| 1. |
- Gullfot, Fredrika, 1967-
(författare)
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Synthesis of xyloglucan oligo- and polysaccharides with glycosynthase technology
- 2009
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Xyloglucans are polysaccharides found as storage polymers in seeds and tubers, and as cross-linking glycans in the cell wall of plants. Their structure is complex with intricate branching patterns, which contribute to the physical properties of the polysaccharide including its binding to and interaction with other glycans such as cellulose. Xyloglucan is widely used in bulk quantities in the food, textile and paper making industries. With an increasing interest in technically more advanced applications of xyloglucan, such as novel biocomposites, there is a need to understand and control the properties and interactions of xyloglucan with other compounds, to decipher the relationship between xyloglucan structure and function, and in particular the effect of different branching patterns. However, due to the structural heterogeneity of the polysaccharide as obtained from natural sources, relevant studies have not been possible to perform in practise. This fact has stimulated an interest in synthetic methods to obtain xyloglucan mimics and analogs with well-defined structure and decoration patterns. Glycosynthases are hydrolytically inactive mutant glycosidases that catalyse the formation of glycosidic linkages between glycosyl fluoride donors and glycoside acceptors. Since its first conception in 1998, the technology is emerging as a useful tool in the synthesis of large, complex polysaccharides. This thesis presents the generation and characterisation of glycosynthases based on xyloglucanase scaffolds for the synthesis of well-defined homogenous xyloglucan oligo- and polysaccharides with regular substitution patterns.
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| 2. |
- Sunner, Hampus, 1981, et al.
(författare)
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Fungal Ferulic Acid Esterases – Specificity and Phylogeny
- 2009
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Ingår i: Italic5 Science and Technology of Biomasses Proceedings Book, M Orlandi, C Crestine (Ed.). Italic5/COST conference, Sept 1-4 2009, Varenna, Italy.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Ferulic Acid Esterases (FAE) is a large heterogeneous group of enzymes with activity on esters of hydroxy- and metoxy- substituted cinnamic acid derivatives, such as ferulic acid. These ester bonds occur in the cell walls of plants and are especially common in grasses. As little systematic knowledge has been collected about this group of enzymes and only a few enzymes have been biochemically characterised to date, we have explored the phylogeny of FAEs using bioinformatic tools. We can conclude that the known Ferulic Acid Esterases belong to several evolutionary distant groups, two of which have dozens of highly related sequences, and a few groups with no members other than the known enzyme. The phylogeny also suggests certain similarities of substrate specificity within groups and proposes enzymes, whose biochemical characterisation would be especially informative for our understanding of the FAE families.
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| 3. |
- Abedinifar, S., et al.
(författare)
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Ethanol production by Mucor indicus and Rhizopus oryzae from rice straw by separate hydrolysis and fermentation
- 2009
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Ingår i: Biomass and Bioenergy. - : Elsevier BV. - 0961-9534 .- 1873-2909. ; 33:5, s. 828-833
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Tidskriftsartikel (refereegranskat)abstract
- Rice straw was successfully converted to ethanol by separate enzymatic hydrolysis and fermentation by Mucor indicus, Rhizopus oryzae, and Saccharomyces cerevisiae. The hydrolysis temperature and pH of commercial cellulase and β-glucosidase enzymes were first investigated and their best performance obtained at 45 °C and pH 5.0. The pretreatment of the straw with dilute-acid hydrolysis resulted in 0.72 g g-1 sugar yield during 48 h enzymatic hydrolysis, which was higher than steam-pretreated (0.60 g g-1) and untreated straw (0.46 g g-1). Furthermore, increasing the concentration of the dilute-acid pretreated straw from 20 to 50 and 100 g L-1 resulted in 13% and 16% lower sugar yield, respectively. Anaerobic cultivation of the hydrolyzates with M. indicus resulted in 0.36-0.43 g g-1 ethanol, 0.11-0.17 g g-1 biomass, and 0.04-0.06 g g-1 glycerol, which is comparable with the corresponding yields by S. cerevisiae (0.37-0.45 g g-1 ethanol, 0.04-0.10 g g-1 biomass and 0.05-0.07 glycerol). These two fungi produced no other major metabolite from the straw and completed the cultivation in less than 25 h. However, R. oryzae produced lactic acid as the major by-product with yield of 0.05-0.09 g g-1. This fungus had ethanol, biomass and glycerol yields of 0.33-0.41, 0.06-0.12, and 0.03-0.04 g g-1, respectively.
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| 4. |
- Enoksson, Peter, 1957, et al.
(författare)
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Micro- and Nanosystems for Sensing in Medicine
- 2008
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Ingår i: Proceedings of Medicinteknikdagarna 2008, 14-15 October, Göteborg, Sweden. ; , s. 117-
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 5. |
- Hjortmo, Sofia, 1978
(författare)
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On Folates in Yeasts -Exploring Yeasts as Vehicles for Biofortification of Folates in Food
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- High intake of the B vitamin folate during pregnancy is known to decrease the risk for development of neural tube defects. In addition, a good folate status may prevent the progression of several diseases such as megaloblastic anaemia, cardiovascular disease, cancer and Alzheimer’s disease. However, reaching sufficient amounts via the diet only is complicated and new strategies must be developed to increase the mean folate intake. The aim of this thesis is to explore the use of yeasts for biofortification of folates in food. Yeasts synthesise folates de novo and may constitute potent vehicles for natural folates. Current work includes investigations of folate content and composition in yeasts as well as studies of the impact of growth rate and chemical environments on folate levels in Saccharomyces cerevisiae (Baker’s yeast). The applicability of the results was then investigated in two food model systems (bread and a cereal-based fermented porridge called togwa) to demonstrate the practical relevance. In a screening of 52 yeast strains, the folate content ranged from 40 to 145 µg per gram dry matter of yeast, showing that inherent variations in yeast folate levels exist. Several S. cerevisiae strains showed at least a two-fold higher folate content than a commercial Baker’s strain, indicating possibilities to increase folates in fermented foods simply by choosing the proper strain. With regard to cultivation conditions, folates in S. cerevisiae were demonstrated to increase linearly with growth rate in a defined medium, showing that high growth rate, i.e. respiro-fermentative metabolism, is most favourable for high folate content. Cultivation in a rich medium yielded cells containing lower amounts of folate compared to cells grown in a poor chemical environment even though the specific growth rate was higher in the rich medium. The results obtained show that the growth rate per se could not predict intracellular folate concentrations and that the chemical environment has a substantial impact on intracellular folates. By applying strain selection and cultivation at optimal conditions prior to baking we were able to increase folates five-fold in white wheat bread compared to bread leavened with commercial Baker’s yeast. In addition, folates increased at most 23-fold during yeast fermentations in a cereal-based porridge (togwa) compared to togwa raw material. Final folate levels were shown to be highly dependent on strain and cultivation time. The results demonstrate that yeasts constitute flexible and controllable vehicles for biofortification of folates in fermented food.
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| 6. |
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| 7. |
- Lennartsson, Patrik R, 1983, et al.
(författare)
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Effects of different growth forms of Mucor indicus on cultivation on dilute-acid lignocellulosic hydrolyzate, inhibitor tolerance, and cell wall composition
- 2009
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Ingår i: Journal of Biotechnology. - : Elsevier BV. - 0168-1656 .- 1873-4863. ; 143:4, s. 255-261
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Tidskriftsartikel (refereegranskat)abstract
- The dimorphic fungus Mucor indicus was grown in different forms classified as purely filamentous, mostly filamentous, mostly yeast-like and purely yeast-like, and the relationship between morphology and metabolite production, inhibitor tolerance and the cell wall composition was investigated. Low concentrations of spores in the inoculum with subsequent aeration promoted filamentous growth, whereas higher spore concentrations and anaerobic conditions promoted yeast-like growth. Ethanol was the main metabolite with glycerol next under all conditions tested. The yields of ethanol from glucose were between 0.39 and 0.42 g g(-1) with productivities of 3.2-5.0 g l(-1) h(-1). The ethanol productivity of mostly filamentous cells was increased from 3.9 to 5.0 g l(-1) h(-1) by the presence of oxygen, whereas aeration of purely yeast-like cells showed no such effect. All growth forms were able to tolerate 4.6 g l(-1) furfural and 10 g l(-1) acetic acid and assimilate the sugars, although with different consumption rates. The cell wall content of the fungus measured as alkali insoluble materials (AIM) of the purely yeast-like cells was 26% of the biomass, compared to 8% of the pure filaments. However, the chitosan concentration of the filaments was 29% of the AIM, compared to 6% of the yeast-like cells.
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| 8. |
- Millati, Ria, 1972, et al.
(författare)
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Ethanol production from xylose and wood hydrolyzate by Mucor indicus at different aeration rates
- 2008
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Ingår i: BioResources. - : North Carolina State University. - 1930-2126. ; 3:4, s. 1020-1029
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Tidskriftsartikel (refereegranskat)abstract
- The fungus Mucor indicus is able to produce ethanol from xylose as well as dilute-acid lignocellulosic hydrolyzates. The fungus completely assimilated 10 g/L xylose as the sole carbon and energy source within 32 to 65 h at an aeration rate of 0.1 to 1.0 vvm. The highest ethanol yield was 0.16 g/g at 0.1 vvm. Xylitol was formed intermediately with a maximum yield of 0.22 g/g at 0.5 vvm., but disappeared towards the end of experiments. During cultivation in a mixture of xylose and glucose, the fungus did not assimilate xylose as long as glucose was present in the medium. The anaerobic cultivation of the fungus in the hydrolyzate containing 20% xylose and 80% hexoses resulted in no assimilation of xylose but complete consumption of the hexoses in less than 15 h. The ethanol yield was 0.44 g/g. However, the xylose in the hydrolyzate was consumed when the media were aerated at 0.067 to 0.333 vvm. The best ethanol yield was 0.44 g/g at 0.067 vvm. The results of this study suggest that M. indicus hydrolyzate can be first fermented anaerobically for hexose assimilation and subsequently continued under oxygen-limited conditions for xylose fermentation.
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| 9. |
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| 10. |
- Taherzadeh, M.J., et al.
(författare)
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Enzymatic-based hydrolysis processes for ethanol from lignocellulosic materials : A review.
- 2007
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Ingår i: BioResources. - : North Carolina State University. - 1930-2126. ; 2:4, s. 707-738
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Tidskriftsartikel (refereegranskat)abstract
- This article reviews developments in the technology for ethanol production from lignocellulosic materials by “enzymatic” processes. Several methods of pretreatment of lignocelluloses are discussed, where the crystalline structure of lignocelluloses is opened up, making them more accessible to the cellulase enzymes. The characteristics of these enzymes and important factors in enzymatic hydrolysis of the cellulose and hemicellulose to cellobiose, glucose, and other sugars are discussed. Different strategies are then described for enzymatic hydrolysis and fermentation, including separate enzymatic hydrolysis and fermentation (SHF), simultaneous saccharification and fermentation (SSF), non-isothermal simultaneous saccharification and fermentation (NSSF), simultaneous saccharification and co-fermentation (SSCF), and consolidated bioprocessing (CBP). Furthermore, the by-products in ethanol from lignocellulosic materials, wastewater treatment, commercial status, and energy production and integration are reviewed.
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| 11. |
- van den Berg, Susanne, et al.
(författare)
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Improved solubility of TEV protease by directed evolution.
- 2006
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Ingår i: Journal of biotechnology. - Amsterdam : Elsevier BV. - 0168-1656 .- 1873-4863. ; 121:3, s. 291-8
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Tidskriftsartikel (refereegranskat)abstract
- The efficiency and high specificity of tobacco etch virus (TEV) protease has made it widely used for cleavage of recombinant fusion proteins. However, the production of TEV protease in E. coli is hampered by low solubility. We have subjected the gene encoding TEV protease to directed evolution to improve the yield of soluble protein. Libraries of mutated genes obtained by error-prone PCR and gene shuffling were introduced into the Gateway cloning system for facilitated transfer between vectors for screening, purification, or other applications. Fluorescence based in vivo solubility screening was carried out by cloning the libraries into a plasmid encoding a C-terminal GFP fusion. Mutant genes giving rise to high GFP fluorescence intensity indicating high levels of soluble TEV-GFP were subsequently transferred to a vector providing a C-terminal histidine tag for expression, purification, and activity tests of mutated TEV. We identified a mutant, TEV(SH), in which three amino acid substitutions result in a five-fold increase in the yield of purified protease with retained activity.
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| 12. |
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| 13. |
- Alminger, Marie, 1957, et al.
(författare)
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Whole-grain cereal products based on a high-fibre barley or oat genotype lower post-prandial glucose and insulin responses in healthy humans
- 2008
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Ingår i: European Journal of Nutrition. - : Springer Science and Business Media LLC. - 1436-6207 .- 1436-6215. ; 47:6, s. 294-300
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Tidskriftsartikel (refereegranskat)abstract
- Background: Several factors can affect glycemic and insulinemic responses from cereal foods. Some suggested factors lowering the responses are; intact botanical structure, high amylose/high β-glucan cereal varieties, organic acid produced during fermentation and food processes inducing retrogradation of starch. Aim of the study: To evaluate the impact of fermented whole grain cereal kernels with high content of amylose (40%) and/or β-glucan (4.6%) on postprandial glucose and insulin responses in healthy adults. Methods: Thirteen healthy volunteers (4 men and 9 women) were given 25 g available carbohydrate portions of: glucose solution; tempe fermented whole-grain barley and tempe fermented whole-grain oat. Blood samples were collected directly before the meal (fasting) and 15, 30, 45, 60, 90 and 120 min after the start of the meal. The GI (glycemic index) and II (insulin index) of meals were calculated for each subject according to FAO/WHO standards. Results: Peak glucose response was lowest after the tempe meal with high-amylose/ high-β-glucan barley tempe while insulin response was lowest after the meal with high β-glucan oat tempe. The mean blood glucose responses for both the barley and the oat tempe meals were significantly lower than from the reference glucose load (P < 0.0001) during the first 60 min. The calculated GI:s for barley and oat tempe were 30 and 63, respectively. Mean serum insulin responses from barley and oat tempe were significantly lower compared with the glucose load (P < 0.002) during the first 60 min, and the calculated II was lower for oat tempe (21) compared with barley tempe (55). Conclusions: The results suggest that cereal products with beneficial influence on postprandial plasma glucose and insulin responses can be tailored by fermentation and enclosure of high-amylose and/or high-β-glucan barley and oat kernels. © 2008 Spinger.
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| 14. |
- Almqvist, Jonas, 1975-
(författare)
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Structural modeling of membrane transporter proteins
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- A fundamental process of all living organisms - the transport of molecules across cellular membranes through membrane transport proteins - is investigated.After a brief review of general properties of biological membranes follows a recollection of the major methods of membrane transport that Nature utilizes (Chapter 1). This is followed by a description of important experimental (Chapter 2) and theoretical methods (Chapter 3) for structural studies of membrane proteins. The findings on membrane protein transport in papers I-IV are then summarized (Chapter 4) and important findings are discussed. The remaining text is a discussion on relevant theoretical and experimental methods.
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| 15. |
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| 16. |
- Andersen, Malin, 1977-
(författare)
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Computational and experimental approaches to regulatory genetic variation
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Genetic variation is a strong risk factor for many human diseases, including diabetes, cancer, cardiovascular disease, depression, autoimmunity and asthma. Most of the disease genes identified so far alter the amino acid sequences of encoded proteins. However, a significant number of genetic variants affecting complex diseases may alter the regulation of gene transcription. The map of the regulatory elements in the human genome is still to a large extent unknown, and it remains a challenge to separate the functional regulatory genetic variations from linked neutral variations. The objective of this thesis was to develop methods for the identification of genetic variation with a potential to affect the transcriptional regulation of human genes, and to analyze potential regulatory polymorphisms in the CD36 glycoprotein, a candidate gene for cardiovascular disease. An in silico tool for the prediction of regulatory polymorphisms in human genes was implemented and is available at www.cisreg.ca/RAVEN. The tool was evaluated using experimentally verified regulatory single nucleotide polymorphisms (SNPs) collected from the scientific literature, and tested in combination with experimental detection of allele specific expression of target genes (allelic imbalance). Regulatory SNPs were shown to be located in evolutionary conserved regions more often than background SNPs, but predicted transcription factor binding sites were unable to enrich for regulatory SNPs unless additional information linking transcription factors with the target genes were available. The in silico tool was applied to the CD36 glycoprotein, a candidate gene for cardiovascular disease. Potential regulatory SNPs in the alternative promoters of this gene were identified and evaluated in vitro and in vivo using a clinical study for coronary artery disease. We observed association to the plasma concentrations of inflammation markers (serum amyloid A protein and C-reactive protein) in myocardial infarction patients, which highlights the need for further analyses of potential regulatory polymorphisms in this gene. Taken together, this thesis describes an in silico approach to identify putative regulatory polymorphisms which can be useful for directing limited laboratory resources to the polymorphisms most likely to have a phenotypic effect.
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| 17. |
- Andersen, M.R., et al.
(författare)
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Current status of systems biology in Aspergilli
- 2009
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1096-0937 .- 1087-1845. ; 46:584-590, s. 180-190
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Tidskriftsartikel (refereegranskat)abstract
- Saccharomyces cerevisiae is a unicellular eukaryal microorganism that has traditionally been regarded either as a model system for investigating cellular physiology or as a cell factory for biotechnological use, for example for the production of fuels and commodity chemicals such as lactate or pharmaceuticals, including human insulin and HPV vaccines. Systems biology has recently gained momentum and has successfully been used for mapping complex regulatory networks and resolving the dynamics of signal transduction pathways. So far, yeast systems biology has mainly focused on the development of new methods and concepts. There are also some examples of the application of yeast systems biology for improving biotechnological processes. We discuss here how yeast systems biology could be used in elucidating fundamental cellular principles such as those relevant for the study of molecular mechanisms underlying complex human diseases, including the metabolic syndrome and ageing.
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| 18. |
- Anderson, Henrik, 1975-
(författare)
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Development of Electroacoustic Sensors for Biomolecular Interaction Analysis
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Biomolecular interaction analysis to determine the kinetics and affinity between interacting partners is important for the fundamental understanding of biology, as well as for the development of new pharmaceutical substances. A quartz crystal microbalance instrument suitable for kinetics and affinity analyses of interaction events was developed. The functionality of the sensor system was demonstrated by development of an assay for relative affinity determination of lectin-carbohydrate interactions.Sensor surfaces allowing for effective immobilization of one interacting partner is a key functionality of a biosensor. Here, three different surfaces and immobilization methods were studied. First, optimized preparation conditions for sensor surfaces based on carboxyl-terminated self assembled monolayers were developed and were demonstrated to provide highly functional biosensor surfaces with low non-specific binding. Second, a method allowing for immobilization of very acidic biomolecules based on the use of an electric field was developed and evaluated. The electric field made it possible to immobilize the highly acidic C-peptide on a carboxylated surface. Third, a method for antibody immobilization on a carboxyl surface was optimized and the influence of immobilization pH on the immobilization level and antigen binding capacity was thoroughly assessed. The method showed high reproducibility for a set of antibodies and allowed for antibody immobilization also at low pH.Three broadly different strategies to increase the sensitivity of electroacoustic sensors were explored. A QCM sensor with small resonator electrodes and reduced flow cell dimensions was demonstrated to improve the mass transport rate to the sensor surface. The use of polymers on QCM sensor surfaces to enhance the sensor response was shown to increase the response of an antibody-antigen model system more than ten-fold. Moreover, the application of high frequency thin film bulk acoustic resonators for biosensing was evaluated with respect to sensing range from the surface. The linear detection range of the thin film resonator was determined to be more than sufficient for biosensor applications involving, for instance, antibody-antigen interactions. Finally, a setup for combined frequency and resistance measurements was developed and was found to provide time resolved data suitable for kinetics determination.
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| 19. |
- Backmark, Anna, 1979
(författare)
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Structural Studies of the Human Water Channel Protein Aquaporin 5
- 2008
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Aquaporins are water channel proteins found in the membranes of all living cells. In humans, thirteen aquaporins have been identified to date. Many of them have been implicated in water imbalance disorders. Water transport through the aquaporins is regulated at several levels. Regulation by trafficking involves translocation of aquaporin containing vesicles from intracellular storage sites to the cell membrane in response to cellular stimuli and after protein phosphorylation. Protein trafficking is a universal mechanism of great importance for cellularfunction.This thesis presents the X-ray structure of human aquaporin 5 (AQP5). It is the first structureof a human aquaporin with enough detail to detect structural features unique to the aquaporinhomologues in man. The structure of AQP5 presents new information regarding the functional role of the putative tetrameric pore of aquaporins. Contradictory to suggestions of a transport function for this pore in other aquaporins, a lipid molecule completely occludes the pore in the centre of the AQP5 tetramer. The structure of AQP5 further provides insights into structural events that may signal the protein for trafficking. Four potential phosphorylationsites are revealed in the structure.The structure of AQP5 was solved using two constructs, one of which included a C-terminal affinity tag (His-tag). Comparison of aquaporin structures with and without a His-tag indicated that the tag influences crystal packing. The tag was found to reduce the diffractionresolution. However, the tag introduced additional spacing and asymmetry in the crystal packing, which reduced or prevented merohedral twinning.
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| 20. |
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| 21. |
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| 22. |
- Boulund, Fredrik, 1985, et al.
(författare)
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An analytical solution for finding voids and bottlenecks within macromolecules
- 2009
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Ingår i: 3DSig 2009: The 5th Structural Bioinformatics and Computational Biophysics Meeting, Stockholm, Sweden, 27-28 June 2009. ; , s. 77-78
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- We present an implementation of a direct analytical method for finding the largest sphere inscribed by four others. This method has been applied to the identification of voids and bottlenecks in protein channels.
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| 23. |
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| 24. |
- Bruns, Volker, et al.
(författare)
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The role of human capital in loan officers' decision policies
- 2008
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Ingår i: Entrepreneurship. - : SAGE Publications. - 1042-2587 .- 1540-6520. ; 32:3, s. 485-506
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Tidskriftsartikel (refereegranskat)abstract
- Using a human-capital perspective and the similarity-attraction paradigm, we examine the role of general and specific human capital in the decision policies of 114 Swedish loan officers in their assessments of small-business loan requests. We found that human capital characteristics had marginal impact on decision policy contingencies and that specific human capital had no significant influence on the probability of loan approval. However, we did find that the similarity between the loan officers’ human capital and the pplicants’ human capital was a significant indicator of loan approval. The findings offer interesting insight into the heterogeneity of loan decision processes and outcomes and future research opportunities are suggested.
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| 25. |
- Buee, Marc, et al.
(författare)
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454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity
- 2009
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Ingår i: New Phytologist. - 0028-646X. ; 184:2, s. 449-456
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Tidskriftsartikel (refereegranskat)abstract
- # Soil fungi play a major role in ecological and biogeochemical processes in forests. Little is known, however, about the structure and richness of different fungal communities and the distribution of functional ecological groups (pathogens, saprobes and symbionts). # Here, we assessed the fungal diversity in six different forest soils using tag-encoded 454 pyrosequencing of the nuclear ribosomal internal transcribed spacer-1 (ITS-1). No less than 166 350 ITS reads were obtained from all samples. In each forest soil sample (4 g), approximately 30 000 reads were recovered, corresponding to around 1000 molecular operational taxonomic units. # Most operational taxonomic units (81%) belonged to the Dikarya subkingdom (Ascomycota and Basidiomycota). Richness, abundance and taxonomic analyses identified the Agaricomycetes as the dominant fungal class. The ITS-1 sequences (73%) analysed corresponded to only 26 taxa. The most abundant operational taxonomic units showed the highest sequence similarity to Ceratobasidium sp., Cryptococcus podzolicus, Lactarius sp. and Scleroderma sp. # This study validates the effectiveness of high-throughput 454 sequencing technology for the survey of soil fungal diversity. The large proportion of unidentified sequences, however, calls for curated sequence databases. The use of pyrosequencing on soil samples will accelerate the study of the spatiotemporal dynamics of fungal communities in forest ecosystems.
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