| 1. |
- Lagman, David, 1987-
(författare)
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Evolution of Vertebrate Vision by Means of Whole Genome Duplications : Zebrafish as a Model for Gene Specialisation
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The signalling cascade of rods and cones use different but related protein components. Rods and cones, emerged in the common ancestor of vertebrates around 500 million years ago around when two whole genome duplications took place, named 1R and 2R. These generated a large number of additional genes that could evolve new or more specialised functions. A third event, 3R, occurred in the ancestor of teleost fish. This thesis describes extensive phylogenetic and comparative synteny analyses of the opsins, transducin and phosphodiesterase (PDE6) of this cascade by including data from a wide selection of vertebrates. The expression of the zebrafish genes was also investigated. The results show that genes for these proteins duplicated in 1R and 2R as well as some in 3R.Expression analyses of the zebrafish genes revealed additional specialisations for the 3R gene duplicates. The transducin beta subunit genes, gnb1a and gnb1b, show co-localisation in rods but are expressed at different levels. Gnb3a and gnb3b show different expression in the adult retina with low expression of gnb3a and expression of gnb3b in cones of the dorso-medial retina. The transducin gamma subunit genes gngt2a and gngt2b are expressed in the ventral and dorso-medial retina respectively. The both of PDE6 gamma subunit genes, pde6ga and pde6gb are both expressed in rods but pde6ga shows rhythmic changes of expression with low daytime levels. Pde6ha and pde6hb are expressed in cones however pde6ha show high daytime expression. All investigated transducin and PDE6 subunit genes, but gnb1b, were also expressed in the adult pineal complex or at some point during development.These results provide compelling evidence that the 1R and 2R genome duplications facilitated the evolution of rods and cones by generating gene duplicates that could evolve distinct expression and function. This supports existence of colour vision before the origin of vertebrates, elaboration of this in the early vertebrate ancestor, along with origin of the black-and-white dim-light vision of rods. Furthermore, the different expression patterns observed in the zebrafish retina for teleost 3R duplicates demonstrate multiple additional specialisations.
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| 2. |
- Wargelius, Hanna-Linn
(författare)
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The Relation between Serotonergic Biomarkers and Behaviour : – studies on human primates, non-human primates and transgenic mice
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Rationale: The serotonergic system is involved in the modulation of emotion and plays an important role for personality and vulnerability for psychiatric disorders. In the papers included in this thesis, we investigate three biological factors that have been studied in relation to psychiatric symptoms: Platelet monoamine oxidase B (MAO-B) activity, and variations in the MAO-A and the serotonin transporter (5HTT) genes. We also study intensity dependent auditory evoked potentials (IAEP) as an intermediate phenotype for serotonergic capacity. Platelet MAO-B has been shown to be a biological marker for the properties of monoamine systems, with low activity being associated with vulnerability for high scores of sensation seeking, monotony avoidance, and impulsiveness, as well as for susceptibility for alcoholism. Functional polymorphisms in the promoter of the genes encoding MAO-A and the serotonin transporter result in high- or low- activity alleles that have been associated with numerous psychiatric symptoms. One hypothesis for the shaping of personality is that these genotype variants have prenatal effects on the wiring of the brain. Thus, exploring how the development of the brain is affected by different prenatal serotonin levels is relevant in this context. Observations: (i) Platelet MAOB activity was associated with monoamine metabolites in cerebrospinal fluid from cisterna magna in monkeys, as well as with voluntary alcohol intake, alcohol-induced aggression, and alcohol sensitivity. (ii) The long 5HTTLPR allele was associated with increased IAEP. (iii) The functional MAOA and 5HTT polymorphisms were associated with symptoms of ADHD-related traits in a population based sample of Swedish adolescents. Associations of these candidate genes with ADHD scores were strenghtened when the platelet MAOB activity was combined with genotype. (iv) Our pilot data showed that treatment of pregnant mice with 5HTT blocking antidepressives resulted in more serotonergic cellbodies in lateral wings of dorsal raphe in the offspring, when compared to saline treatment. Conclusions: Our studies support the notion that platelet MAOB activity and IAEP are endophenotypes for monoaminergic capacity and related behaviours. The functional candidate polymorphisms in MAOA and 5HTT were linked to behaviour, however, the cause-relationship is unclear and the explanation for the associations need to be further investigated, possibly with focus on prenatal effects of the polymorphisms.
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| 3. |
- Ocampo Daza, Daniel, 1984-
(författare)
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Evolution of Vertebrate Endocrine and Neuronal Gene Families : Focus on Pituitary and Retina
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The duplication of genes followed by selection is perhaps the most prominent way in which molecular biological systems gain multiplicity, diversity and functional complexity in evolution. Whole genome duplications (WGDs) therefore have the potential of generating an extraordinary amount of evolutionary innovation. It is now accepted that the vertebrate lineage has gone through two rounds of WGD in its early stages, after the divergence of invertebrate chordates and before the emergence of jawed vertebrates. These basal vertebrate WGDs are called 2R for two rounds of whole genome duplication. An additional WGD called 3R occurred early in the evolution of teleost fishes, before the radiation of this species-rich group. This thesis describes the evolution of several endocrine and neuronal gene families in relation to the vertebrate WGDs, through a comparative genomic approach including both phylogenetic analyses and chromosomal location data across a wide range of vertebrate taxa.These results show that numerous endocrine gene families have expanded in 2R and in several cases also in 3R. These include the gene families of oxytocin and vasopressin receptors (OT/VP-R), somatostatin receptors (SSTR) and insulin-like growth factor binding proteins (IGFBP). For the OT/VP-R and SSTR families, previously undescribed subtypes were identified. The protein hormone family that includes growth hormone (GH), prolactin (PRL) and somatolactin (SL) acquired a new PRL gene in 2R, however the origins of GH, PRL and SL likely predate 2R. The corresponding family of receptors diversified during different time periods through a combination of local duplications and 3R.Neuronal gene families of the visual system have also expanded in 2R and 3R. The results presented here demonstrate that the vertebrate repertoire of visual opsin genes arose in 2R as part of chromosomal blocks that also include the OT/VP-R genes. The gene families including the transducin alpha, beta and gamma subunits also arose in 2R, hinting at the importance of these events in the diversification and specialization of phototransduction cascades for rods and cones.Thus, the whole genome duplications have been important contributors to the evolution of both vision and endocrine regulation in the vertebrates.
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| 4. |
- Shebanits, Kateryna
(författare)
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The human pancreatic polypeptide receptor Y4 : Genetic and functional variation
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Humans are evolutionarily adapted to an environment where food is scarce, but today many live in a world of food abundance. Paired with low physical activity, this may lead to weight gain and obesity. Efficient anti-obesity treatments require understanding of the mechanisms that control hunger, satiety, energy metabolism and body weight. This thesis investigates possible genetic and physiological mechanisms behind these processes.Genetic correlation between body-mass index (BMI) and a highly polymorphic region on chromosome 10 was analysed with regard to single nucleotide polymorphisms (SNPs) and gene copy number variation (CNV). This region contains the gene NPY4R encoding the pancreatic polypeptide (PP) receptor Y4, which has been reported to reduce appetite.The results show that the NPY4R gene was duplicated before the divergence of modern humans from the Neanderthals and the Denisovans (approximately to 400,000–800,000 years ago). The CNV of the NPY4R gene region was investigated by read depth analysis based on genome sequences and droplet digital PCR (ddPCR). The read depth results revealed a CNV range of 3-7 copies per genome, while the ddPCR results demonstrated a range of 2–11. Most humans have a total of 4–5 copies, in contrast to the two copies presumed by previous studies.Investigation of an association between the NPY4R CNV and body mass index (BMI) led to interesting and ambiguous results. A study of 558 Swedish individuals with a wide range of BMI suggested, surprisingly, a positive correlation between NPY4R copy number and BMI for women. On the other hand, a study of 1009 individuals from Northern Sweden found no correlation between BMI and NPY4R copy number. These diverging findings may be due to geographical variation or lack of power in one of these studies.Twelve naturally-occurring amino acid variants of the Y4 receptor were investigated pharmacologically in cell culture. Three of these showed no functional response, which may be explained by altered conformation of the receptors. For two receptor variants PP had a significantly decreased potency. A 3D model of the Y4 receptor was generated based on the crystal structure of the human Y1 receptor. The functional responses of the Y4 variants agree well with the 3D model and with the degree of evolutionary conservation of the positions.In conclusion, these studies reveal unexpectedly large CNV as well as extensive SNP for the NPY4R gene and a possible correlation with BMI that may be due to the differing responses of the naturally occurring receptor variants.
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| 5. |
- Sundström, Görel, 1977-
(författare)
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Evolution of the Neuropeptide Y and Opioid Systems and their Genomic Regions
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Two whole genome duplications (2R) occurred early in vertebrate evolution. By using combined information from phylogenetic analyses and chromosomal location of genes, this thesis delineates the evolutionary history of two receptor-ligand systems that expanded by these large scale events. A third whole genome duplication (3R) took place in the teleost fish lineage and has also contributed to the complexity of the gene families. New members of neuropeptide Y (NPY) peptide and receptor families were generated in 2R and 3R. Evolutionary comparisons show that the ancestral teleost fish had four peptides; subsequently, differential losses of the peptide genes occurred. In zebrafish the peptides and receptors display differences in tissue distribution and have evolved binding preferences. In the frog Silurana tropicalis three peptides and six receptors werev identified, also displaying some differences in tissue distribution and receptor-ligand preferences. The findings in these experimental animals highlight both evolutionary conservation and lineage-specific features of the NPY system. The opioid system consists of four receptors and several peptides originating from four precursors. These results show that the receptor family was formed in 2R and 3R and that 2R together with one local duplication gave rise to the peptide family. The ancestral receptor and peptide genes were located on the same chromosome, suggesting coevolution. The Hox gene clusters, important in early development, provided the first strong evidence for 2R. Several neighboring gene families were analyzed and found to have expanded in 2R and 3R. In depth analyses of insulin-like growth factor binding protein (IGFBP) and voltage-gated sodium channel (SCN) gene families illustrates the importance of local duplications in combination with whole genome duplications in the formation of gene families. These findings provide additional strong evidence for two genome duplications in early vertebrate evolution and show that these events generated many new genes that could evolve new or more specialized functions.
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| 6. |
- Xu, Bo, 1980-
(författare)
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Evolutionary and Pharmacological Studies of NPY and QRFP Receptors
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The neuropeptide Y (NPY) system consists of 3-4 peptides and 4-7 receptors in vertebrates. It has powerful effects on appetite regulation and is involved in many other biological processes including blood pressure regulation, bone formation and anxiety. This thesis describes studies of the evolution of the NPY system by comparison of several vertebrate species and structural studies of the human Y2 receptor, which reduces appetite, to identify amino acid residues involved in peptide-receptor interactions.The NPY system was studied in zebrafish (Danio rerio), western clawed frog (Xenopus tropicalis), and sea lamprey (Petromyzon marinus). The receptors were cloned and functionally expressed and their pharmacological profiles were determined using the native peptides in either binding studies or a signal transduction assay. Some peptide-receptor preferences were observed, indicating functional specialization.A receptor family closely related to the NPY receptors, called the QRFP receptors, was investigated. A QRFP receptor was cloned from amphioxus, Branchistoma floridae, showing that the receptor arose before the origin of the vertebrates. Evolutionary studies demonstrated that the ancestral vertebrate had as many as four QRFP receptors, only one of which remains in mammals today. This correlates with the NPY receptor family, located in the same chromosomal regions, which had seven members in the ancestral vertebrate but only 4-5 in living mammals. Some vertebrates have considerably more complex NPY and QRFP receptor systems than humans and other mammals.Two studies investigated interactions of NPY-family peptides with the human Y2 receptor. Candidate residues, selected based on structural modeling and docking, were mutated to disrupt possible interactions with peptide ligands. The modified receptors were expressed in cultured cells and investigated by measuring binding and functional responses. Several receptor residues were found to influence peptide-receptor interactions, some of which are involved in maintaining receptor structure. In a pilot study, the kinetics of peptide-receptor interaction were found to be very slow, of the order several hours.In conclusion, this thesis clarifies evolutionary relationships for the complex NPY and QRFP peptide-receptor systems and improves the structural models of the human NPY-family receptors, especially Y2. These results will hopefully facilitate drug design for targeting of NPY-family receptors.
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| 7. |
- Dyakova, Olga
(författare)
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The processing of natural images in the visual system
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Any image can be described in terms of its statistics (i.e. quantitative parameters calculated from the image, for example RMS-contrast, the skewness of image brightness distribution, and slope constant of an average amplitude spectrum).It was previously shown that insect and vertebrate visual systems are optimised to the statistics common among natural scenes. However, the exact mechanisms of this process are still unclear and need further investigation.This thesis presents the results of examining links between some image statistics and visual responses in humans and hoverflies.It was found that while image statistics do not play the main role when hoverflies (Eristalis tenax and Episyrphus balteatus) chose what flowers to feed on, there is a link between hoverfly (Episyrphus balteatus) active behaviours and image statistics. There is a significant difference in the slope constant of the average amplitude spectrum, RMS contrast and skewness of brightness distribution between photos of areas where hoverflies were hovering or flying. These photos were also used to create a prediction model of hoverfly behaviour. After model validation, it was concluded that photos of both the ground and the surround should be used for best prediction of behaviour. The best predictor was skewness of image brightness distribution.By using a trackball setup, the optomotor response in walking hoverflies (Eristalis tenax) was found to be influenced by the slope constant of an average amplitude spectrum. Intracellular recording showed that the higher-order neuron cSIFE (The centrifugal stationary inhibited flicker excited) in the hoverfly (Eristalis tenax) lobula plate was inhibited by a range of natural scenes and that this inhibition was strongest in a response to visual stimuli with the slope constant of an average amplitude spectrum of 1, which is the typical value for natural environments. Based on the results of psychophysics study in human subjects it was found that sleep deprivation affects human perception of naturalistic slope constants differently for different image categories (“food” and “real world scenes”).These results help provide a better understanding of the link between visual processes and the spatial statistics of natural scenes.
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| 8. |
- Fällmar, Helena, 1980-
(författare)
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Studies of the Neuropeptide Y Receptor Y2 in Human and Zebrafish
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The G-protein coupled receptors (GPCRs) comprise the largest family of receptors in humans and other vertebrates. They are embedded in the cell membrane and are activated by many different signaling molecules. Activation modulates cellular signal transduction pathways and influences many physiological processes. Therefore the GPCRs are important as targets for numerous drugs. The receptors for NPY (neuropeptide Y) belong to GPCRs of Class A (rhodopsin-like). NPY and its related peptides PYY and PP are involved in the regulation of appetite, blood pressure and many other processes. They share a common structure and interact with the receptors Y1, Y2, Y4 and Y5 in mammals, and, in addition, Y7 and Y8 in amphibians and bony fishes. This thesis is focused on the human Y2 receptor, known to reduce appetite, by investigating the importance of thirteen amino acid residues for ligand binding. Mutagenesis followed by functional expression and receptor binding was conducted. During the course of this work several new GPCR crystal structures have been resolved, thereby improving the receptor modeling in papers I-III. The major finding is that even though the Y1 and Y2 receptors have evolved from a common ancestor, their points of ligand interaction differ and have thus changed during evolution. In general, the positions investigated resulted in milder changes in the ligands’ affinities for Y2 compared to Y1. These findings were incorporated in the design of new Y1 and Y2 receptor models, leading to improved understanding of how such divergent receptors, sharing only 30 percent sequence identity, can still interact with the same ligands. Notably, several of the mutations introduced in Y2 resulted in increased affinity. A novel NPY receptor gene named Y2-2 was identified in the genomes of zebrafish and medaka. This brings the number of zebrafish NPY receptors to seven. The binding characteristics of zebrafish Y2-2 differed from zebrafish Y2 mainly in the interaction with NPY13-36 and the antagonist BIIE0246. In conclusion, these results increase our understanding of ligand interactions with GPCRs and will be useful for refinement of ligand-receptor models for future development of receptor subtype-selective drugs.
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| 9. |
- Göktürk, Camilla, 1967-
(författare)
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Semicarbazide-sensitive Amine Oxidase (SSAO) – Regulation and Involvement in Blood Vessel Damage with Special Regard to Diabetes : A Study on Mice Overexpressing Human SSAO
- 2004
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Semicarbazide-sensitive amine oxidase (SSAO, EC 1.4.3.6) belongs to a family of copper-containing amine oxidases. SSAO exists as a membrane bound protein in endothelial-, smooth muscle-, and adipose cells as well as soluble in plasma. SSAO catalyses oxidative deamination of primary monoamines, which results in the production of corresponding aldehydes, hydrogen peroxide and ammonia. These compounds are very reactive and potentially cytotoxic, and are able to induce vascular damage if produced in high levels. Patients with diabetes mellitus, and with diabetic complications in particular, have a higher SSAO activity in plasma compared to healthy controls. It has therefore been speculated that high SSAO activity is involved in the development of vascular complications associated with diabetes. The aim of this thesis is to investigate the importance of SSAO in the development of disorders of a vascular origin. We have studied the transcriptional regulation of the SSAO gene, by inducing diabetes in NMRI and in transgenic mice, overexpressing the human form of SSAO in smooth muscle cells. We found that the increase in SSAO activity in diabetes is accompanied by reduced mRNA levels of the endogenous mouse gene, suggesting a negative feedback on the transcription of the SSAO gene. In addition, the transgenic mice exhibited an abnormal phenotype in the elastic tissue of aorta and renal artery. These mice have a lower mean artery pressure and an elevated pulse pressure. These results indicate that high SSAO activity in smooth muscle cells is associated with a change in the morphology of large arteries. This is likely contributing to the development of vascular complications in diabetes.
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| 10. |
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