitful for students to learn protein synthesis from both contexts to build a meaningful understanding.

  • 22.
    Ölund, David
    Karlstad University, Faculty of Technology and Science, Department of Chemistry and Biomedical Sciences.
    Konstruktion av reporterplasmider innehållande möjliga promotorregioner för kloratreduktas respektive kloritdismutas från Ideonella dechloratans2012Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Ideonella dechloratans is one of several isolated strains of bacteria with the ability to use chlorate in its metabolism in an anaerobic environment. This can be utilized by, for example, the paper industry where chlorate is an environmentally dangerous pollutant after chlorine dioxine bleaching. 

       Chlorate and perchlorate have been found to have negative effects in humans, animals and plants which give rise to a need for more research on improved purification methods. If the gene regulation of the enzymes that handle the breakdown of chlorate, chlorate reductase and chlorite dismutase, could be improved to work in an aerobic environment then both the purification and cost efficiency could improve.

       By inserting the promoter regions for chlorate reductase and chlorite dismutase in a broad-host-range reporterplasmid, pQlacZ-1, they can be evaluated in several different conditions and different strains of gram-negative bacteria.

       Through double cleaving of pQlacZ-1 with BamHI and EcoRI, PCR products of Clrp and Cldp from Ideonella dechloratans have been ligated into E. coli, XL-1 Blue.

       Gel extraction was found to be the most efficient method of purification before ligation but further screening needs to be performed on the transformants to ensure the efficiency of the method.

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