| 1. |
- Berglund, Björn, 1983-
(författare)
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Deliberations on the impact of antibiotic contamination on dissemination of antibiotic resistance genes in aquatic environments
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The great success of antibiotics in treating bacterial infectious diseases has been hampered by the increasing prevalence of antibiotic resistant bacteria. Not only does antibiotic resistance threaten to increase the difficulty in treating bacterial infectious diseases, but it could also make medical procedures such as routine surgery and organ transplantations very dangerous to perform. Traditionally, antibiotic resistance has been regarded as a strictly clinical problem and studies of the problem have mostly been restricted to a clinical milieu. Recently, non-clinical environments, and in particular aquatic environments, have been recognised as important factors in development and dissemination of antibiotic resistance. Elevated concentrations of antibiotics in an environment are likely to drive a selection pressure which favours resistant bacteria, and are also believed to promote horizontal gene transfer among the indigenous bacteria. Antibiotic resistance genes are often located on mobile genetic elements such as plasmids and integrons, which have the ability to disseminate among taxonomically unrelated species. The environmental bacteria can thus serve as both reservoirs for resistance and hot spots for the development of new antibiotic resistance determinants.There is still a lack of data pertaining to how high antibiotic concentrations are necessary to drive a selection pressure in aquatic environments. The aim of this thesis is to determine the effect of high and low concentrations of antibiotics on environmental bacterial communities from different aquatic environments. In the studies performed, antibiotics were measured using liquid chromatography-mass spectrometry. Bacterial diversity and evenness were assessed using molecular fingerprints obtained with 16S rRNA gene-based denaturing gradient gel electrophoresis, and antibiotic resistance genes and class 1 integrons were quantified using real-time PCR.Water and sediment samples were collected from different rivers and canals in Pakistan. The environments differed in anthropogenic exposure from undisturbed to heavily contaminated. A general trend could be observed of high concentrations of antibiotics correlating to elevated concentrations of antibiotic resistance genes and integrons. Extremely high concentrations of antibiotic resistance genes and integrons were found in the sediments downstream of an industrial drug formulation site, which likely correlated to the high load of antibiotics found in the water. Antibiotic and antibiotic resistance gene concentrations were also shown to increase downstream of Ravi river, which flows through Lahore, a city of more than 10 million inhabitants. Rivers not impacted by anthropogenic contamination were found to contain antibiotics and resistance gene concentrations of similar levels as in Europe and the U.S. Similar measurements were performed in the Swedish river Stångån. The concentrations of antibiotic resistance genes and class 1 integrons were shown to increase in the river after it had passed, and received urban wastewater effluent from the city of Linköping.A series of constructed wetlands were exposed to a mixture of different antibiotics at environmentally relevant concentrations over a few weeks. The antibiotic exposure did not observably affect the bacterial diversity or integron concentrations. Antibiotic resistance genes were found at low background concentrations, but the antibiotic exposure did not observably affect the concentrations. The constructed wetlands were also found to reduce most antibiotics at levels comparable to conventional wastewater treatment schemes, suggesting that constructed wetlands may be useful supplementary alternatives to conventional wastewater treatment.To investigate the effect of antibiotics on an uncontaminated aquatic environment in a more controlled setting, microcosms were constructed from lake water and sediments and subsequently exposed to varying concentrations of antibiotics (ranging from wastewater-like concentrations to 1,000 times higher). The water and sediments were gathered from the lake Nydalasjön, near Umeå, which is not exposed to urban waste. While antibiotic resistance genes and class 1 integrons were found in the lake sediments, no increase in the concentrations of these genes could be observed due to the antibiotic additions.In conclusion, although antibiotic resistance genes and integrons are part of the environmental gene pool, low concentrations of antibiotics do not seem to immediately impact their prevalence. However, aquatic environments exposed to anthropogenic waste do exhibit elevated levels of antibiotic resistance genes and integrons. Aquatic environments heavily polluted with antibiotics also clearly display correspondingly high concentrations of antibiotic resistance genes and integrons. These results clearly indicate the necessity to keep down pollution levels as well as the need to establish the range of antibiotic concentrations which do promote resistance. This must be done in order to enable risk assessments and to establish acceptable levels of antibiotic pollution. It should also be stressed that more research is required to elucidate what effect low levels of antibiotic exposure has on environmental bacterial communities.
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| 2. |
- Chen, Shan, 1986-
(författare)
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Stability and inactivation mechanisms of two transaminases
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In the past decades, more and more enzymes are employed as biocatalysts in industrial processes because of their advantages, such as high efficiency, substrate selectivity and stereoselectivity. Among them, amine transaminases (ATAs) are pyridoxal 5’-phosphate (PLP) dependent enzymes. ATAs have gained attention for their excellent performance in chiral amine synthesis, and their broad substrate acceptance. However, the low operational stability of amine transaminases still limits their application in industry.The amine transaminase from Chromobacterium violaceum (Cv-ATA) has been selected for further investigation for its relatively low operational stability. Co-solvents and various additives have been added to the enzyme storage solution to improve its storage stability at various temperatures. Co-lyophilization of Cv-ATA with surfactants has been applied to improve its enzymatic activity in neat organic solvents.As a PLP-dependent dimeric enzyme, the Cv-ATA is not primarily inactivated due to tertiary structural changes. Instead, both dimer dissociation and PLP release may affect the enzyme stability. Therefore, the inactivation pathway of the Cv-ATA during operational conditions was explored. The unfolding of the enzyme was detected by several methods, and the detection of fluorescence intensity spectrum of tryptophan is extensively applied for its high sensitivity. The phosphate group of PLP can be coordinated into the phosphate group binding cup, which may influence the enzyme structural stability. Therefore, the effect of both PLP and inorganic phosphate ions (present in phosphate buffer) on the enzyme stability was explored.The amine transaminase from Vibrio fluvialis (Vf-ATA) is another amine transaminase, which catalyses the same biocatalytic reaction and has a similar substrate scope as Cv-ATA. However, there is still a lack of data on the stability of Vf-ATA. Consequently, the operational stability of Vf-ATA in various environments was studied.
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| 3. |
- Engelmark Cassimjee, Karim
(författare)
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Tools in biocatalysis : enzyme immobilisation on silica and synthesis of enantiopure amines
- 2010
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis presents two techniques in the field of biocatalysis: An enzyme immobilisation method based on the His6-tag for attachment on modified silica oxide beads, and it’s employment in aqueous and organic medium for synthesis applications. The method functions as a one step extraction and immobilisation protocol. An equilibrium displacement system which enables complete conversion in reactions with ω-transaminases where isopropylamine is the donor, a route for synthesis of pharmaceutically interesting enantiopure amines. Biocatalysis is predicted to be a paramount technology for an environmentally sustainable chemical industry, to which every newly developed method represents a small but important step. The work done here is aimed to be a part of this development.
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| 4. |
- Engelmark Cassimjee, Karim
(författare)
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ω-Transaminase in Biocatalysis : Methods, Reactions and Engineering
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Biocatalysis offers an alternative to classic chemistry by using enzymes, the protein catalysts of Nature, for production of fine chemicals. Evolution has created enzymes capable of catalysis at moderate temperature of a specific reaction in the presence of a plethora of compounds in the aqueous cell environment. The focal point of biocatalysis is to utilise these traits in vitro, for creation of valuable molecules. The ω-transaminase is an enzyme capable of producing chiral amines, compounds used to great extent in pharmaceuticals. Much effort has in recent years been invested in the research and engineering of this enzyme type since the catalysed reaction offers an advantageous alternative to classical techniques. Nevertheless, there is a need for method development, adaptation of the enzyme and increased understanding of the catalytic mechanism for feasibility as an effective biocatalyst for unnatural substrates. This thesis addresses a chosen set of obstacles as a contribution to meeting the demands at hand. ω-Transaminase from Chromobacterium violaceum and Arthrobacter citreus was used. Many homologous ω-transaminases are available, which are also subject to engineering where variants are produced. To accurately compare their kinetic constants an active site quantification method is required but has not been available. Here such a method is presented (Paper 1) which encompasses a virtually irreversible half transamination reaction. In stereoselective synthesis the ω-transaminase catalysed equilibrium reaction inherently results in incomplete conversion. An equilibrium displacement system is presented (Paper II) where isopropylamine is the amino donor for transamination of acetophenone and derivatives thereof, coupled to an enzymatic cascade reaction. For many unnatural substrates the specificity and enantiospecificity is insufficient. Rationally redesigned variants were produced with improved properties for chosen substrates (Paper III and IV). The catalytic contributions of field and resonance of a variant compared to the wild type were investigated (Paper IV) for increased knowledge of the mechanism. For rational redesign of an enzyme the three-dimensional structure is required, of which only a few are available for the ω-transaminases. X-ray crystallographic structures of the holo and apo form of Chromobacterium violaceum ω-transaminase were made (Paper V) which revealed significant structural rearrangements upon coenzyme binding which may be of consequence for future engineering.
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| 5. |
- Gustavsson, Martin, 1984-
(författare)
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Surface expression using the AIDA autotransporter : Towards live vaccines and whole-cell biocatalysis
- 2011
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The area of surface expression has gathered a lot of interest from research groups all over the world and much work is performed in the area. Autotransporters have been used for surface expression in Gram-negative bacteria. One of the more commonly used autotransporters is the Adhesin Involved in Diffuse Adherence (AIDA) of pathogenic Escherichia coli. The surface expression of enzymes and vaccine epitopes offer several advantages. Surface expressed enzymes gain similar properties to immobilised enzymes, mainly simplified handling and separation using centrifugation. Surface expressed vaccine epitopes can have longer half-lives inside the animal that is to be immunized and surface groups on the host cell can act as adjuvants, increasing the immune response and leading to a better immunisation. However, while much basic research is directed towards mechanisms of surface expression using autotransporters there are few reports regarding production of surface expressed protein. Thus the aim of this work was the optimisation of the yield and productivity of surface expressed protein. Protein Z, an IgG-binding domain of Staphylococcal protein A, was used as a model protein for the investigation of which cultivation parameters influenced surface expression. The choice of cultivation medium gave the largest impact on expression, which was attributed to effects based on the induction of the native promoter of AIDA. The AIDA system was then used for the expression of two Salmonella surface proteins, SefA and H:gm, with potential for use as vaccine epitopes. SefA was verified located on the cell surface, and H:gm was found in the outer membrane of the host cell, though only in proteolytically truncated forms lacking the His6-tag used for detection. This proteolysis persisted in E. coli strains deficient for the outer membrane protease OmpT and was concluded to be dependent on other proteases. The removal of proteolysis and further optimisation of the yield of surface-expressed protein are important goals of further work.
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| 6. |
- Land, Henrik, 1987-
(författare)
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Amine Transaminases in Biocatalytic Amine Synthesis
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The use of enzymes, nature´s own catalysts, both isolated or as whole cells to perform chemical transformations is called biocatalysis. As a complement to classical chemical catalysis, biocatalysis can be an environmentally friendly and more economical option in the production and synthesis of chemicals. Research on the application of amine transaminases in synthesis of chiral amines have exploded over the last two decades and interest from the industry is increasing. Amine transaminases are promising catalysts due to their ability to perform reductive amination of ketones with excellent enantioselectivity.For a process to be efficient, high substrate specificity of the applied enzyme is an important factor. A variant of Chromobacterium violaceum amine transaminase that was obtained through rational design has an increased specific activity toward (S)-1-phenylethylamine and a set of 4´-substituted acetophenones. This result makes this variant a promising catalyst for the asymmetric synthesis of similar amines.Amine transaminase catalyzed asymmetric synthesis of amines generally suffers from unfavorable equilibrium. Two methods that include spontaneous tautomerization and biocatalytic amidation for equilibrium displacement have therefore been developed.Efficient assays and screening methods are demanded for the discovery and development of novel amine transaminases. For this purpose, a sensitive fluorescence-based assay that holds promise as a high-throughput screening method was developed.One of the major obstacles for application of enzymes in industrial processes is the instability of the enzyme toward harsh conditions. The stability of Chromobacterium violaceum amine transaminase was investigated and improved using co-solvents and other additives. Co-lyophilization with surfactants was also applied to improve the performance of the same enzyme in organic solvents.
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| 7. |
- Larsson, Per A., 1980-
(författare)
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Dimensional Stability of Paper : Influence of Fibre-Fibre Joints and Fibre Wall Oxidation
- 2008
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Papper är ett mycket mångsidigt material. Trots detta finns det ett flertal egenskaper som begränsar papperets användbarhet. Ett av de större problemen med cellulosa- och lignocellulosafibrer är att de sänker sin fria energi genom att sorbera vatten, och denna sorption förändrar papperets dimensioner. Detta fenomen kallas vanligtvis för bristfällig dimensionsstabilitet och uppträder i form av registerfel vid flerfärgstryck eller som krullning, buckling och vågiga papperskanter vid utskrift, kopiering och lagring, eller med en vidare definition som förkortad livslängd hos lådor på grund av mekanosorptivt kryp. Avsikten med denna avhandling har varit att studera och kvantifiera vilka egenskaper som styr, och hur de påverkar, den vatteninducerade dimensionsförändringen som sker hos ett fibernätverk, samt hur dess dimensionsstabilitet kan förbättras. Detta har studerats både genom att ändra fiberns fuktsorptionsegenskaper och genom att förändra adhesionen och kontaktgraden mellan fibrerna i fiber-fiberfogarna. Fogegenskaperna har också varierats genom att tillverka laboratorieark torkade under inspänning samt ark torkade fritt för att minimera mängden inbyggda spänningar i arket. Blekt kraftmassa har behandlats med polyelektrolytmultilager (PEM) för att förbättra adhesionen mellan fibrerna och för att öka kontaktgraden mellan fibrerna i fogen. Kontaktgraden har även minskats genom förhorning av fibrerna före arkformning. För de ark som fick torka fritt gav PEM-behandlingen en ökad hygroexpansionskoefficient, det vill säga dimensionsförändringen normaliserad mot förändringen i fuktinnehåll, vid samma förändring i relativ luftfuktighet medan förhorningen minskade hygroexpansionskoefficienten något. Om arken emellertid torkades under inspänning observerades ingen skillnad i hygroexpansionskoefficient mellan de olika fibermodifieringarna. Detta tolkades som ett resultat av en ökad kontaktzon och en större utbredning ut ur fogens plan, när arken torkades utan inspänning. En utbredning som medför att en större del av fiberns transversella expansion överförs som expansion i pappersplanet. Fibrernas fuktsorptionsegenskaper förändrades genom natriumperjodatoxidering av 1,4-glukanernas C2-C3-bindning. Detta skapade sannolikt tvärbindningar i fiberväggen som förbättrade fiberväggens tålighet både genom att låsa fibrillerna närmare varandra och genom att ta bort potentiella adsorptionssäten som annars är tillgängliga för vattenadsorption. Perjodatoxidationen minskar också fibrernas kristallinitet och således frigjorde oxidationen hydroxylgrupper där vattenmolekyler kan adsorbera. Detta innebar att oxidationen både minskade och ökade interaktionen mellan vatten och fibervägg, men dock på olika strukturell nivå. Tvärbindningarna visade sig också märkbart reducera sorptionshastigheten när arken utsattes för en förändrad luftfuktighet så länge de inte tidigare utsatts för relativa luftfuktigheter nära mättnad. Som ett resultat av den lägre förändringen i fuktinnehåll vid en förändring i luftfuktighet från 20 till 85 % RF minskade dimensionsförändringens amplitud för de tvärbundna arken upp till 30 %. Emellertid uppvisade de tvärbundna arken en högre hygroexpansionskoefficeint, vilket innebär att de blev mer känsliga för absoluta förändringar i fuktinnehåll.
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| 8. |
- Modén, Carl S., 1979-
(författare)
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Micromechanics of softwoods in the transverse plane : effects on cell and annual ring scales
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Transverse mechanical properties of wood are important in many practial applications and an interesting scientific subject. A very low transverse shear modulus has been identified in spruce, which causes large strain concentrations in wood structures. In this thesis, experimental characterization of local density variations as well as local strain fields are carried out using the SilviScan apparatus and digital speckle photography, respectively. This is combined with micromechanical modeling based on hexagonal wood cells in combination with finite element analysis. Problems addressed include the moduli in the transverse plane, including variations at the scale of individual annual rings. The relative importance of cell wall bending and stretching deformation mechanisms is analysed as a function of wood cell geometry, relative density and direction of loading (radial, tangential and shear). Transverse anisotropy is also analyzed, including its dependency of earlywood and latewood characteristics. The wood cell shape angle variation and density effects are sufficient to explain transverse anisotropy in softwoods (no ray effects), and the influence of earlywood/latewood ratio is explained. As a practical test method for shear modulus measurements, an off-axis compression test with full-field strain determination is proposed. The advantage is a simple fixture and large region of representative strain required for a heterogeneous material such as wood. As an alternative, the single cube apparatus (SCA) for shear tests is evaluated. The SCA is used to determine the shear strain distribution within the annual rings. Based on the density distribution of the shear test specimen and a micromechanics model, a finite element model is developed, and predictions are compared with the measured shear strains. The agreement between predicted and measured shear strains at the annual ring scale are remarkably good. It shows that the low GRT of spruce is due to the low earlywood density and the large cell wall bending deformation resulting from shear loading. Furthermore, it illustrates the need for improved understanding of annual ring scale effects. For example, fairly low transverse global loads will lead to lage local shear strains.
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| 9. |
- Roos, Fredrica, 1988-
(författare)
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Scoring the World: The Musical Imagery of Orchestration in Gustav Mahler's Symphonies no. 4 and 5
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Gustav Mahler’s comment to Sibelius in 1907 that a symphony must be like the world is one of classical music’s most cited and has functioned as a crucial springboard for interpretations of the composer’s works. However, these have mostly centred on autobiographical, programmatic, or narrative aspects, with a focus on temporally unfolding plots or generic and semiotic connotations. In this study, I use the ‘world’ concept in exploring Mahler’s music as a ‘sound-world’ and its imaginative production through listening, with a particular focus on the often-bypassed features of timbre and orchestration. This investigation proceeds from the theoretical framework of world-making and narrative, although references to theatre and film are also made. The ‘storyworld’ notion and the related possible worlds theory form the vantage point for examining ‘world’ from various perspectives. Together with the constructional categories of space and temporality, content matters of voice, virtual agency, and gesture are analytically applied to Mahler’s Fourth and Fifth Symphonies, which represent generic worlds of fairy tale and realism, respectively. The results of the study show that it is Mahler’s rich and shifting orchestral combinations that generate the multitude of different worlds and their continuous interrelationships. By means of spatial and temporal mobility, the listener is actively integrated in the sound-world as an actual agent, perceiving it from alternating positions determined by instrumentation. Through his particular treatment of timbre, Mahler expands the symphonic genre into a sort of intermedial drama in sound, while suggesting other approaches to musical narration based on textual simultaneity and expressive mode. Hearing his symphonies as worlds also permits new means of analysing musical works, making analysis a more dynamic process highlighting the imaginative and structural possibilities of sound.
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| 10. |
- Ruggieri, Federica, 1990-
(författare)
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Transaminase Biocatalysis: Applications and Fundamental Studies
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Biocatalysis is the branch of science at the intersection between chemistry and biology and specifcally dedicated to the application of natural evolvable catalysts, i.e. enzymes, in human-designed chemical processes. Among the array of promising biocatalysts, transaminases (EC 2.6.1.x) are possibly one of the enzyme classes with the largest unrealized potential. Fast inactivation, poor acceptance towards unnatural substrates and limited tolerance to cosolvents are some of the main factors hampering their implementation in chemical synthesis. In the present thesis work advances in both transaminase application and molecular understanding are presented. Indeed, these two topics are deeply interconnected, as a better molecular understanding is expected to ease the generation of novel enzyme variants suitable for new desired applications.From the application perspective, the design of an effective one-pot transaminase-based racemization system offers new possibilities for the design of fully biocatalytic dynamic kinetic resolutions of valuable chiral amines. Similarly, the successful structure-guided redesign of the small substrate binding pocket of the Chromobacterium violaceum (S)-selective transaminase (Cv-TA) granted access to a new enzyme variant active on semi-preparative scale towards the unnatural substrate 1,2-diphenylethylamine.From the molecular understanding perspective, the combination of crystallographic and computational techniques led to the formulation of a dimer dissociation model valid for Cv-TA and possibly for other enzymes belonging to the same fold type. This model, which aided the improvement of the Cv-TA stability by structure-based engineering, will hopefully enable similar results in other structurally related enzymes.
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