| 1. |
- Tapani, Sofia, 1982
(författare)
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Stochastic modelling and analysis of early mouse development
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The aim of this thesis is to model and describe dynamical events for biological cells using statistical and mathematical tools. The thesis includes five papers that all relate to stochastic modelling of cells. In order to understand the development and patterning of the early mammalian embryo, stochastic modelling has become a more important tool than ever. It allows for studying the processes that mediate the transition from pluripotency of the embryonic cells to their differentiation. It is still unclear whether the positions of cells determine their future fates. One alternative possibility is that cells are pre-specified at random positions and then sort according to a already set fate. Mouse embryonic cells are thought to be equivalent in their developmental properties until approaching the eight-cell stage. Some biological studies show, in comparison, that patterning can be present already at sperm entry and in the pronuclei migration. We investigate in Paper I the dynamics of the pronuclei migration by analysing their trajectories and find that not only do the pronuclei follow a noise corrupted path towards the centre of the egg but they also have some attraction to each other which affects their dynamics. Continuing in Paper II and III, we use these results to model this behaviour with a coupled stochastic differential equation model. This enables us to simulate distributions that describe the meeting plane between pronuclei which in turn can be related to the orientation of the first cleavage of the egg. Our results show that adding randomness in sperm entry point is different from the randomness added through the environment of the egg. We are also able to show that data sets with normal eggs and eggs treated with an actin growth inhibitor give rise to considerably different model dynamics, suggesting that the treatment is affecting the migration in an invasive way. Altering the pronuclei dynamics can alter the polarity of the egg and may transfer into the later axis-formation process. Invasiveness of experimental procedures is a difficult issue to handle. The alternative to invasive procedures is not appealing since it means that important developmental features may not be discovered because of individual variability and noise, leading to guesswork of the underlying mechanisms. The embryonic cells are easily affected by treatments performed to make the measuring, made by hand, easier or by the light exposure of the microscope. Treatments as such are used for example for producing flourescent proteins in membranes or slowing processes down. Paper IV and Paper V serve to analyse how light induced stress affects yeast cells and we employ a method for analysing the noisy non-stationary time series, which are a result of the yeast experiments, using wavelet decomposition.
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| 2. |
- Nilsson, R. Henrik, 1976
(författare)
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Fungal taxonomy and systematics in the digital era, with an outlook on the cantharelloid clade (Basidiomycota)
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Fungi form a large and ubiquitous group of organisms where species identification and delimitation on morphological grounds often fall short. DNA sequences have proved an invaluable information source for these pursuits and are now routinely used in most mycological laboratories. Newl generated DNA sequences are typically compared with the entries of the large INSD sequence database for inference of taxonomic affiliations and other properties using the sequence similarity search tool BLAST. This thesis highlights some practical difficulties in using BLAST for these purposes it is for example very sensitive to the length of the sequences - and shows that improper use of BLAST appears to have had considerable repercussion on the general level of taxonomic reliability of the fungal sequences in INSD, more than 10% of which may be incorrectly identified to species level. An initiative to build a new DNA sequence database for taxonomically reliable DNA-based identification of mycorrhizal (plant-mutualistic) fungi is described. The database differs from similar initiatives in that its entries are determined to species level by pertinent experts; it allows for integrative sequence annotations, including photos and morphological descriptions; and it employs new, phylogeny-based tools for sequence identification to alleviate the concerns with simplistic, similarity-based tools as arbiters of taxonomic affiliation. That phylogenetic analyses can be beneficial also to classification and nomenclatural projects is shown in the mor enterprise, which is a weekly automaton of Agaricomycetes (mushroom-forming fungi) phylogeny. All fungal sequences from the nuclear ribosomal large subunit gene are assembled on a weekly basis; automated phylogenetic analyses are undertaken; and the resulting phylogenetic trees are displayed and analyzed for changes in clade topology and inclusiveness. The enigmatic cantharelloid clade of the Agaricomycetes is studied using a four-gene phylogenetic approach. While this heterogeneous assembly of mushroom-like, resupinate, clavarioid, and lichen-forming fungi defies any morphological attempt at indicating a close relatedness for its species, the results from the molecular analyses show that there is indeed strong evidence to support that these fungi form a monophyletic group; a restrictive circumscription of the clade to include the genera Botryobasidium, Sistotrema, Multiclavula, Membranomyces, Hydnum, Clavulina, Cantharellus, and Craterellus is advocated. Stichic basidia, and to a lesser extent parenthesome ultrastructure, are found to be characteristic of the clade, and the previously reported divergent rates of evolution for the genera Cantharellus and Craterellus are shown to be limited to the nuclear ribosomal genes. The largely resupinate, and purportedly wood-decaying, genus Sistotrema is demonstrated to hold mycorrhizal lineages, and the molecular evidence to consider the genus polyphyletic is found to be very convincing.
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| 3. |
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| 4. |
- Fallahshahroudi, Amir, 1981-
(författare)
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Domestication Effects on the Stress Response in Chickens : Genetics, Physiology, and Behaviour
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Animal domestication, the process where animals become adapted to living in proximity to humans, is associated with the alteration of multiple traits, including decreased fearfulness and stress response. With an estimated population of 50 billion, the domesticated chicken is the most populous avian species in the world. Hundreds of chicken breeds have been developed for meat and egg production, hobby or research purposes. Multidirectional selection and the relaxation of natural selection in captivity have created immense phenotypic diversity amongst domesticates in a relatively short evolutionary time. The extensive phenotypic diversity, existence of the wild ancestor, and feasibility of intercrossing various breeds makes the chicken a suitable model animal for deciphering genetic determinants of complex traits such as stress response. We used chicken domestication as a model to gain insights about the mechanisms that regulate stress response in an avian species. We studied behavioural and physiological stress response in the ancestral Red Junglefowl and one of its domesticated progenies, White Leghorn. An advanced intercross between the aforementioned breeds was later used to map genetic loci underlying modification of stress response. The general pattern of the stress response in chickens was comparable with that reported in mammals, however we identified distinctive differences in the stress modulatory pathways in chickens. We showed that changes in the expression levels of several stress modulatory genes in the brain, the pituitary and the adrenal glands underlie the observed modified stress response in domesticated chickens. Using quantitative trait loci (QTL) mapping, several QTL underlying stress induced corticosterone, aldosterone and baseline dehydroepiandrosterone (DHEA) levels were detected. As a next step, we combined QTL mapping with gene expression (eQTL) mapping and narrowed two QTL down to the putative causal genes, SERPINA10 and PDE1C. Both of these genes were differentially expressed in the adrenal glands of White Leghorn and the Red Junglefowl, had overlapping eQTL with hormonal QTL, and their expression levels in the adrenal glands were correlated with plasma levels of corticosterone and al-dosterone. These two genes thus serve as strong candidates for further functional investigation concerning modification of the stress response during domestication. This dissertation increase the knowledge about genetics and physiology of the stress response in an avian species and its modification during domestication. Our findings expand the basic knowledge about the stress response in chicken, which can potentially be used to improve welfare through appropriate genetic selection.
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| 5. |
- Sundman, Ann-Sofie, 1982-
(författare)
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Dog behaviour : Intricate picture of genetics, epigenetics, and human-dog relations
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Dogs, Canis familiaris, share the lives of humans all over the world. That dogs, and the behavior of dogs, are of interest to many is therefore no surprise. In this thesis, the main aim has been to identify factors that affect dogs’ behaviours.The dog, Canis familiaris, is our first domesticated animal. Since domestication, various types of dogs have developed through adaptation to an environment shared with humans and through our selective breeding, resulting in a unique variation in morphology and behaviour. Although there is an individual variation in the behaviour of dogs, there is also a difference between breeds. Moreover, selection during the last decades has split some breeds into divergent types. Labrador and golden retrievers are divided into a common type, for show and companionship, and a field type, for hunting. By comparing the breed types, we can study the effects of recent selection. In Paper I, we investigate differences in general behavioural traits between Labrador and golden retriever and between common and field type within the two breeds by using results from the standardized behaviour test Dog Mentality Assessment. There were differences between breeds and types for all behavioural traits. However, there was also an interaction between breed and type. Thus, a common/field-type Labrador does not behave like a common/field-type golden retriever. Even though they have been selected for similar traits, the selection has affected the general behavioural traits differently in the two breeds.In paper II, we were interested in dogs’ human-directed social skills. Dogs have a high social competence when it comes to humans. Two experiments commonly used to study these skills are the problem-solving test, where dogs’ human-directed behaviours when faced with a problem are measured, and the pointing test, where dogs are tested on how well they understand human gestures. We compared the social skills of German shepherds and Labrador retrievers, and of common- and field-type Labradors. Labradors were more successful in the pointing test and German shepherds stayed closer to their owners during the problem solving. Among Labrador types, the field type had more human eye contact than the common type. Importantly, when comparing the two experiments, we found no positive correlations between the problem-solving test and the pointing test, suggesting that the two tests measure different aspects of human-directed social behaviour in dogs.A previous study has identified two suggestive genetic regions for human-directed social behaviours during the problem-solving test in beagles. In paper III, we show that these SNPs are also associated to social behaviours in Labrador and golden retrievers. Moreover, the Labrador breed types differed significantly in allele frequencies. This indicates that the two SNPs have been affected by recent selection and may have a part in the differences in sociability between common and field type.The behaviour of dogs cannot simply be explained by genetics, there is also an environmental component. In paper IV, we study which factors that affect long-term stress in dogs. Long-term cortisol can be measured by hair samples. We found a clear synchronization in hair cortisol concentrations between dogs and their owners. Neither dogs’ activity levels nor their behavioural traits affected the cortisol, however, the personality of the owners did. Therefore, we suggest that dogs mirror the stress level of their owners.The mediator between genes and the environment is epigenetics, and one epigenetic factor is DNA methylation. In paper V, we compared methylation patterns of wolves and dogs as well as dog breeds. Between both wolves and dogs and among dogs there were substantial differences in methylated DNA regions, suggesting that DNA methylation is likely to contribute to the vast variation among canines. We hypothesize that epigenetic factors have been important during domestication and in breed formation.In this thesis, I cover several aspects on how dogs’ behaviours can be affected, and paint an intricate picture on how genetics, epigenetics, and human-dog relations forms dog behaviour.
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| 6. |
- Roufidou, Chrysoula, 1987-
(författare)
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Reproductive physiology of the female three-spined stickleback, Gasterosteus aculeatus
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Reproduction in vertebrates, including fishes, is under control of the brain-pituitary-gonad (BPG) axis. The female three-spined stickleback, Gasterosteus aculeatus, produces egg clutches at intervals of a few days and spawns them in a nest built by male. Following ovulation, eggs are stored in the ovarian cavity surrounded by the ovarian fluid (OF). If spawning or spontaneous release do not occur, the eggs can undergo overripening, a phenomenon occurring both in nature and captivity.In this PhD thesis, the changes of reproductive hormones and vitellogenesis were studied at overripening of eggs and over the natural spawning cycle. OF properties were also examined at overripening of eggs and after treatment with sex steroids.Plasma levels of steroids: testosterone (T), estradiol (E2), 17,20β-dihydroxypregn-4-en-3-one (17,20β-P) and 17,20β,21-trihydroxypregn-4-en-3-one (17,20β,21-P) were measured by radioimmunoassay, and relative mRNA levels of the pituitary gonadotropins (fsh-β/lh-β), brain gonadotropin-releasing hormones (gnrh2/gnrh3) and kisspeptin and its receptor (kiss2/gpr54) by qPCR. Overripening of eggs was accompanied with a significant reduction in most of endocrine parameters of BPG axis (T, E2, 17,20β-P; lh-β; kiss2, gpr54). Low level of hormones could be advantageous for the overripe egg-bound females, since this would reduce further ovulations giving higher chances to survive and reproduce again. Over the 3-day spawning cycle, T and E2 were highly correlated, showed cyclicity with low levels at ovulation and increasing from 24 and 6 hours post-spawning (hps), respectively. Spawning may give rise to this increase as these rises did not occur if release of the eggs does not happen (overripe females). A peak at pituitary lh-β mRNA levels appeared 48 hps, a day before the next ovulation. No significant changes were found for the other studied hormones.Vitellogenesis was studied by measurement of the vitellogenin mRNA levels in the liver by qPCR. The levels were highest at 24 and 48 hps and were positively correlated to both E2 and T over the cycle. However, changes were small suggesting a rather continuous vitellogenesis over the stickleback spawning cycle which could be an advantage for a multiple spawner with a limited spawning season. Overripening reduced vitellogenin mRNA levels but did not abolish it.OF amount was diminished in overripe females and had a lower viscocity but higher dry weight and protein levels than in non-overripe ovulated females, suggesting that changes in OF properties are related to the egg overripening. The effects of steroids were studied using Silastic capsules. T and 17,20β-P induced an increase of OF amount, but protein levels were only increased in 17,20β-P-treated females, proposing a role of this steroid in the control of OF secretion. 1-D SDS-PAGE showed that OF contained several proteins, some of them came from eggs, but no consistent differences between groups.Concluding, the knowledge of the reproductive physiological changes is important for understanding their essential roles in the production of viable eggs in this species but also in the reproductive physiology of female fishes in general.
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| 7. |
- Gräns, Albin, 1979
(författare)
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The Effects of Temperature on Gut Blood Flow and Gut Motility in Fish
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In order for a fish to grow and thrive, the gut must function efficiently. This is achieved through a range of processes, including controlled patterns of gut motility and modifications in gut blood flow. How these processes are affected by long and short-term changes in ambient temperature was the main focus of this thesis. After acclimation to a higher temperature, the interdigestive motility of rainbow trout was higher. This indicates an increased demand for movements involved in the housekeeping functions of the gut. Temperature acclimation did not affect the postprandial response, in neither gut blood flow nor gut motility. These results indicate that thermal compensation processes work to neutralize acute thermal effects, so that these two functions are maintained at a certain rate. Also, in vitro preparations of isolated intestine showed signs of thermal compensation processes, as the acute temperature effects on the response to the cholinergic agonist carbachol were abolished after a temperature acclimation period. Fish species studied responded very differently to an acute change in temperature. A relatively linear correlation with temperature was seen in, both gut blood flow and gut motility, in two species of sculpins (shorthorn and Arctic sculpin). The gut blood flow, in both green and white sturgeon, was unaffected by moderate fluctuations in water temperature during the interdigestive state. White sturgeon were also studied after feeding and a correlation between gut blood flow and temperature was observed, in a similar fashion as for the unfed sculpins. Thermoregulatory behaviours observed in white sturgeon, show that moving between different temperatures, after a meal, will have a great influence on the volume of blood distributed to the gut. An increase in gut blood flow is probably an important factor explaining why it can be beneficial to migrate into warmer waters after feeding. However, if combining the presented data with data from previous studies, it shows that perfusion of the gut can also be a limiting factor when the environmental temperature changes. This is probably the reason why some fish species forage in warm waters and then move into colder areas when digesting the meal. A leading hypothesis suggests that the temperature limitations for a fish are mainly set by a reduction in metabolic scope. However, experimental data has shown that temperature can have significant effects on both appetite and growth before metabolic scope is reduced. The findings in this thesis suggest that oxygen-limited thermal tolerance in the gut of fish could also be a significant variable in determining the temperature range that fish can tolerate.
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| 8. |
- Martinsson, Svante, 1985
(författare)
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Exploring the species boundaries in terrestrial clitellates (Annelida: Clitellata)
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The biological diversity in the soil is much higher than most people can imagine, and a very important group of animals living there are earthworms and other clitellate worms. It has been found that several clitellate morphospecies are in fact complexes of so called cryptic species, and the number of species in this group may be much higher than previously believed. In this thesis, I explore the species boundaries of terrestrial clitellates by combining various data sources and methods as a basis for taxonomical decisions. A widely used approach for studying cryptic species is DNA-barcoding, where a single standardised marker is used for the identification of organisms and discovering new species. For animals, the marker generally used is the mitochondrial COI gene. In the thesis, I present four different cases, from three different clitellate families: 1) A variety of Rhyacodrilus falciformis was shown to be a distinct species, whereas other COI clusters were found to be part of the same species. 2) Extensive cryptic diversity was found in the genus previously known as Cognettia, a group that includes C. sphagnetorum, a well-studied model in soil biology. This taxon and C. glandulosus were both found to be complexes of cryptic species. The generic taxonomy of Cognettia was revised and the genus split into its two senior synonyms, Euenchytraeus and Chamaedrilus, and the species in the C. sphagnetorum complex were revised and described. 3) In the earthworm Aporrectodea longa, two well separated COI lineages were found to be part of the same species. 4) In the earthworm genus Lumbricus, the previously noted split between L. terrestris and L. herculeus was verified using nuclear data, and in the morphospecies L. rubellus seven cryptic species were found. The first evidence of limited hybridisation within the genus was also found, between L. terrestris and L. herculeus, as well as and between species within L. rubellus s.lat. To conclude, I have shown that the species diversity among terrestrial clitellates is larger than previously known based on morphology, and that species can be robustly delimited using a combination of mitochondrial and nuclear markers, supported with morphology. I have also found that using DNA-barcoding alone will often overestimate the number of clitellate species, and caution is required when using it.
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| 9. |
- Andersson, Anastasia, 1987-
(författare)
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Hidden biodiversity in an alpine freshwater top predator : Existence, characteristics, and temporal dynamics of cryptic, sympatric brown trout populations
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Intraspecific genetic diversity is imperative to the survival of species in a changing environment, and it plays a vital role in ecosystem function. Since this type of diversity can be difficult to detect it is sometimes referred to as “hidden biodiversity”. When separate and genetically distinct populations of the same species coexist within the same habitat, without apparent barriers to migration and obvious phenotypic divergence, this form of hidden biodiversity is called cryptic sympatry. Knowledge of cryptic sympatry is limited, however, and the aim of this thesis is to increase our understanding of this phenomenon by focusing on a species group where several cases of sympatry have been documented – the salmonids.Using the brown trout (Salmo trutta) as a model, I characterized two previously reported cases of cryptic sympatry occurring in small Swedish alpine lakes with respect to both phenotypic and genetic characteristics. I explored the hypothesis that cryptic sympatry is more common than currently recognized by reviewing literature documenting sympatry, as well as by assessing the statistical power to detect sympatric populations with varying degrees of divergence using commonly applied sample sizes for loci and individuals. Further, I performed a large-scale search for sympatric populations in alpine lakes in central Sweden.I found that cryptic, sympatric populations can coexist while apparently utilizing the same food resources and exhibiting the same adaptive plasticity to their shared environment (Paper I). In one of the empirical cases there were indications that the populations used different creeks for spawning, suggesting that segregation in spawning location contributes to the maintenance of sympatry (Paper II). Further, I found that differences between cryptic, sympatric populations of the same lake may be large with respect to levels of genetic diversity, inbreeding, and connectivity with populations in nearby lakes (Papers II and III). I found support for the hypothesis that cryptic sympatry is more common than generally acknowledged (Papers IV and V). In the literature, cryptic sympatry is rarely reported and typically associated with higher divergence levels than between sympatric populations that differ phenotypically. My results suggest that this to a large extent may be due to limited statistical power when commonly used sample sizes in terms of individuals and loci are applied and the amount of divergence between populations is small (Paper IV). Cryptic sympatry was observed in over 40% of the screened localities (27 lakes), and was shown to be temporally stable over at least 40 years (Paper V).
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| 10. |
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