| 1. |
- Olsson, Mia, 1978-
(författare)
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Uncovering a Novel Pathway for Autoinflammation : With a Little Help from a Wrinkled Friend
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- A major challenge in medical genetics is to identify the mutations underlying heritable diseases. Dogs are excellent genetic models in the search for causative mutations, as they constitute a large library of naturally occurring heritable diseases many of which are analogous to those suffered by man. In addition, these animals have a genome structure well suited to gene mapping. The Shar-Pei dog has two breed-specific features; a strongly selected for wrinkled skin and a high predisposition to an autoinflammatory disease (AID). Abnormalities in the innate immune system cause this type of disease, presenting as spontaneous attacks of inflammation. Persistent inflammation puts an affected Shar-Pei at risk of amyloidosis, organ failure and premature death. In humans, similar AIDs occur and for a majority of cases, no underlying genetic cause has yet been identified. The aim of this thesis was to use the Shar-Pei as a genetic model for autoinflammation in order to find new genes and signalling pathways involved in disease. In paper I, a pleiotropic mutation was identified that could explain both the wrinkled skin and autoinflammation in Shar-Pei. The mutation is associated with an up-regulation of Hyaluronic Acid Synthase 2 (HAS2). Increased expression of HAS2 leads to abnormal depositions of hyaluronic acid (HA) in the skin, resulting in the wrinkled appearance. When fragmented, HA also function as a damage signal sensed by the innate immune system which then responds with inflammation. By selecting for the wrinkled skin, the autoinflammatory disease has inadvertently been enriched in the breed. In paper II, five different inflammatory signs could be associated with the same genetic risk factor, allowing the introduction of a new terminology: Shar-Pei autoinflammatory disease (SPAID) to describe the whole disease complex. In addition, a modifying locus containing several biologically attractive genes was suggested to contribute to varying incidence of amyloidosis in Shar-Pei. In paper III, signs of pathological changes in HA metabolism were investigated in human AID. HA concentration was found to be both higher in subjects with no molecular diagnosis and also associated to disease activity and severity. Taken together, this suggests HA is also involved in human AID.
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| 2. |
- Jiang, Lin
(författare)
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Functional Studies of Genes Associated with Muscle Growth in Pigs and Hair Greying in Horses
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Domestic animals have become very different from their wild ancestors during domestication and animal breeding. This provides a good model to unravel the molecular mechanisms underlying phenotypic variation. In my thesis I have studied genes affecting two important traits, leanness in pigs and hair greying-associated melanoma in horses.In the first part of the thesis, I focused on an intronic mutation leading to more muscle growth and less fat deposition in domestic pigs to identify a transcription factor (TF) that binds to the regulatory element overlapping with the mutation. The aim has been to further study the function of the previously unknown TF in mouse myoblast cells and in insulin-producing cells (Paper I-III). We discovered a new TF ZBED6 binding to intron 3 of the IGF2 gene, in which a single nucleotide substitution in pigs abrogates the binding and causes increased leanness in domestic pigs. Silencing of ZBED6 expression in mouse myoblasts increased Igf2 expression, cell proliferation and migration, and myotube formation. This result is in line with the increased leanness phenotype in mutant pigs. Chromatin Immunoprecipitation-sequencing (ChIP-seq) using an anti-ZBED6 antibody identified 1200 ZBED6 target genes besides IGF2 and many are TFs controlling fundamental biological processes. In the first follow-up study we found ZBED6 mainly affected the expression of muscle protein genes by directly regulating Igf2 and Twist2 expression, in agreement with our previous observation of faster myotube formation in ZBED6-silenced cells. ChIP-seq with antibodies against six different histone modifications revealed that ZBED6 preferentially binds to active promoters and modulates transcriptional activity by a novel mechanism rather than by recruiting repressive histone modifications. The second follow-up study revealed that ZBED6 affects the morphology and insulin content and release in pancreatic ß cells.In the second part (Paper IV), we investigate the functional significance of an intronic duplication in the Syntaxin 17 (STX17) gene causing hair greying and melanoma in horses. We found two Microphtalmia-associated transcription factor (MITF) binding sites within the duplication and showed that the duplicated sequence up-regulates reporter gene expression in a melanocyte-specific manner both by reporter assays in mouse melanocytes and in transgenic zebrafish. These results established that the intronic duplication acts as a melanocyte-specific enhancer that becomes much stronger when it is duplicated.
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| 3. |
- Andersson, Yvette, 1972-
(författare)
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Sentinel Node in Clinical Practice : Implications for Breast Cancer Treatment and Prognosis
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The introduction of sentinel lymph node biopsy (SLNB) has conveyed several new issues, such as the risk of false negativity, long-term consequences, the prognostic significance of micrometastases and whether ALND can be omitted in sentinel lymph node- (SLN) positive patients.Archived SLN specimens from 50 false negative patients and 107 true negative controls were serially sectioned and stained with immunohistochemistry. The detection rate of previously unknown metastases did not differ between the false and the true negative patients. The risk of false negativity was higher in patients with multifocal or hormone receptor-negative tumours, or if only one SLN was found.In a Swedish multicentre cohort, 2216 SLN-negative patients in whom ALND was omitted were followed up for a median of 65 months. The isolated axillary recurrence rate was only 1.0%, and the overall survival was high (93%).The survival of 3369 breast cancer patients (2383 node-negative (pN0), 107 isolated tumour cells (pN0(i+), 123 micrometastases (pN1mi) and 756 macrometastases (pN1)) was analysed. The 5-year cause-specific and event-free survival was worse for pN1mi and pN1 patients than for pN0 patients. There was no difference in survival between pN0(i+) and pN0 patients.Tumour and SLN characteristics in 869 SLN-positive patients were compared between those with and without non-SLN metastases, and the Tenon score was calculated. The risk of non-SLN metastases was higher in case of SLN macrometastases (compared with micrometastases), a high positive/total SLN ratio and Elston grade 3 tumours, and increased with increasing tumour size. The area under the curve (AUC) for the Tenon score was 0.65, and the test thus performed inadequately in this population.In conclusion, despite the risk of false negativity, SLNB with omission of ALND in SLN-negative patients appears to be safe even in the long term. The presence of micrometastases is of prognostic importance and should entail adjuvant treatment. The need for ALND in patients with SLN micro- and even macrometastases has been questioned, but the occurrence of non-SLN metastases is hard to predict, and strong evidence for the safe omission of ALND is lacking.
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| 4. |
- Berglund, Jonas, 1983-
(författare)
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Meiotic Recombination in Human and Dog : Targets, Consequences and Implications for Genome Evolution
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Understanding the mechanism of recombination has important implications for genome evolution and genomic variability. The work presented in this thesis studies the properties of recombination by investigating the effects it has on genome evolution in humans and dogs.Using alignments of human genes with chimpanzee and macaque orthologues we studied substitution patterns along the human lineage and scanned for evidence of positive selection. The properties mirror the situation in human non-coding sequences with the fixation bias ‘GC-biased gene conversion’ (gBGC) as a driving force in the most rapidly evolving regions. By assigning candidate genes to distinct classes of evolutionary forces we quantified the extent of those genes affected by gBGC to 20%. This suggests that human-specific characters can be prompted by the fixation bias of gBGC, which can be mistaken for selection.The gene PRDM9 controls recombination in most mammals, but is lacking in dogs. Using whole-genome alignments of dog with related species we examined the effects of PRDM9 inactivation. Additionally, we analyzed genomic variation in the genomes of several dog breeds. We identified that non-allelic homologous recombination (NAHR) via sequence identity, often GC-rich, creates structural variants of genomic regions. We show that these regions, which are also found in dog recombination hotspots, are a subset of unmethylated CpG-islands (CGIs). We inferred that CGIs have experienced a drastic increase in biased substitution rates, concurrent with a shift of recombination to target these regions. This enables recurrent episodes of gBGC to shape their distribution.The work presented in this thesis demonstrates the importance of meiotic recombination on patterns of molecular evolution and genomic variability in humans and dogs. Bioinformatic analyses identified mechanisms that regulate genome composition. gBGC is presented as an alternative to positive selection and is revealed as a major factor affecting allele configuration and the emergence of accelerated evolution on the human lineage. Characterization of recombination-induced sequence patterns highlights the potential of non-methylation and establishes unmethylated CGIs as targets of meiotic recombination in dogs. These observations describe recombination as an interesting process in genome evolution and provide further insights into the mechanisms of genomic variability.
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| 5. |
- Zody, Michael C., 1968-
(författare)
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Investigation of Mechanics of Mutation and Selection by Comparative Sequencing
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The process of evolution is of both scientific and medical interest. This thesis presents several studies using complete genomic reference sequences, comparative genomic data, and intraspecific diversity data to study the two key processes of evolution: mutation and selection. Large duplications, deletions, inversions, and translocations of DNA contribute to genomic variation both between and within species. Human chromosomes 15 and 17 contain a high percentage of dispersed, recently duplicated sequences. Examination of the relationships between these sequences showed that the majority of all duplications within each chromosome could be linked through core sequences that are prone to duplication. Comparison to orthologous sequences in other mammals allowed a reconstruction of the ancestral state of the human chromosomes, revealing that regions of rearrangement specific to the human lineage are highly enriched in chromosome-specific duplications. Comparison to copy number variation data from other studies also shows that these regions are enriched in current human structural variation. One specific region, the MAPT locus at 17q21.31, known to contain an inversion polymorphism in Europeans, was resequenced completely across both human orientation haplotypes and in chimpanzee and orangutan, revealing complex duplication structures at the inversion breakpoints, with the human region being more complex than chimpanzee or orangutan. Fluorescent in-situ hybridization analysis of human, chimpanzee, and orangutan chromosomes showed inversion polymorphisms of independent origin in all three species, demonstrating that this region has been a hotspot of genomic rearrangement for at least twelve million years. These results reveal a mechanistic relationship between sequence duplication and rearrangement in the great apes. We also generated a draft sequence of the chimpanzee genome and compared it to that of the human. Among other findings, this showed that CpG dinucleotides contribute 25% of all single base mutations, with a rate of mutation ~10-fold that of other bases, and that the male mutation rate in great apes is ~5-6 times the female rate, a higher ratio than had been observed in comparisons of primates and rodents. We detected six regions of probable recent positive selection in humans with a statistical method relying on chimpanzee sequence to control for regional variation in mutation rates. Finally, resequencing of several lines of domestic chicken and comparison to the reference chicken genome identified a number of gene deletions fixed in domestic lines and also several potential selective sweeps. Of particular interest are a missense mutation in TSHR nearly fixed in all domestic chickens and a partial deletion of SH3RF2 fixed in a high growth line. The TSHR mutation may play a role in relaxation of seasonal reproduction. A high-resolution QTL mapping experiment showed that the SH3RF2 deletion is significantly associated with increased growth. This work provides important new insights into the mechanics of evolutionary change at both the single nucleotide and structural level and identifies potential targets of natural and artificial selection in humans and chickens.
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| 6. |
- Andersson, Joacim, 1978-
(författare)
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Kroppsliggörande, erfarenhet och pedagogiska processer : en undersökning av lärande av kroppstekniker
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The overall aim of this thesis is to theoretically explore and empirically analyse practical embodied knowledge in educational settings. In accordance to this aim an approach of body pedagogics is used in combination with classical pragmatism, using foremost William James’ and John Dewey’s concepts of experience, meaning, inquiry and habit. In addition, these concepts are combined with an idea of reflexive body techniques.A main focus lies on investigating the learning of body techniques in dinghy sailing by studying the process and the product of teaching and learning, the role of the instructor for sailors’ learning and the interplay between teaching and learning. The thesis entails three case studies consisting of video recordings of dinghy sailing, all using a combination of theoretical explorations and practical epistemology analysis (PEA). Empirical focus lies on how sailors grow into purposeful body techniques by taking the measure of their ongoing, continuous experience while coordinating their movements with the environment. The analyses show how understandings and bodily skills are simultaneously used in the educational situations where the dinghy sailors have to handle both the environment and various instructions given by the trainer. The result is presented through a descriptive model, comprising theoretical explorations and empirical analysis, through which it is possible to emphasise both the process and the content of the learning of body techniques. The methodological contribution of the thesis thus also consists of developed tools for analysing processes of body pedagogics at a micro level.
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| 7. |
- Eriksson, Jonas
(författare)
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Genetic and Genomic Studies in Chicken : Assigning Function to Vertebrate Genes
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- A major challenge in the post-genomic era is to understand how genome sequence variants (genotype) give rise to the enormous diversity observed in terms of morphology, physiology and behavior (phenotype) among living organisms. Domestic animals—with their tremendous phenotypic variation—are excellent model organisms for determining the relationships between genotype and phenotype. In this thesis, I describe the utilization of the chicken, in combination with modern genetic and genomic approaches, in developing our understanding of the genetic mechanisms underlying phenotypic variation. These studies provide novel information on the genetics behind variation in carotenoid- and melanin-based pigmentation—observed in many organisms—and also cast light on the genetic basis of chicken domestication. In paper I, we report that the yellow skin phenotype—observed in most commercial chickens—is caused by one or several tissue-specific mutations altering the expression of beta-carotene oxygenase 2 (BCO2 or BCDO2) in skin. In addition, we present the first conclusive evidence of a hybrid origin of the domestic chicken, since the allele causing yellow skin most likely originates from the grey jungle fowl (Gallus sonneratii) and not from the previously described sole ancestor, the red jungle fowl (Gallus gallus). In paper II, we detect a number of loci that were likely important during the domestication process of chicken and the later specialization into meat (broiler) and egg (layer) producing lines. One of the major findings was that worldwide, almost all domestic chickens carry a missense mutation in TSHR (thyroid stimulating hormone receptor) in a position that is completely conserved amongst vertebrates. We speculate that this “domestication-mutation” has played an important role in the transformation of the wild red jungle fowl ancestor into the modern domestic chicken. In paper III, we demonstrate that the dilution of red (pheomelanin) pigmentation—observed in the plumage of the Inhibitor of Gold chicken—is caused by a frame-shift mutation in the catechol-O-methyltransferase domain containing 1 (COMTD1) gene. The production and regulation of pheomelanin is poorly understood and this discovery advances our current knowledge of this pathway.
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| 8. |
- Lamichhaney, Sangeet, 1984-
(författare)
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The genetic basis for adaptation in natural populations
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Many previous studies in evolutionary genetics have been based on few model organisms that can be reared at ease in the laboratory. In contrast, genetic studies of non-model, natural populations are desirable as they provide a wider range of adaptive phenotypes throughout evolutionary timescales and allow a more realistic understanding of how natural selection drives adaptive evolution. This thesis represents an example of how modern genomic tools can be effectively used to study adaptation in natural populations.Atlantic herring is one of the world’s most numerous fish having multiple populations with phenotypic differences adapted to strikingly different environments. Our study demonstrated insignificant level of genetic drift in herring that resulted in minute genetic differences in the majority of the genome among these populations. In contrast, a small percentage of the loci showed striking genetic differentiation that were potentially under natural selection. We identified loci associated with adaptation to the Baltic Sea and with seasonal reproduction (spring- and autumn-spawning) and demonstrated that ecological adaptation in Atlantic herring is highly polygenic but controlled by a finite number of loci.The study of Darwin’s finches constitutes a breakthrough in characterizing their evolution. We identified two loci, ALX1 and HMGA2, which most likely are the two most prominent loci that contributed to beak diversification and thereby to expanded food utilization. These loci have played a key role in adaptive evolution of Darwin’s finches. Our study also demonstrated that interspecies gene flow played a significant role in the radiation of Darwin’s finches and some species have a mixed ancestry.This thesis also explored the genetic basis for the remarkable phenotypic differences between three male morphs in the ruff. Identification of two different versions of a 4.5 MB inversion in Satellites and Faeders that occurred about 4 million years ago revealed clues about the genetic foundation of male mating strategies in ruff. We highlighted two genes in the inverted region; HSD17B2 that affects metabolism of testosterone and MC1R that has a key role in regulating pigmentation, as the major loci associated with this adaptation.
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| 9. |
- Naboulsi, Rakan
(författare)
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Animal genomics – gene discovery and gene characterization
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis involves two projects. The aim in the first project was to identify genomic regions associated with spontaneous autoimmune thyroiditis (SAT), which is a hereditary autoimmune disease that affects the obese strain (OS) of chicken, an animal model for human Hashimoto’s thyroiditis (HT). In the second project, we study ZBED6, a highly conserved protein unique to placental mammals. Here we explore the functional significance of ZBED6 in general, and its effect on the regulation of Igf2 and miR483 in specific. To identify genomic regions predisposing to SAT, a nine-generation intercross between OS and their wild ancestor, the red junglefowl (RJF), was previously generated. In paper I, we developed a cell-based assay to phenotype the F9 chickens by measuring the TSH levels in their serum. We found that 1) SAT is similar to HT in the sense that the serum-TSH levels increase in affected individuals, and 2) that TSH levels in SAT-affected chickens starts to increase after 20 weeks of age. In paper II, a whole genome sequencing experiment was performed to compare a healthy and a severely SAT-affected groups of chicken. This analysis revealed 12 genomic loci to be significantly different between the two groups. In the second project, we utilized a mouse myoblast cell line, C2C12, to characterize the function of ZBED6. In paper III, we affect ZBED6 function, by either mutating its binding site in Igf2 (Igf2dGGCT), or by completely knocking it out (Zbed6-/-). Functional analysis of the mutant cells revealed that ZBED6 overexpression induces cell cycle arrest and apoptosis, that ZBED6 directly affects mitochondrial activity, and that ZBED6 in myoblast cells mainly exerts its effect through regulating Igf2. In paper IV, we use ZBED6 knock-out and knock-in mice to investigate the effect of ZBED6 on the regulation of miRNA expression. We found that ZBED6 is not a general regulator for miRNA, with the exception of miR483, which exists in an intron of Igf2. Thereafter, we generated miR483-/- cells, using the Igf2dGGCT cell line. In this analysis we found that the main function of miR483 in myoblast cells is to regulate the expression of Igf2, and that ZBED6 partially regulates Igf2 through regulating miR483.
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| 10. |
- Wahlberg, Per, 1975-
(författare)
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Chicken Genomics - Linkage and QTL mapping
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis presents results from genetic studies conducted in the chicken (Gallus gallus). The domestication of chicken is believed to have been initiated approximately 7,000 – 9,000 years ago in Southeast Asia. Since that time, selective breeding has altered the appearance of the wild ancestor, creating highly specialized chicken lines developed for egg and meat production. The first part of this thesis describes a detailed genetic analysis conducted on an F2 intercross between two phenotypically diverse chicken lines. The two parental lines used in this experiment originated from the same base population and have been developed by divergent selection for juvenile body-weight. Selection during forty generations has resulted in an eight-fold difference in body-weight between the High-Weight Selected (HWS) and Low-Weight Selected (LWS) line. In an attempt to identify the genetic factors differentiating the two lines, a large intercross population was bred to map Quantitative Trait Loci (QTL) affecting body-weight traits. A linkage map was constructed which included 434 genetic markers covering 31 of the 38 chicken autosomes. Although there is a dramatic phenotypic difference between the two founder lines, the QTL analysis for marginal effect could only identify seven QTL, each with small additive effects, influencing body-weight. We extended the genetic analysis to also include a model testing for pair-wise interactions between loci (epistasis). The analysis revealed 15 QTL pairs that affect body-weight and several of those formed a network of interacting loci. These results suggest that the genetic basis for the large difference in body-weight is most likely a result of a combined effect of multiple genetic factors, including QTL with small additive effects in combination with pair-wise interactions between QTL. The second part of this thesis presents two linkage maps. The first map constructed was of the chicken Z chromosome, the second used a genome-wide marker set, including 12,945 SNP markers, to build an updated consensus map of the chicken genome. The resulting consensus map includes 9,268 genetic markers and covers 33 chromosomes, still leaving five microchromosomes without marker coverage. The genome average rate of recombination was estimated to 3.1 cM/Mb, but varied considerably between and within chromosomes. A general trend of elevated recombination rates towards telomeric ends and lower rates near centromeres was observed. This was in concordance to previous reports from mammalian species. Recombination rates in chicken were also found to be highly positively correlated with GC-rich sequences.
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