| 1. |
- Aagaard, Sunniva Margrethe Due
(författare)
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Reticulate Evolution in Diphasiastrum (Lycopodiaceae)
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis relationships and the occurrence of reticulate evolutionary events in the club moss genus Diphasiastrum are investigated. Diphasiastrum is initially established as a monophyletic group within Lycopodiaceae using non recombinant chloroplast sequence data. Support is obtained for eight distinct parental lineages in Diphasiastrum, and relationships among the putative parent taxa in the hypothesized hybrid complexes; D. alpinum, D. complanatum, D. digitatum, D. multispicatum, D. sitchense, D. tristachyum and D. veitchii are presented. Feulgen DNA image densitometry data and sequence data obtained from three nuclear regions, RPB2, LEAFY and LAMB4, were used to infer the origins of three different taxa confirmed to be allopolyploid; D. zanclophyllum from South Africa, D. wightianum from Malaysia and an undescribed taxon from China. The two Asian polyploids have originated from two different hybrid combinations, D. multispicatum x D. veitchii and D. tristachyum x D. veitchii. Diphasiastrum zanclophyllum originates from a cross between D. digitatum and an unidentified diploid taxon. The occurrence of three homoploid hybrid combinations commonly recognized in Europe, D. alpinum x D. complanatum, D. alpinum x D. tristachyum and D. complanatum x D. tristachyum, are verified using the same three nuclear regions. Two of the three hybrid combinations are also shown to have originated from reciprocal crosses. Admixture analyses performed on an extended, dataset similarly identified predominately F1 hybrids and backcrosses. The observations and common recognition of hybrid species in the included populations are hence most likely due to frequent observations of neohybrids in hybrid zones. Reticulate patterns are, however, prominent in the presented dataset. Hence future studies addressing evolutionary and ecological questions in Diphasiastrum should emphasize the impact of gene flow between parent lineages rather than speciation as the result of hybridization.
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| 2. |
- Abenius, Erik, 1971-
(författare)
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Direct and Inverse Methods for Waveguides and Scattering Problems in the Time Domain
- 2005
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Numerical simulation is an important tool in understanding the electromagnetic field and how it interacts with the environment. Different topics for time-domain finite-difference (FDTD) and finite-element (FETD) methods for Maxwell's equations are treated in this thesis. Subcell models are of vital importance for the efficient modeling of small objects that are not resolved by the grid. A novel model for thin sheets using shell elements is proposed. This approach has the advantage of taking into account discontinuities in the normal component of the electric field, unlike previous models based on impedance boundary conditions (IBCs). Several results are presented to illustrate the capabilities of the shell element approach. Waveguides are of fundamental importance in many microwave applications, for example in antenna feeds. The key issues of excitation and truncation of waveguides are addressed. A complex frequency shifted form of the uniaxial perfectly matched layer (UPML) absorbing boundary condition (ABC) in FETD is developed. Prism elements are used to promote automatic grid generation and enhance the performance. Results are presented where reflection errors below -70dB are obtained for different types of waveguides, including inhomogeneous cases. Excitation and analysis via the scattering parameters are achieved using waveguide modes computed by a general frequency-domain mode solver for the vector Helmholtz equation. Huygens surfaces are used in both FDTD and FETD for excitation in waveguide ports. Inverse problems have received an increased interest due to the availability of powerful computers. An important application is non-destructive evaluation of material. A time-domain, minimization approach is presented where exact gradients are computed using the adjoint problem. The approach is applied to a general form of Maxwell's equations including dispersive media and UPML. Successful reconstruction examples are presented both using synthetic and experimental measurement data. Parameter reduction of complex geometries using simplified models is an interesting topic that leads to an inverse problem. Gradients for subcell parameters are derived and a successful reconstruction example is presented for a combined dielectric sheet and slot geometry.
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| 3. |
- Abrahamson, Alexandra, 1978-
(författare)
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Gill EROD Activity in Fish : A Biomarker for Waterborne Ah-receptor Agonists
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Induction of the cytochrome P450(CYP)1A protein and the connected increase in 7-ethoxyresorufin O-deethylase (EROD) activity are common biomarkers in fish. Enhanced activity of this protein signals exposure to Ah-receptor agonists such as chlorinated dioxins, co-planar polychlorinated biphenyls (PCBs) and certain polycyclic aromatic hydrocarbons (PAHs). The EROD biomarker is commonly analyzed in liver microsomes. However, the gill is directly exposed to waterborne pollutants, and in this thesis the gill filament EROD assay was therefore evaluated as a monitoring tool for waterborne CYP1A inducers in fish. Originally developed in rainbow trout (Oncorhynchus mykiss), the assay was here applied in various limnic and marine species. Following exposure to low waterborne concentrations of the readily metabolized CYP1A inducers benzo(a)pyrene (BaP) and indigo, a strong EROD induction was observed in the gill but not in the liver. This likely reflected metabolic clearance of the inducers in gill and other extrahepatic tissues. The high sensitivity of the gill was confirmed in studies of fish caged in waters in urban and rural areas in Sweden where the gill consistently showed a more pronounced EROD induction compared with the liver and the kidney. Fish caged in the reference waters showed surprisingly strong gill EROD induction and CYP1A immunostaining. Consequently, there may be CYP1A inducers present in the aquatic environment that are not yet identified. The assay was further applied in Atlantic cod (Gadus morhua) as a biomarker of exposure to crude oil and produced water (PW) from oil fields in the North Sea. The assay was finally adapted to detect inhibiting compounds, and an imidazole, a triazole and a plant flavonoid turned out to be potent gill EROD inhibitors. The overall conclusion from the studies of this thesis is that the gill filament EROD assay is a practical and sensitive biomarker of exposure to waterborne CYP1A inducers in various fish species. The induction of gill EROD activity in fish also at the reference sites in the field studies calls for further studies on background contamination in Swedish waters.
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| 4. |
- Abrahamsson, Maria, 1975-
(författare)
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Tuning of the Excited State Properties of Ruthenium(II)-Polypyridyl Complexes
- 2006
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Processes where a molecule absorbs visible light and then converts the solar energy into chemical energy are important in many biological systems, such as photosynthesis and also in many technical applications e.g. photovoltaics. This thesis describes a part of a multidisciplinary project, aiming at a functional mimic of the natural photosynthesis, with the overall goal of production of a renewable fuel from sun and water. More specific, the thesis is focused on design and photophysical characterization of new photosensitizers, i.e. light absorbers that should be capable of transferring electrons to an acceptor and be suitable building blocks for supramolecular rod-like donor-photosensitizer-acceptor arrays. The excited state lifetime, the excited state energy and the geometry are important properties for a photosensitizer. The work presented here describes a new strategy to obtain longer excited state lifetimes of the geometrically favorable Ru(II)-bistridentate type complexes, without a concomitant substantial decrease in excited state energy. The basic idea is that a more octahedral coordination around the Ru will lead to longer excited state lifetimes. In the first generation of new photosensitizers a 50-fold increase of the excited state lifetime was observed, going from 0.25 ns for the model complex to 15 ns for the best photosensitizer. The second generation goes another step forward, to an excited state lifetime of 810 ns. Furthermore, the third generation of new photosensitizers show excited state lifetimes in the 0.45 - 5.5 microsecond region at room temperature, a significant improvement. In addition, the third generation of photosensitizers are suitable for further symmetric attachment of electron donor and acceptor motifs, and it is shown that the favorable properties are maintained upon the attachment of anchoring groups. The reactivity of the excited state towards light-induced reactions is proved and the photostability is sufficient so the new design strategy has proven successful.
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| 5. |
- Acharya, Sandipta, 1972-
(författare)
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Some Aspects of Physicochemical Properties of DNA and RNA
- 2006
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis is based on nine research publications (I – IX) on structure and reactivity of RNA vis-à-vis DNA. The DNA and RNA are made of flexible pentose sugar units, polyelectrolytic phosphodiester backbone, and heterocyclic nucleobases. DNA stores our genetic code, whereas RNA is involved both in protein biosynthesis and catalysis. Various ligand-binding and recognition properties of DNA/RNA are mediated through inter- and intra-molecular H-bonding and stacking interactions, beside hydration, van der Waal and London dispersion forces. In this work the pH dependant chemical shift, pKa values of 2'-OH group as well as those the nucleobases in different sequence context, alkaline hydrolysis of the internucleotidic phosphodiester bonds and analysis of NOESY footprints along with NMR constrained molecular dynamics simulation were used as tools to explore and understand the physico-chemical behavior of various nucleic acid sequences, and the forces involved in their self-assembly process. Papers I – II showed that the ionization of 2'-OH group is nucleobase-dependant. Paper III showed that the chemical characters of internucleotidic phosphate are non-identical in RNA compared to that of DNA. Papers IV – VI show that variable intramolecular electrostatic interactions between electronically coupled nearest neighbor nucleobases in a ssRNA can modulate their respective pseudoaromatic character, and result in creation of a unique set of aglycons with unique properties depending on propensity and geometry of nearest neighbor interaction. Paper VII showed that the cross-modulation of the pseudoaromatic character of nucleobases by the nearest neighbor is sequence-dependant in nature in oligonucleotides. Paper VIII showed that the purine-rich hexameric ssDNA and ssRNA retain the right-handed helical structure (B-type in ssDNA and A-type in ssRNA) in the single-stranded form even in absence of intermolecular hydrogen bonding. The directionality of stacking geometry however differs in ssDNA compared to ssRNA. In ssDNA the relatively electron-rich imidazole stacks above the electron-deficient pyrimidine in the 5' to 3' direction, in contradistinction, the pyrimidine stacks above the imidazole in the 5' to 3' direction in ssRNA. Paper IX showed that the pKa values of the nucleobases in monomeric nucleotides can be used to show that a RNA-RNA duplex is more stable than a DNA-DNA duplex. The dissection of the relative strength of base-pairing and stacking showed that the relative contribution of former compared to that of the latter in an RNA-RNA over the corresponding DNA-DNA duplexes decreases with the increasing content of A-T/U base pairs in a sequence.
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| 6. |
- Adams, Christopher, 1978-
(författare)
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Secondary and Higher Order Structural Characterization of Peptides and Proteins by Mass Spectrometry
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The work in this thesis has demonstrated the advantages and limitations of using MS based technologies in protein and peptide structural studies. Tandem MS, specifically electron capture dissociation (ECD) have shown the ability to provide structural insights in molecules containing the slightest of all modifications (D-AA substitution). Additionally, it can be concluded that charge localization in molecular ions is best identified with ECD and to a lesser degree using CAD. Fragment ion abundances are a quantifiable tool providing chiral recognition (RChiral). An analytical model demonstrating the detection and quantification of D-AAs within proteins and peptides has been achieved. ECD has demonstrated the ability to quantify stereoisomeric mixtures to as little as 1%. Chirality elucidation on a nano LC-MS/MS time scale has been shown. The structures of various stereoisomers of the mini protein Trp Cage were explored, each providing unique ECD fragment ion abundances suggestive of gas phase structural differences. The uniqueness of these abundances combined with MDS data have been used in proposing a new mechanism in c and z fragment ion formation in ECD. This mechanism suggests initial electron capture on a backbone amide involved in (neutral) hydrogen bonding.The wealth of solution phase (circular dichroism), transitition phase (charge state distribution, CSD) and gas phase (ECD) data for Trp Cage suggest that at low charge states (2+) the molecule has a high degree of structural similarity in solution- and gas- phases. Furthermore, quantitative information from CSD studies is garnered when using a “native” deuteriated form as part of the stereoisomeric mixture. It has also been shown that the stability of the reduced species after electron capture is indicative of the recombination energy release, which in turn is linked to the coulombic repulsion- a structural constraint that can be used for approximation of the inter-charge distance for various stereoisomers.
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| 7. |
- Agervald, Åsa
(författare)
-
Maturation and Regulation of Cyanobacterial Hydrogenases
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Accelerated global warming plus an increasing need for energy is an equation not easily solved, thus new forms of sustainable energy production are urgently requested. In this context hydrogen production based on a cyanobacterial system offers an environmentally friendly alternative for energy capture and conversion. Cyanobacteria can produce hydrogen gas from sun light and water through the combination of photosystems and hydrogenases, and are suitable to cultivate in large scale. In the present thesis the maturation process of [NiFe]-hydrogenases is investigated with special focus on transcription of the accessory genes encoding proteins needed for assembly of the large and possibly also for the small hydrogenase subunit. The cyanobacteria used are two N2-fixing, filamentous, heterocystous strains; Nostoc sp. strain PCC 7120 and Nostoc punctiforme PCC 73102. For a biotechnological exploration of hydrogen production tools for regulatory purposes are important. The transcription factor CalA (cyanobacterial AbrB like) (Alr0946 in the genome) in Nostoc sp. strain PCC 7120 was found to be involved in hydrogen metabolism by regulating the transcription of the maturation protein HypC. Further the bidirectional hydrogenase activity was down-regulated in the presence of elevated levels of CalA, a result important to take into account when optimizing cyanobacteria for hydrogen production. CalA regulates at least 25 proteins in Nostoc sp. strain PCC 7120 and one of the down-regulated proteins was superoxide dismutase, FeSOD. The characterization of FeSOD shows that it has a specific and important function in the oxidative stress tolerance of Nostoc sp. stain PCC 7120. Since CalA is involved in regulation of both the hydrogen metabolism as well as stress responses these findings indicate that Alr0946 is an important transcription factor in Nostoc sp. strain PCC 7120 active on a global level in the cell. This thesis adds more knowledge concerning maturation and regulation of cyanobacterial hydrogenases which might be useful for future large scale hydrogen.
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| 8. |
- Agåker, Marcus, 1976-
(författare)
-
Double Excitations in Helium Atoms and Lithium Compounds
- 2006
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis addresses the investigation of doubly excited 2l´nl states in helium atoms and double core excitations in solid lithium compounds.Measurements on He are made in field free environments and under the influence of electric and magnetic fields, using synchrotron based inelastic photon scattering. Cross sections for scattering to singly excited final states are directly determined and compared to theoretical results and are found to be in excellent agreement. Radiative and spin-orbit effects are quantified and are shown to play an important role in the overall characterization of highly excited He states below the N =2 threshold. A dramatic electric field dependence is also observed in the flourecence yield already for relatively weak fields. This signal increase, induced by electric as well as magnetic fields, is interpreted in terms of mixing with states of higher fluorescence branching ratios.Double core excitations at the lithium site in solid lithium compounds are investigated using resonant inelastic x-ray scattering (RIXS). The lithium halides LiF, LiCl, LiBr and LiI are studied as well as the molecular compounds Li2O, Li2CO3 and LiBF4. States with one, as well as both, of the excited electrons localized at the site of the bare lithium nucleus are identified, and transitions which involve additional band excitations are observed. A strong influence of the chemical surrounding is found, and it is discussed in terms of the ionic character of the chemical bond.
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| 9. |
- Ahlgren, Joakim, 1972-
(författare)
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Organic Phosphorus Compounds in Aquatic Sediments : Analysis, Abundance and Effects
- 2006
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Phosphorus (P) is often the limiting nutrient in lacustrine and brackish eco-systems, and enhanced input of P into an aquatic system might therefore negatively impact the environment. Because modern waste water manage-ment have reduced external P input to surface waters, internal P loading from the sediment has become one of the main P sources to aquatic ecosys-tems, in which relatively unknown organic P compounds seem to be more active in P recycling than previously thought. This thesis focus is on improving analysis methods for organic P com-pounds in lacustrine and brackish sediments, as well as determining which of these compounds might be degraded, mobilized and subsequently recycled to the water column and on what temporal scale this occur. In both lacustrine and brackish environments, the most labile P compound was pyrophosphate, followed by different phosphate diesters. Phosphate monoesters were the least labile organic P compounds and degraded the slowest with sediment depth. In regulated lakes, it was shown that pyrophosphate and polyphos-phate compound groups were most related to lake trophic status, thus indi-cating their involvement in P cycling. This thesis also indicates faster P turn-over in sediment from the brackish environment compared to sediment from the lacustrine environment. A comparison of organic P extraction procedures showed that pre-extraction with EDTA, and NaOH as main extractant, was most efficient for total P extraction. Using buffered sodium dithionite (BD) as a pre-extractant and NaOH as main extractant was most efficient for extracting the presuma-bly most labile organic P compound groups, pyrophosphate and polyphos-phate. Furthermore, it was determined that organic P compounds associated with humic substances were more recalcitrant than other P compounds, that the BD step used in traditional P fractionation might extract phosphate monoesters, and that NMR is a statistically valid method for quantification of organic P compounds in sediment extracts.
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| 10. |
- Al-Ramadan, Khalid, 1976-
(författare)
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Impact of Diagenetic Alterations on Reservoir Quality and Heterogeneity of Paralic and Shallow Marine Sandstones : Links to Depositional Facies and Sequence Stratigraphy
- 2006
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis constrains the distribution of diagenetic alterations and their impact on reservoir-quality and heterogeneity evolution pathways in relation to depositional environments and sequence stratigraphy (systems tracts and key sequence stratigraphic surfaces) of four selected paralic and shallow marine siliciclastic successions. Typical eogenetic alterations encountered include the dissolution and kaolinitization of framework silicates, which are closely associated to shoreface facies of forced regressive systems tract (FRWST), lowstand systems tract (LST), upper part of the highstand systems tract (HST), and below the sequence boundary (SB). These alterations are attributed to incursion of meteoric water owing to rapid and considerable fall in the relative sea level. Extensive carbonate cementation is most evident below marine and maximum flooding surfaces (MFS), whereas dissolution of carbonate cement and detrital dolomite occur in LST, HST and below SB. Parameters controlling the patterns and texture (microcrystalline vs. poikilotopic) of calcite cement have been constrained within sequence stratigraphic framework of the sandstones. Coarse crystalline to poikilotopic calcite textures of meteoric water origin are thus closely linked to the FRWST, LST and upper part of the HST sandstones and occur mainly as stratabound concretions, whereas microcrystalline calcite, which was precipitated from marine porewaters, occurs as continuously cemented layers in the transgressive systems tract (TST) and lower part of the HST sandstones.Eogenetic alterations impose, in turn, profound control on the distribution pattern of mesogenetic alterations, and hence on reservoir quality evolution (destruction vs. preservation) pathways of sandstones. Eogenetic infiltrated clays, which occur in the tidal estuarine TST and HST sandstones, have helped preserving porosity in deeply buried sandstone reservoirs (≈ 5 km) through inhibition of extensive cementation by quartz overgrowths. Other essential findings of this thesis include deciphering the control on the formation of authigenic illite and chlorite by ultra-thin (≤ 1 µm thick), grain-coating clay mineral substrate.
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| 11. |
- Alfredsson, Ylvi, 1973-
(författare)
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Electronic and Structural Properties of Thin Films of Phthalocyanines and Titanium Dioxide
- 2005
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis is based on experimental studies in chemical physics. Titanium dioxide (TiO2) and phthalocyanine’s (Pc’s), interesting in many future perspectives, have been deposited as thin films and studied as follows. Information has been obtained on e.g. molecular orientation, crystal structure, depth profile of the chemical composition, electrochemical properties and electronic structure. This has been achieved by means of a combination of techniques: X-ray photoelectron spectroscopy (XPS), near edge x-ray absorption fine structure (NEXAFS), density functional theory calculations (DFT), UV-visible absorption spectroscopy (UVVIS) and cyclic voltammetry (CV).Metal-free phthalcyanine (H2Pc) has been shown to form films with different crystal structure and molecular orientation depending on deposition method, evaporation/sublimation or powder deposition, on commercial conducting glass (fluorine doped tin oxide, FTO), which is used e.g. in solar cells and organic light emitting devices (OLEDs). The unoccupied molecular orbitals are divided in x, y and z space coordinates of the molecule and also divided in inequivalent nitrogen components.The electronic structure is also studied for a sublimated titanyl phthalocyanine (TiOPc) film and related to the metal-free phthalocyanine. The ligand field around the titanium atom in TiOPc is compared with that of TiO2 to delineate the unoccupied levels recorded by means of x-ray absorption spectroscopy.Nanostructured TiO2 films were manufactured by screen printing/doctor blading on FTO. Such films were additionally covered with lutetium diphthalocyanine (LuPc2) by means of surface assembly from solution. LuPc2-, LuPc2+ and LuPc2H were identified and the stability of the electrochromic reactions in this system was monitored.Chemical vapor deposition (CVD) has been used to grow nanometer sized anatase TiO2 crystals on pre-oxidized Si (111) without formation of interfacial carbon and with an interface layer of the size of 15- 25Å. The interface layer was found to be amorphous TiSixOy with graded stoichiometry.
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| 12. |
- Allard, Erik, 1976-
(författare)
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Metabolic Studies with Liquid Separation Coupled to Mass Spectrometry
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Metabolism is the sum of all chemical processes with the purpose to maintain life, as well as enable reproduction, in a living organism. Through the study of metabolism, increased understanding of pharmacological mechanisms and diseases can be achieved. This thesis describes several ways of doing so, including targeted analysis of selected metabolites and investigations of systematic metabolic differences between selected groups through pattern recognition. A method for exploring metabolic patterns in urine samples after intake of coffee or tea was developed. The methodology was later used with the aim to find biomarkers for prostate cancer and urinary bladder cancer. Furthermore, a fully automated quantitative method was developed for concentration measurements of the double prodrug ximelagatran and its metabolites in pig liver. The method was then used to study the roll of active transporters in pig liver cells. Moreover, a fundamental study was conducted to investigate how monitoring of small, doubly charged analytes can improve the limit of detection and precision in a quantitative method. The techniques used for the experiments were liquid separation coupled to electrospray mass spectrometry. Extra efforts were made to make the separation and the ionization as compatible as possible to each other for increased quality of the collected data.
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| 13. |
- Alm, Oscar, 1977-
(författare)
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Heterogeneous Photolytic Synthesis of Nanoparticles
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Nanoparticles of iron, cobalt and tungsten oxide were synthesised by photolytic laser assisted chemical vapour deposition (LCVD). An excimer laser (operating at 193 nm) was used as an excitation source. The LCVD process, was monitored in situ by optical emission spectroscopy (OES). The synthesised particles were further analysed using transmission electron spectroscopy (TEM), X-ray diffraction (XRD), high resolution scanning electron microscopy (HRSEM), X-ray fluorescence spectroscopy (XRF), X-ray photoelectron spectroscopy (XPS) and Raman spectroscopy.Iron and cobalt single crystalline nanoparticles were synthesized using ferrocene and cobaltocene precursors. The diameter of the particles could be tailored by the experimental parameters (e.g., partial pressure and laser power) and were in the range 1 - 50 nm in diameter. In both cases, the particles were covered by a carbon shell, typically 7 nm thick. A thin graphitic layer was observed at the interface metal-carbon. Amorphous carbon was deposited on top of the graphitic carbon. Particle temperature, reaching the boiling point of the respective metal, was observed by OES of the thermal emission during the laser-induced particle formation process (and subsequent heating). Both bcc and fcc Fe phases were formed, both hcp and fcc for the Co phases. Size dependent magnetic properties were observed using superconducting quantum interference device (SQUID) measurements, where super-paramagnetic magnetic domains dominated for d < 10 nm. The iron particles were further processed, whereby the amorphous shell was removed by refluxing in nitric acid. In a subsequent step, the graphitic surface was functionalized by attaching an octyl ester, rendering the particles hydrophobic.Tungsten oxides were synthesized from combinations of WF6/H2/O2 as precursors. No particles could be deposited if H2 was removed from the gas-mixture. The as-deposited oxide nanoparticle film was amorphous. A monoclinic WO3 particle film could be achieved by annealing the amorphous oxide. Above 400°C, the oxide particles increased in size from ca. 20 nm to 60 nm through coalescence. The gas-sensing properties of the tungsten oxide were tested by conductance measurements using H2S as analyte. The sensitivity of the amorphous oxide nanoparticle film was found to be superior to that of a crystalline oxide nanoparticle film.
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| 14. |
- Almlöf, Martin, 1977-
(författare)
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Computational Methods for Calculation of Ligand-Receptor Binding Affinities Involving Protein and Nucleic Acid Complexes
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented.For a test case of several hydrophobic ligands binding to P450cam it is found that the LIE parameters do not change when simulations are performed with three different force fields. The nonpolar contribution to binding of these ligands is best reproduced with a constant offset and a previously determined scaling of the van der Waals interactions.A new methodology for prediction of binding free energies of protein-protein complexes is investigated and found to give excellent agreement with experimental results. In order to reproduce the nonpolar contribution to binding, a different scaling of the van der Waals interactions is neccesary (compared to small ligand binding) and found to be, in part, due to an electrostatic preorganization effect not present when binding small ligands.A new treatment of the electrostatic contribution to binding is also proposed. In this new scheme, the chemical makeup of the ligand determines the scaling of the electrostatic ligand interaction energies. These scaling factors are calibrated using the electrostatic contribution to hydration free energies and proposed to be applicable to ligand binding.The issue of codon-anticodon recognition on the ribosome is adressed using LIE. The calculated binding free energies are in excellent agreement with experimental results, and further predict that the Leu2 anticodon stem loop is about 10 times more stable than the Ser stem loop in complex with a ribosome loaded with the Phe UUU codon. The simulations also support the previously suggested roles of A1492, A1493, and G530 in the codon-anticodon recognition process.
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| 15. |
- Alwall, Johan, 1975-
(författare)
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Quark Distributions and Charged Higgs Boson Production : Studies of Proton Structure and New Physics
- 2005
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The Standard Model describes all elementary particles known today, but at larger energies it will have to be complemented with new particles and interactions. To be able to distinguish new physics at proton colliders such as LHC at CERN, it is essential to have an appropriate description of the colliding protons and their interactions. The study of the proton is important also in itself, to get a better understanding of the non-perturbative aspects of the strong interaction.In paper I-IV of this thesis, a model for the non-perturbative dynamics of quarks and gluons is developed, based on quantum fluctuations in hadrons. The parton distributions of the proton are given by momentum fluctuations, with sea quark distributions generated by fluctuations into baryon-meson pairs. This model can reproduce proton structure function data, as well as measured asymmetries between up and down valence quark distributions and between the anti-up and anti-down sea. It provides an intrinsic charm quark component as indicated by data. It also predicts an asymmetry in the strange sea of the proton, which can explain the NuTeV anomaly first attributed to new physics beyond the Standard Model.Charged Higgs bosons are predicted by several theories for new physics, including Supersymmetry. At proton colliders, the predicted dominant production mechanism is in association with top and bottom quarks. In paper V-VII, different contributions to this production are studied, and an algorithm is developed for combining the two dominant processes gb -> tH+/- and gg -> tbH+/-. The algorithm gives a smooth transition from small to large transverse momenta of the b-quark, which is important when the b-quark is observed. It also gives arguments for the choice of factorisation scale in the process.
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| 16. |
- Ameur, Adam, 1977-
(författare)
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A Bioinformatics Study of Human Transcriptional Regulation
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Regulation of transcription is a central mechanism in all living cells that now can be investigated with high-throughput technologies. Data produced from such experiments give new insights to how transcription factors (TFs) coordinate the gene transcription and thereby regulate the amounts of proteins produced. These studies are also important from a medical perspective since TF proteins are often involved in disease. To learn more about transcriptional regulation, we have developed strategies for analysis of data from microarray and massively parallel sequencing (MPS) experiments.Our computational results consist of methods to handle the steadily increasing amount of data from high-throughput technologies. Microarray data analysis tools have been assembled in the LCB-Data Warehouse (LCB-DWH) (paper I), and other analysis strategies have been developed for MPS data (paper V). We have also developed a de novo motif search algorithm called BCRANK (paper IV).The analysis has lead to interesting biological findings in human liver cells (papers II-V). The investigated TFs appeared to bind at several thousand sites in the genome, that we have identified at base pair resolution. The investigated histone modifications are mainly found downstream of transcription start sites, and correlated to transcriptional activity. These histone marks are frequently found for pairs of genes in a bidirectional conformation. Our results suggest that a TF can bind in the shared promoter of two genes and regulate both of them.From a medical perspective, the genes bound by the investigated TFs are candidates to be involved in metabolic disorders. Moreover, we have developed a new strategy to detect single nucleotide polymorphisms (SNPs) that disrupt the binding of a TF (paper IV). We further demonstrated that SNPs can affect transcription in the immediate vicinity. Ultimately, our method may prove helpful to find disease-causing regulatory SNPs.
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| 17. |
- Amira, Sami, 1971-
(författare)
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Classical and Car-Parrinello Molecular Dynamics Simulations of Polyvalent Metal Ions in Water
- 2005
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The aqueous solvation of metal ions is one of the long-standing and complex problems in chemistry, with implications for and applications in a broad range of biochemical and electrochemical systems, where water is the all-pervasive medium.This thesis describes computer simulations of Al3+(aq), Fe2+(aq), Fe3+(aq) and Cu2+(aq). Various aspects of the solvation of these polyvalent metal ions in water are addressed, at different levels of theory, using Car-Parrinello molecular dynamics, classical molecular dynamics and quantum-mechanical cluster calculations. Polyvalent metal ions are particularly interesting because of their large influence on the solvent structure, dynamics and thermodynamics, as well as on the properties of the individual solvent molecules. Polyvalent metal ions in aqueous solution also constitute a challenging subject for computer simulations since a sophisticated interaction model is needed to incorporate the large many-body effects. All the ion-water coordination figures in this thesis are octahedral, except in the Cu2+(aq) solution, where the ion is penta-coordinated with four equatorial neighbours in a plane and one axial neighbour located ~0.45 Å further out from the ion. The equatorial ion-water bonds have covalent character, while the axial water molecule is only electrostatically bound. For all the ions, the OD stretching frequencies of the first-shell water molecules are much more downshifted than in liquid water. In the case of Cu2+(aq), however, only the OD frequencies of the equatorial water molecules are downshifted with respect to bulk water whereas the OD frequencies of the axial water molecule are slightly upshifted. Various limitations of the Car-Parrinello molecular dynamics simulations have been explored and compared, such as finite system-size effects and shortcomings in the electronic structure calculations. The Car-Parrinello simulations are found to give reasonable descriptions of the polyvalent metal ions in aqueous solution.
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| 18. |
- Amoignon, Olivier, 1969-
(författare)
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Numerical Methods for Aerodynamic Shape Optimization
- 2005
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Gradient-based aerodynamic shape optimization, based on Computational Fluid Dynamics analysis of the flow, is a method that can automatically improve designs of aircraft components. The prospect is to reduce a cost function that reflects aerodynamic performances.When the shape is described by a large number of parameters, the calculation of one gradient of the cost function is only feasible by recourse to techniques that are derived from the theory of optimal control. In order to obtain the best computational efficiency, the so called adjoint method is applied here on the complete mapping, from the parameters of design to the values of the cost function. The mapping considered here includes the Euler equations for compressible flow discretized on unstructured meshes by a median-dual finite-volume scheme, the primal-to-dual mesh transformation, the mesh deformation, and the parameterization. The results of the present research concern the detailed derivations of expressions, equations, and algorithms that are necessary to calculate the gradient of the cost function. The discrete adjoint of the Euler equations and the exact dual-to-primal transformation of the gradient have been implemented for 2D and 3D applications in the code Edge, a program of Computational Fluid Dynamics used by Swedish industries.Moreover, techniques are proposed here in the aim to further reduce the computational cost of aerodynamic shape optimization. For instance, an interpolation scheme is derived based on Radial Basis Functions that can execute the deformation of unstructured meshes faster than methods based on an elliptic equation.In order to improve the accuracy of the shape, obtained by numerical optimization, a moving mesh adaptation scheme is realized based on a variable diffusivity equation of Winslow type. This adaptation has been successfully applied on a simple case of shape optimization involving a supersonic flow. An interpolation technique has been derived based on a mollifier in order to improve the convergence of the coupled mesh-flow equations entering the adaptive scheme.The method of adjoint derived here has also been applied successfully when coupling the Euler equations with the boundary-layer and parabolized stability equations, with the aim to delay the laminar-to-turbulent transition of the flow. The delay of transition is an efficient way to reduce the drag due to viscosity at high Reynolds numbers.
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| 19. |
- Andér, Martin, 1979-
(författare)
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Computational Analysis of Molecular Recognition Involving the Ribosome and a Voltage Gated K+ Channel
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Over the last few decades, computer simulation techniques have been established as an essential tool for understanding biochemical processes. This thesis deals mainly with the application of free energy calculations to ribosomal complexes and a cardiac ion channel. The linear interaction energy (LIE) method is used to explore the energetic properties of the essential process of codon–anticodon recognition on the ribosome. The calculations show the structural and energetic consequences and effects of first, second, and third position mismatches in the ribosomal decoding center. Recognition of stop codons by ribosomal termination complexes is fundamentally different from sense codon recognition. Free energy perturbation simulations are used to study the detailed energetics of stop codon recognition by the bacterial ribosomal release factors RF1 and RF2. The calculations explain the vastly different responses to third codon position A to G substitutions by RF1 and RF2. Also, previously unknown highly specific water interactions are identified. The GGQ loop of ribosomal RFs is essential for its hydrolytic activity and contains a universally methylated glutamine residue. The structural effect of this methylation is investigated. The results strongly suggest that the methylation has no effect on the intrinsic conformation of the GGQ loop, and, thus, that its sole purpose is to enhance interactions in the ribosomal termination complex. A first microscopic, atomic level, analysis of blocker binding to the pharmaceutically interesting potassium ion channel Kv1.5 is presented. A previously unknown uniform binding mode is identified, and experimental binding data is accurately reproduced. Furthermore, problems associated with pharmacophore models based on minimized gas phase ligand conformations are highlighted. Generalized Born and Poisson–Boltzmann continuum models are incorporated into the LIE method to enable implicit treatment of solvent, in an effort to improve speed and convergence. The methods are evaluated and validated using a set of plasmepsin II inhibitors.
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| 20. |
- Anderson, Cajsa Lisa, 1972-
(författare)
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Dating Divergence Times in Phylogenies
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis concerns different aspects of dating divergence times in phylogenetic trees, using molecular data and multiple fossil age constraints.Datings of phylogenetically basal eudicots, monocots and modern birds (Neoaves) are presented. Large phylograms and multiple fossil constraints were used in all these studies. Eudicots and monocots are suggested to be part of a rapid divergence of angiosperms in the Early Cretaceous, with most families present at the Cretaceous/Tertiary boundary. Stem lineages of Neoaves were present in the Late Cretaceous, but the main divergence of extant families took place around the Cre-taceous/Tertiary boundary.A novel method and computer software for dating large phylogenetic trees, PATHd8, is presented. PATHd8 is a nonparametric smoothing method that smoothes one pair of sister groups at a time, by taking the mean of the added branch lengths from a terminal taxon to a node. Because of the local smoothing, the algorithm is simple, hence providing stable and very fast analyses, allowing for thousands of taxa and an arbitrary number of age constraints.The importance of fossil constraints and their placement are discussed, and concluded to be the most important factor for obtaining reasonable age estimates.Different dating methods are compared, and it is concluded that differences in age estimates are obtained from penalized likelihood, PATHd8, and the Bayesian autocorrelation method implemented in the multidivtime program. In the Bayesian method, prior assumptions about evolutionary rate at the root, rate variance and the level of rate smoothing between internal edges, are suggested to influence the results.
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| 21. |
- Andersson, Carin, 1972-
(författare)
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Evaluation of Biomarker Responses in Fish : with Special Emphasis on Gill EROD Activity
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Many chemicals present in the aquatic environment can interfere with physiological functions in fish. Exposure to chemicals can be revealed by the use of biomarkers. Induction of 7-ethoxyresorufin O-deethylase (EROD) activity is a commonly used biomarker for exposure to CYP1A inducers such as dioxins and polyaromatic hyrdrocarbons. Vitellogenin is a frequently used biomarker for estrogenic compounds in various fish species whereas a biomarker for androgens, spiggin, is only found in sticklebacks. The main objectives of this thesis were to evaluate gill EROD activity as a biomarker and the three-spined stickleback as a model species in ecotoxicological studies. EROD activities were measured in gill, liver and kidney in rainbow trout (Oncorhynchus mykiss) caged in urban areas in Sweden. EROD induction was most pronounced in the gill. Also in fish caged at reference sites, with an expected low level of known CYP1A inducers, a marked gill EROD induction was found. One suggested inducer in rural waters is humic substances (HS). To evaluate the EROD-inducing capacity of HS, three-spined sticklebacks (Gasterosteus aculeatus) were exposed to HS of natural or synthetic origin. Both kinds of HS caused significant EROD induction. Gill EROD activities were also induced in sticklebacks exposed to ethynylestradiol (EE2) and β-naphthoflavone (βNF), alone and in combinations. Production of vitellogenin was induced in sticklebacks exposed to ≥50 ng EE2/l and a significant decrease in spiggin production was observed in individuals exposed to 170 ng EE2/l. Results from this thesis further strengthen the contention that gill EROD activity is a very sensitive biomarker for CYP1A inducers and that the stickleback is a suitable biomonitoring species, especially for exposure to CYP1A inducers. The finding that not only classical CYP1A inducers but also HS and high EE2 concentrations stimulate gill EROD activity is of significance for the interpretation of biomonitoring data.
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| 22. |
- Andersson, Cecilia, 1976-
(författare)
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Exploring the Magnetism of Ultra Thin 3d Transition Metal Films
- 2006
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis the magnetic and structural properties of ultra-thin 3d transition metals films have been investigated, in particular Fe, Ni and Co films. X-ray Magnetic Circular Dichroism (XMCD) has provided element specific spin (ms ) and orbital (ml ) moments per atom by utilizing the magneto optic sum-rules. Element specific hysteresis curves have been measured by means of X-ray Resonant Magnetic Scattering (XRMS), and the local crystallographic structure has been investigated using Extended X-ray Absorption Fine Structure (EXAFS).By performing XMCD on Fe/Ag(100) we observe a spin reorientation from in-plane to out-of-plane as the Fe thickness is lowered. At temperatures below 300K it occurs around 5-7 mono layers (ML) of Fe. While reorienting the magnetization out-of-plane the orbital moment increases with 125% but only a minor increase (5%) of the spin moment is observed. Extended X-ray Absorption Fine Structure (EXAFS) measurements indicate that films 6 ML and thicker have a bulk-like bcc structure. For the thin out-of-plane films, the local crystallographic structure is more complicated.The spin reorientation of the Au/Co/Au tri-layer system has been studied as a function of temperature, Co layer and Au cap thickness. An unexpected behavior of the orbital moment upon spin reorientation is found in these systems. An ex-situ prepared sample shows a smooth spin reorientation from an in-plane to an out-of-plane easy magnetization direction as the temperature is lowered from 300K to 200K. In-situ prepared samples have also been investigated and a novel phase diagram has been identified. The Au/Co interface has been explored during the Au capping by means of photoemission measurements.In the bi- and tri-layer system of Fe and Ni we have been able to manipulate the spin reorientation by varying the Fe and Ni thickness. A novel non-collinear interlayer exchange interaction for 3d ferro magnets in direct contact has been discovered for a set of samples. This exchange interaction is found to be strongly dependant on the preparation conditions.
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| 23. |
- Andersson, Claes, 1978-
(författare)
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Fusing Domain Knowledge with Data : Applications in Bioinformatics
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Massively parallel measurement techniques can be used for generating hypotheses about the molecular underpinnings of a biological systems. This thesis investigates how domain knowledge can be fused to data from different sources in order to generate more sophisticated hypotheses and improved analyses. We find our applications in the related fields of cell cycle regulation and cancer chemotherapy. In our cell cycle studies we design a detector of periodic expression and use it to generate hypotheses about transcriptional regulation during the course of the cell cycle in synchronized yeast cultures as well as investigate if domain knowledge about gene function can explain whether a gene is periodically expressed or not. We then generate hypotheses that suggest how periodic expression that depends on how the cells were perturbed into synchrony are regulated. The hypotheses suggest where and which transcription factors bind upstreams of genes that are regulated by the cell cycle. In our cancer chemotherapy investigations we first study how a method for identifiyng co-regulated genes associated with chemoresponse to drugs in cell lines is affected by domain knowledge about the genetic relationships between the cell lines. We then turn our attention to problems that arise in microarray based predictive medicine, were there typically are few samples available for learning the predictor and study two different means of alleviating the inherent trade-off betweeen allocation of design and test samples. First we investigate whether independent tests on the design data can be used for improving estimates of a predictors performance without inflicting a bias in the estimate. Then, motivated by recent developments in microarray based predictive medicine, we propose an algorithm that can use unlabeled data for selecting features and consequently improve predictor performance without wasting valuable labeled data.
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| 24. |
- Andersson, Eva, 1975-
(författare)
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Benthic-Pelagic Microbial Interactions and Carbon Cycling in Clearwater Lakes
- 2005
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis focuses on the interactions among microbiota in clearwater lakes. Field sampling and field experiments were performed to evaluate interactions among microbiota and the importance of benthic versus pelagic microbiota in terms of biomass and production. In addition, carbon cycling in an oligotrophic clearwater lake was calculated. Biomass and production of microbiota was clearly focused to the benthic habitat. During natural nutrient concentrations growth of heterotrophic bacteria (benthic and pelagic) was coupled to production of microphytobenthos in Lake Eckarfjärden, indicating interactions between autotrophic and heterotrophic microbiota in, as well as between, habitats. At increased nutrient concentrations, growth of heterotrophic bacteria was not correlated to microphytobenthos production. This was explained by less release of dissolved organic carbon (DOC) from microphytobenthos when they got access to more nutrients. Further investigations showed different scenarios in oligotrophic clearwater lakes following increased nutrient concentrations. The interactions between microbiota may be altered following increased nutrient concentrations and the microbial mat either positively or negatively affect the pelagic microbiota. The most striking result was that the expected shift towards dominance of pelagic primary production does not necessarily occur. Major flows of carbon were identified between different habitats in the oligotrophic clearwater Lake Eckarfjärden, and the net result was that the benthic habitat provided carbon to the pelagial. High DOC concentrations in the lake together with low pelagic production are factors that would indicate net heterotrophy. Accordingly, the pelagial of Lake Eckarfjärden was net heterotrophic but when the benthic and littoral habitats were included in the calculations, the lake turned out to be net autotrophic. In conclusion, the benthic microbiota contributed significantly to the total production in the investigated lakes and had a major role in the lake metabolism. Thus, this thesis emphasises the importance of benthic microbiota in shallow clearwater lakes.
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| 25. |
- Andersson, Mattias K., 1978-
(författare)
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Cleavage Specificity of Mast Cell Chymases
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Mast cells (MC) are potent inflammatory cells that are known primarily for their prominent role in IgE mediated allergies. However, they also provide beneficial functions to the host, e.g. in bacterial and parasitic defence. MCs react rapidly upon stimulation by releasing potent granule-stored mediators, and serine proteases of the chymase or tryptase families are such major granule constituents. As a first step towards a better understanding of the biological function of these proteases, we have determined the extended cleavage specificities of four mammalian mast cell chymases, by utilizing a substrate phage display approach. The specificities of these enzymes have then been used to compare their functional characteristics.The major mucosal MC chymase in mice, mMCP-1, was found to possess a strict preference in four amino acid positions of the peptide substrate. Using this sequence to search the mouse proteome for potential in vivo substrates led to the identification of several very interesting potential novel substrates. Some of them may explain the increased epithelial permeability provided by this enzyme.Human MCs, express only one single α-chymase, and the rodent α-chymases have secondarily gained elastase-like primary cleavage specificity. However, rodents express additional chymases, the β-chymases, and rodent β-chymases may have adopted the function of the α-chymases. The cleavage specificities of the human chymase and two rodent β-chymases were therefore determined (rat rMCP-1 and mouse mMCP-4). N-terminal of the cleaved bond the three chymases showed similar preferences, but C-terminal the human chymase and mMCP-4 shared a high preference for acidic amino acids in the P2´ position and therefore seem to be functional homologues. The molecular interactions mediating the preference for acidic amino acids in position P2´ were further investigated. By site-directed mutagenesis of the human chymase, amino acids Arg143 and Lys192 were concluded to synergistically mediate this preference.Our data show that chymases, of different MC subpopulations, display quite different extended cleavage specificities. However mouse do possess a MC chymase with almost identical cleavage specificity as the human MC chymase indicating a strong evolutionary pressure to maintain this enzyme specificity.
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