| 1. |
- Tedersoo, Leho, et al.
(författare)
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Response to Comment on “Global diversity and geography of soil fungi”
- 2015
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 349:6251
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Schadt and Rosling (Technical Comment, 26 June 2015, p. 1438) argue that primer-template mismatches neglected the fungal class Archaeorhizomycetes in a global soil survey. Amplicon-based metabarcoding of nine barcode-primer pair combinations and polymerase chain reaction (PCR)–free shotgun metagenomics revealed that barcode and primer choice and PCR bias drive the diversity and composition of microorganisms in general, but the Archaeorhizomycetes were little affected in the global study. We urge that careful choice of DNA markers and primers is essential for ecological studies using high-throughput sequencing for identification.
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| 2. |
- Öhman, Sebastian, 1991-
(författare)
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Exploring Crystallisation Phenomena in Al2TiO5-Based Chemically Vapour Deposited Coatings by in situ Transmission Electron Microscopy
- 2023
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Ingår i: Crystal Growth & Design. - Washington : American Chemical Society (ACS). - 1528-7505.
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Understanding crystallization is crucial to enable improved design approaches for inorganic materials. Despite this importance, a deepened understanding of the mechanisms controlling this phase transition is still lacking. Herein, we employ in situ heating in a transmission electron microscope (TEM) to unravel crystallization phenomena in the Al–Ti–O system. Specifically, annealing of amorphous chemical vapour deposited (CVD) Al2TiO5-based coatings has been carried out in the temperature interval 750–900 °C. Crystallization typically occurs through a two-step process, where numerous smaller (< 10 nm) crystals are initially formed, followed by rapid crystal growth. Examinations of the initial crystallization stages indicate that the amorphous-to-crystalline transformation is polymorphic and that several phases may nucleate simultaneously, including Al6Ti2O13 and Al16Ti5O34. A transient (time-dependent) nucleation rate is discovered based on the displayed nucleation behaviour. Subsequent evaluations of the growth stages also reveal a preferential growth into larger crystals, and the coherent findings of this study indicate that crystallization occurs through a diffusionless (displacive) mechanism.
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| 3. |
- Öhman, Sebastian, 1991-
(författare)
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The Role of Oxygen in Vacancy-Induced Phase Formation and Crystallization of Al2TiO5-Based Chemically Vapor Deposited Coatings
- 2023
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Ingår i: The Journal of Physical Chemistry C. - Washington. - 1932-7447 .- 1932-7455.
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Oxygen is a commonly overlooked element influencing the properties of many metal oxides. By combining several in situ analytical techniques and theoretical calculations, we demonstrate that oxygen plays a vital part in the phase formation and crystallization of Al2TiO5-based chemical vapour deposition coatings. Rutherford backscattering spectrometry (RBS) corroborates a polymorphic transformation during crystallization. Subsequent hard X-ray photoelectron spectroscopy (HAXPES) shows that crystallization occurs through a displacive (diffusionless) mechanism. Combined with theoretical calculations, the crystallization and co-formation of Al2TiO5, Al6Ti2O13 and Al16Ti5O34 are suggested to be driven by the migration of oxygen ions and their corresponding vacancies.
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| 4. |
- Nettelblad, Carl, 1985-
(författare)
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Two Optimization Problems in Genetics : Multi-dimensional QTL Analysis and Haplotype Inference
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The existence of new technologies, implemented in efficient platforms and workflows has made massive genotyping available to all fields of biology and medicine. Genetic analyses are no longer dominated by experimental work in laboratories, but rather the interpretation of the resulting data. When billions of data points representing thousands of individuals are available, efficient computational tools are required. The focus of this thesis is on developing models, methods and implementations for such tools.The first theme of the thesis is multi-dimensional scans for quantitative trait loci (QTL) in experimental crosses. By mating individuals from different lines, it is possible to gather data that can be used to pinpoint the genetic variation that influences specific traits to specific genome loci. However, it is natural to expect multiple genes influencing a single trait to interact. The thesis discusses model structure and model selection, giving new insight regarding under what conditions orthogonal models can be devised. The thesis also presents a new optimization method for efficiently and accurately locating QTL, and performing the permuted data searches needed for significance testing. This method has been implemented in a software package that can seamlessly perform the searches on grid computing infrastructures.The other theme in the thesis is the development of adapted optimization schemes for using hidden Markov models in tracing allele inheritance pathways, and specifically inferring haplotypes. The advances presented form the basis for more accurate and non-biased line origin probabilities in experimental crosses, especially multi-generational ones. We show that the new tools are able to reconstruct haplotypes and even genotypes in founder individuals and offspring alike, based on only unordered offspring genotypes. The tools can also handle larger populations than competing methods, resolving inheritance pathways and phase in much larger and more complex populations. Finally, the methods presented are also applicable to datasets where individual relationships are not known, which is frequently the case in human genetics studies. One immediate application for this would be improved accuracy for imputation of SNP markers within genome-wide association studies (GWAS).
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| 5. |
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| 6. |
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| 7. |
- Asfaw, Habtom Desta
(författare)
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Multifunctional Carbon Foams by Emulsion Templating : Synthesis, Microstructure, and 3D Li-ion Microbatteries
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Carbon foams are among the existing electrode designs proposed for use in 3D Li-ion microbatteries. For such electrodes to find applications in practical microbatteries, however, their void sizes, specific surface areas and pore volumes need be optimized. This thesis concerns the synthesis of highly porous carbon foams and their multifunctional applications in 3D microbatteries. The carbon foams are derived from polymers that are obtained by polymerizing high internal phase water-in-oil emulsions (HIPEs).In general, the carbonization of the sulfonated polymers yielded hierarchically porous structures with void sizes ranging from 2 to 35 µm and a BET specific surface area as high as 630 m2 g-1. Thermogravimetric and spectroscopic evidence indicated that the sulfonic acid groups, introduced during sulfonation, transformed above 250 oC to thioether (-C-S-) crosslinks which were responsible for the thermal stability and charring tendency of the polymer precursors. Depending on the preparation of the HIPEs, the specific surface areas and void-size distributions were observed to vary considerably. In addition, the pyrolysis temperature could also affect the microstructures, the degree of graphitization, and the surface chemistry of the carbon foams.Various potential applications were explored for the bespoke carbon foams. First, their use as freestanding active materials in 3D microbatteries was studied. The carbon foams obtained at 700 to 1500 oC suffered from significant irreversible capacity loss during the initial discharge. In an effort to alleviate this drawback, the pyrolysis temperature was raised to 2200 oC. The resulting carbon foams were observed to deliver high, stable areal capacities over several cycles. Secondly, the possibility of using these structures as 3D current collectors for various active materials was investigated in-depth. As a proof-of-concept demonstration, positive active materials like polyaniline and LiFePO4 were deposited on the 3D architectures by means of electrodeposition and sol-gel approach, respectively. In both cases, the composite electrodes exhibited reasonably high cyclability and rate performance at different current densities. The syntheses of niobium and molybdenum oxides and their potential application as electrodes in microbatteries were also studied. In such applications, the carbon foams served dual purposes as 3D scaffolds and as reducing reactants in the carbothermal reduction process. Finally, a facile method of coating carbon substrates with oxide nanosheets was developed. The approach involved the exfoliation of crystalline VO2 to prepare dispersions of hydrated V2O5, which were subsequently cast onto CNT paper to form oxide films of different thicknesses.
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| 8. |
- Edelbroek, Bart
(författare)
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Function and Evolution of Small Regulatory RNAs and their Associated Proteins : A Journey from Genome to Proteome
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Organisms throughout the tree of life have evolved distinct ways to regulate gene expression. Some of these processes involve non-coding RNAs (ncRNAs), which are not translated but functional nonetheless. These ncRNAs are of utmost importance, with dysregulation of some causing severe developmental effects or even being lethal.In order to get a better fundamental understanding of gene regulation, and the ncRNAs that evolved to regulate gene expression, we study this in Amoebozoa. Members of this taxon vary greatly in lifestyle and organismal complexity. Some are strictly unicellular, free-living, whereas others, such as the social amoeba Dictyostelium discoideum can transition between unicellular and multicellular lifestyles. D. discoideum features a variety of small ncRNAs. Among these are the microRNAs. microRNAs have mostly been studied in plants and animals, where they are believed to have evolved convergently, and hypothesized to have played a role when these taxa evolved multicellular lifestyles. At what point the D. discoideum microRNAs evolved, how they function, and if they are involved in its multicellular lifestyle are fundamental questions addressed in this thesis. Here, we studied the evolution and function of microRNAs in a broad set of species belonging to Amoebozoa. We could identify microRNAs in all studied amoebae, and concluded that they are probably not involved in the evolution of multicellularity. To in detail investigate the evolution of microRNAs, we performed comparative genomics using D. discoideum and the close relative Dictyostelium firmibasis. For this, we sequenced, assembled and annotated the genome of the latter. At this point, our findings suggest that the microRNAs evolved several times in Amoebozoa, although we cannot rule out if they have a deep evolutionary history.The Class I RNAs are another type of ncRNAs. These, on the other hand, are only present in the social amoebae. They are hypothesized to regulate the transition from unicellular to multicellular in these species, potentially in a post-transcriptional manner. In order to investigate this, it is essential to understand to what extent the proteome and transcriptome correlate. Hence, we performed paired transcriptomics and proteomics in a time-series during multicellular development. By including a strain in which a specific Class I RNA is knocked out, we have initiated studies of its role during the transition to multicellularity.In conclusion, we were able to answer broad evolutionary and functional questions about gene regulation and ncRNAs by studying Amoebozoa from genome to proteome.
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| 9. |
- Ahlgren, Gunnel, et al.
(författare)
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Fatty Acid Ratios in Freshwater Fish, Zooplankton and Zoobenthos - Are There Specific Optima?
- 2009
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Ingår i: Lipids in Aquatic Ecosystems. - New York : Springer-Verlag New York. - 9780387886077 - 9780387893662 ; , s. 147-178
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Two groups of polyunsaturated fatty acids (PUFA), termed omega-3 and omega-6 in food (or here as n-3 and n-6 PUFA, respectively), are essential for all vertebrates and probably also for nearly all invertebrates. The absolute concentrations of the different PUFA are important, as is an appropriate balance between the two. The optimal ratio of n-3/n-6 is not known for most organisms but is anticipated to be more or less species-specific (Sargent et al. 1995). The three most important PUFA in vertebrates are eicosapentaenoic acid (EPA, 20:5n-3), docosahexaenoic acid (DHA, 22:6n-3) and arachidonic acid (ARA, 20:4n-6). Both EPA and ARA are precursors for biologically active eicosanoids that are vital components of cell membranes and play many dynamic roles in mediating and controlling a wide array of cellular activities (Crawford et al. 1989; Harrison 1990; Henderson et al. 1996; see Chap. 9). Since n-3 and n-6 PUFA cannot be synthesized de novo by most metazoans, they must be included in the diet, either as EPA, DHA and ARA, or as their precursors, such as α-linolenic acid (ALA, 18:3n-3, precursor of EPA and DHA) and linoleic acid (LIN, 18:2n-6, precursor of ARA) (Bell et al. 1986; Sargent et al. 1995). Both ALA and LIN are produced in the thylacoid membranes of algae and plants with chlorophyll (Sargent at al. 1987).
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| 10. |
- Blicharska, Malgorzata, et al.
(författare)
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Old Trees: Cultural Value
- 2013
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 339, s. 904-
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Annan publikation (övrigt vetenskapligt/konstnärligt)
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