<p>Analysis of genetic relatedness is of great importance in forensic casework such as immigration and identification cases. The conventional methods for relationship testing are not sufficient in the most complicated cases, because more genetic markers are required to obtain results with satisfactory statistical security. This study demonstrates that microarrays, which can be used to genotype thousands of single nucleotide polymorphisms (SNPs), could be a promising solution to this problem. The microarray technique used in this study performed very well on blood samples and also worked well in combination with whole genome amplification, but did not generate any results when used on severely degraded materials.</p><p>Markers suitable for relatedness analysis were selected from the microarray and were successfully tested on families with known genetic relations. Although a maximum of 64 autosomal markers were used, there is a great potential of selecting the hundreds or thousands of markers that may be required in some cases of relatedness investigation.</p>

<p>This thesis describes the application of multivariate methods in analyses of genomic DNA sequences, gene expression and protein synthesis, which represent each of the steps in the central dogma of biology. The recent finalisation of large sequencing projects has given us a definable core of genetic data and large-scale methods for the dynamic quantification of gene expression and protein synthesis. However, in order to gain meaningful knowledge from such data, appropriate data analysis methods must be applied.</p><p>The multivariate projection methods, principal component analysis (PCA) and partial least squares projection to latent structures (PLS), were used for clustering and multivariate calibration of data. By combining results from these and other statistical methods with interactive visualisation, valuable information was extracted and further interpreted.</p><p>We analysed genomic sequences by combining multivariate statistics with cytological observations and full genome annotations. All oligomers of di- (16), tri- (64), tetra- (256), penta- (1024) and hexa-mers (4096) of DNA were separately counted and normalised and their distributions in the chromosomes of three Drosophila genomes were studied by using PCA. Using this strategy sequence signatures responsible for the differentiation of chromosomal elements were identified and related to previously defined biological features. We also developed a tool, which has been made publicly available, to interactively analyse single nucleotide polymorphism data and to visualise annotations and linkage disequilibrium.</p><p>PLS was used to investigate the relationships between weather factors and gene expression in field-grown aspen leaves. By interpreting PLS models it was possible to predict if genes were mainly environmentally or developmentally regulated. Based on a PCA model calculated from seasonal gene expression profiles, different phases of the growing season were identified as different clusters. In addition, a publicly available dataset with gene expression values for 7070 genes was analysed by PLS to classify tumour types. All samples in a training set and an external test set were correctly classified. For the interpretation of these results a method was applied to obtain a cut-off value for deciding which genes could be of interest for further studies.</p><p>Potential biomarkers for the efficacy of radiation treatment of brain tumours were identified by combining quantification of protein profiles by SELDI-MS-TOF with multivariate analysis using PCA and PLS. We were also able to differentiate brain tumours from normal brain tissue based on protein profiles, and observed that radiation treatment slows down the development of tumours at a molecular level.</p><p>By applying a multivariate approach for the analysis of biological data information was extracted that would be impossible or very difficult to acquire with traditional methods. The next step in a systems biology approach will be to perform a combined analysis in order to elucidate how the different levels of information are linked together to form a regulatory network.</p>

<p>Predisposition to autoimmune diseases such as, rheumatoid arthritis, diabetes, and multiple sclerosis, is caused by the effect of multiple genes and a strong influence from the environment. </p><p>In this study, I have investigated genetic factors that confer susceptibility to rheumatoid arthritis in a rat model. This work has led to the identification of several chromosomal regions, containing uncharacterized genes that directly or indirectly are associated to the arthritis development in these rats. We have observed that timing, gender, and genetic interactions are features that play a part in the effect that these genetic factors exert. </p><p>Unarguably, animal models for human disorders display differences to the human form of disease. An important fact is however that the same chromosomal regions are identified in both rodent and human studies, which suggests that there are genetic factors that we have in common, which are involved directly or indirectly with an autoimmune response. </p><p>Focusing the interest on these similarities, and on the possibility to apply a wide set of genetic tools, make animal models an invaluable, and probably necessary, instrument to dissect the genetic component of complex disorders. To fully comprehend the genetic basis for a complex disorder like this, will require understanding of how multiple genes interact with each other to cause disease. </p><p>We have been able to demonstrate that chronic arthritis, in a rat model for rheumatoid arthritis, is regulated by several genes and that these act during different temporal phases of the disease. These findings will hopefully contribute to our understanding of the etiology and progression of rheumatoid arthritis.</p>

<p>Synthetic and physicochemical studies on appropriately functionalized ODN-conjugates have been performed to evaluate their abilities to act as antisense agents against RNA or as intramolecular DNA cross-linking agents. Intercalating aromatic systems [phenazine (Pnz), dipyridophenazine (DPPZ)] and metallointercalators such as Ru²⁺(phen)₂(DPPZ) and Ru²⁺(tpy)(DPPZ)<b>L</b> [where <b>L</b> = chemically or photochemically labile ligand, phen = phenanthroline, tpy = terpyridine], which are covalently tethered to the oligo-deoxynucleotides (ODNs), have been chosen for this purpose. The ODN-conjugates were typically prepared by automated solid phase synthesis using phosphoramidite building blocks, or on solid supports, both functionalized with the chromophore groups. The photosensitive metal complex, Ru²⁺(tpy)(DPPZ)(CH₃CN), has been incorporated by post-synthetic coupling to the amino-linker modified ODNs <i>via</i> an amide bond. The intercalating ability of the tethered chromophores gave enhanced stability of the duplexes and triplexes formed with ODN-conjugates and their complementary targets: DNA, RNA, or double-stranded DNA. The conjugation of DPPZ chromophore to ODN (at 3', 5' or at the middle) led us to incorporate Ru²⁺(phen)₂(DPPZ) through the DPPZ ligand, for the first time. The corresponding (Ru²⁺-ODN)•DNA duplexes showed dramatic stabilization (ΔT_m = 19.4 – 22.0ºC). The CD and DNase I footprinting experiments suggest that the stabilization is owing to metallointercalation by threading of the Ru²⁺(phen)₂ moiety through the ODN•DNA duplex core, thus "stapling" the two helical strands from the minor to major groove. On the other hand, Ru²⁺(tpy)(DPPZ)(CH₃CN)-ODN conjugates represent a new class of oligonucleotides containing the photoactivatible Ru²⁺ complexes, which can successfully crosslink to the complementary strand. The mechanism of cross-linking upon photoirradiation of [Ru²⁺(tpy)(DPPZ)(CH₃CN)-ODN]•DNA involves <i>in situ</i> conversion to the reactive [Ru²⁺(tpy)(DPPZ)(H₂O)-ODN]•DNA which are subsequently cross-linked through the G residue of the complementary DNA strand. All starting materials and products have been purified by HPLC and/or by PAGE and subsequently characterized by MALDI-TOF as well as ESI mass spectroscopy. Terminal conjugation of the planar Pnz and DPPZ groups through the flexible linkers were also shown to improve thermal stability of the ODN•RNA hybrid duplexes without alteration of the initial AB-type global helical structure as revealed from CD experiments. As a result, RNase H mediated cleavage of the RNA strand in the intercalator-tethered ODN•RNA duplexes was more efficient compared to the natural counterpart. The RNase H cleavage pattern was also found to be dependent on the chemical nature of the chromophore. It appeared that introduction of a tether at the 3'-end of the ODN can be most easily tolerated by the enzyme regardless of the nature of the appending chromophore. The tethered DPPZ group has also been shown to chelate Cu²⁺ and Fe³⁺, like phenanthroline group, followed by the formation of redox-active metal complex which cleaves the complementary DNA strand in a sequence-specific manner. This shows that the choice of appropriate ligand is useful to (i) attain improved intercalation giving Tm enhancement, and (ii) sequence-specifically inactivate target RNA or DNA molecules using multiple modes of chemistry (RNase H mediated cleavage, free-radical, oxidative pathways or photocross-linkage).</p>

<p>This thesis focuses on the identification of genetic factors underlying two inherited human phenotypes: hearing loss and monoamine oxidase activity. </p><p>Non-syndromic hearing loss segregating in a Swedish family was tested for linkage to 13 previously reported candidate loci for hearing disabilities. Linkage was found to two loci: DFNA12 (llq22-q24) and DFNA2 (lp32). A detailed analysis of the phenotypes and haplotypes shared by the affected individuals supported the hypothesis of digenic inheritance of hearing disability in the Swedish family. Mutation screening of α-tectorin, a gene residing within the DFNA12 region revealed a mutation of a conserved amino acid (Cys to Ser), that segregated with the disease. The identification of the mutation added support to the involvement of α-tectorin in hearing disabilities. In contrast, no mutations were identified in two candidate genes at the DFNA2 locus, that were reported to cause hearing loss in other families. It is possible that the DFNA2 locus contains a third, not yet identified, hearing loss gene. </p><p>Monoamine oxidase A (MAOA) and B (MAOB) catalyze the degradation of certain neurotransmitters in the central nervous system and are associated with specific behavioral and neuropsychiatric human traits. Activity levels of both monoamine oxidases (MAO) are highly variable among humans and are determined by unknown genetic factors. This study investigated the relationship of different MAO alleles with MAO mRNA levels and enzyme activity in human brain. Several novel DNA polymorphisms were identified in a group of Swedish individuals. Haplotypes containing several closely located MAOA polymorphisms were assessed in Asian, African, and Caucasian populations. The haplotype distribution and diversity pattern found among the three populations supported the occurrence of a bottleneck during the dispersion of modem humans from Africa. </p><p>Allelic association studies conducted on postmortem human brain samples, revealed the association between a SNP in the MAOB intron 13, and different levels of both MAO enzyme activities. This suggested that this SNP is in linkage disequilibrium with at least one novel functional DNA polymorphism that controls MAO enzyme activities in human brain. The identification of functional polymorphisms regulating the activity of these enzymes will help to elucidate the involvement of MAO in human behavior and neuropsychiatric conditions. </p>

<p>&nbsp / </p> <p align="left">The domesticated apple (<i><font face="TimesNewRomanPS-ItalicMT">Malus </font><font face="TimesNewRomanPSMT">x </font><i><font face="TimesNewRomanPS-ItalicMT">domestica </font><font face="TimesNewRomanPSMT">Borkh.), belonging to the </font><i><font face="TimesNewRomanPS-ItalicMT">Malus </font><font face="TimesNewRomanPSMT">genus of the Rosaceae family, is one of the edible pomaceous fruits. Since it is one of the important commercial fruit crops worldwide, the quality of the fruit is crucial to breeders and farmers as it ultimately determines acceptance of a cultivar for consumption. Fruit quality is also a critical determinant factor that is used to estimate the potential of apples to have a long shelf life. The introduction of marker-assisted selection (MAS) has allowed hastening of traditional breeding and selection of high-quality apple cultivars. The availability of genetic linkage maps, constructed by positioning molecular markers throughout the apple genome, enables the detection and analysis of major genes and quantitative trait loci (QTLs) contributing to the quality traits of a given genotype.&nbsp / herefore, the primary aim of this study was to construct a genetic linkage map of the &lsquo / Golden Delicious&rsquo / x &lsquo / Dietrich&rsquo / population for the identification of QTLs associated with fruit quality traits and then to examine the apple fruit pulp proteome with a specific focus on fruit firmness. In this regard, genomic DNA was extracted from leaves of the &lsquo / Golden Delicious&rsquo / x Dietrich&rsquo / population and used in megaplex PCR reactions. The PCR products were analysed prior to scoring of alleles. Polymorphic markers were then used to construct genetic linkage maps. The genetic linkage maps constructed in this study comprise of 167 simple sequence repeats (SSR) markers, 33 of these were newly developed markers. The 17 linkage groups of apple were constructed and aligned to existing apple genetic maps. The maps span 1,437.8 cM and 1,491.5 cM for &lsquo / Golden Delicious&rsquo / and &lsquo / Dietrich&rsquo / , respectively.</font></i></i></i></p>

This thesis focuses on the identification of genetic factors underlying two inherited human phenotypes: hearing loss and monoamine oxidase activity. Non-syndromic hearing loss segregating in a Swedish family was tested for linkage to 13 previously reported candidate loci for hearing disabilities. Linkage was found to two loci: DFNA12 (llq22-q24) and DFNA2 (lp32). A detailed analysis of the phenotypes and haplotypes shared by the affected individuals supported the hypothesis of digenic inheritance of hearing disability in the Swedish family. Mutation screening of α-tectorin, a gene residing within the DFNA12 region revealed a mutation of a conserved amino acid (Cys to Ser), that segregated with the disease. The identification of the mutation added support to the involvement of α-tectorin in hearing disabilities. In contrast, no mutations were identified in two candidate genes at the DFNA2 locus, that were reported to cause hearing loss in other families. It is possible that the DFNA2 locus contains a third, not yet identified, hearing loss gene. Monoamine oxidase A (MAOA) and B (MAOB) catalyze the degradation of certain neurotransmitters in the central nervous system and are associated with specific behavioral and neuropsychiatric human traits. Activity levels of both monoamine oxidases (MAO) are highly variable among humans and are determined by unknown genetic factors. This study investigated the relationship of different MAO alleles with MAO mRNA levels and enzyme activity in human brain. Several novel DNA polymorphisms were identified in a group of Swedish individuals. Haplotypes containing several closely located MAOA polymorphisms were assessed in Asian, African, and Caucasian populations. The haplotype distribution and diversity pattern found among the three populations supported the occurrence of a bottleneck during the dispersion of modem humans from Africa. Allelic association studies conducted on postmortem human brain samples, revealed the association between a SNP in the MAOB intron 13, and different levels of both MAO enzyme activities. This suggested that this SNP is in linkage disequilibrium with at least one novel functional DNA polymorphism that controls MAO enzyme activities in human brain. The identification of functional polymorphisms regulating the activity of these enzymes will help to elucidate the involvement of MAO in human behavior and neuropsychiatric conditions.

Predisposition to autoimmune diseases such as, rheumatoid arthritis, diabetes, and multiple sclerosis, is caused by the effect of multiple genes and a strong influence from the environment. In this study, I have investigated genetic factors that confer susceptibility to rheumatoid arthritis in a rat model. This work has led to the identification of several chromosomal regions, containing uncharacterized genes that directly or indirectly are associated to the arthritis development in these rats. We have observed that timing, gender, and genetic interactions are features that play a part in the effect that these genetic factors exert. Unarguably, animal models for human disorders display differences to the human form of disease. An important fact is however that the same chromosomal regions are identified in both rodent and human studies, which suggests that there are genetic factors that we have in common, which are involved directly or indirectly with an autoimmune response. Focusing the interest on these similarities, and on the possibility to apply a wide set of genetic tools, make animal models an invaluable, and probably necessary, instrument to dissect the genetic component of complex disorders. To fully comprehend the genetic basis for a complex disorder like this, will require understanding of how multiple genes interact with each other to cause disease. We have been able to demonstrate that chronic arthritis, in a rat model for rheumatoid arthritis, is regulated by several genes and that these act during different temporal phases of the disease. These findings will hopefully contribute to our understanding of the etiology and progression of rheumatoid arthritis.

Synthetic and physicochemical studies on appropriately functionalized ODN-conjugates have been performed to evaluate their abilities to act as antisense agents against RNA or as intramolecular DNA cross-linking agents. Intercalating aromatic systems [phenazine (Pnz), dipyridophenazine (DPPZ)] and metallointercalators such as Ru2+(phen)2(DPPZ) and Ru2+(tpy)(DPPZ)<b>L</b> [where <b>L</b> = chemically or photochemically labile ligand, phen = phenanthroline, tpy = terpyridine], which are covalently tethered to the oligo-deoxynucleotides (ODNs), have been chosen for this purpose. The ODN-conjugates were typically prepared by automated solid phase synthesis using phosphoramidite building blocks, or on solid supports, both functionalized with the chromophore groups. The photosensitive metal complex, Ru2+(tpy)(DPPZ)(CH3CN), has been incorporated by post-synthetic coupling to the amino-linker modified ODNs via an amide bond. The intercalating ability of the tethered chromophores gave enhanced stability of the duplexes and triplexes formed with ODN-conjugates and their complementary targets: DNA, RNA, or double-stranded DNA. The conjugation of DPPZ chromophore to ODN (at 3', 5' or at the middle) led us to incorporate Ru2+(phen)2(DPPZ) through the DPPZ ligand, for the first time. The corresponding (Ru2+-ODN)•DNA duplexes showed dramatic stabilization (ΔTm = 19.4 – 22.0ºC). The CD and DNase I footprinting experiments suggest that the stabilization is owing to metallointercalation by threading of the Ru2+(phen)2 moiety through the ODN•DNA duplex core, thus "stapling" the two helical strands from the minor to major groove. On the other hand, Ru2+(tpy)(DPPZ)(CH3CN)-ODN conjugates represent a new class of oligonucleotides containing the photoactivatible Ru2+ complexes, which can successfully crosslink to the complementary strand. The mechanism of cross-linking upon photoirradiation of [Ru2+(tpy)(DPPZ)(CH3CN)-ODN]•DNA involves in situ conversion to the reactive [Ru2+(tpy)(DPPZ)(H2O)-ODN]•DNA which are subsequently cross-linked through the G residue of the complementary DNA strand. All starting materials and products have been purified by HPLC and/or by PAGE and subsequently characterized by MALDI-TOF as well as ESI mass spectroscopy. Terminal conjugation of the planar Pnz and DPPZ groups through the flexible linkers were also shown to improve thermal stability of the ODN•RNA hybrid duplexes without alteration of the initial AB-type global helical structure as revealed from CD experiments. As a result, RNase H mediated cleavage of the RNA strand in the intercalator-tethered ODN•RNA duplexes was more efficient compared to the natural counterpart. The RNase H cleavage pattern was also found to be dependent on the chemical nature of the chromophore. It appeared that introduction of a tether at the 3'-end of the ODN can be most easily tolerated by the enzyme regardless of the nature of the appending chromophore. The tethered DPPZ group has also been shown to chelate Cu2+ and Fe3+, like phenanthroline group, followed by the formation of redox-active metal complex which cleaves the complementary DNA strand in a sequence-specific manner. This shows that the choice of appropriate ligand is useful to (i) attain improved intercalation giving Tm enhancement, and (ii) sequence-specifically inactivate target RNA or DNA molecules using multiple modes of chemistry (RNase H mediated cleavage, free-radical, oxidative pathways or photocross-linkage).

Patients with Alzheimer's disease (AD) often have a family history of the disease, implicating genetics as a major risk factor. Three genes are currently known to cause familial early-onset AD (&lt;65 years): the amyloid precursor protein (APP) and the presenilins (PSEN1 and PSEN2). For the much more common late-onset disease (&gt;65 years), only the APOE gene has repeatedly been associated to AD, where the ε4 allele increases disease risk and decreases age at onset. As APOE ε4 only explains part of the total estimated disease risk, more genes are expected to contribute to AD. This thesis has focused on the study of genetic risk factors involved in AD. In the first study, we conducted a linkage analysis of six chromosomes previously implicated in AD in a collection of affected relative pairs from Sweden, the UK and the USA. An earlier described linkage peak on chromosome 10q21 could not be replicated in the current sample, while significant linkage was demonstrated to chromosome 19q13 where the APOE gene is located. The linkage to 19q13 was further analyzed in the second study, demonstrating no significant evidence of genes other than APOE contributing to this peak. In the third study, the prevalence of APP duplications, a recently reported cause of early-onset AD, was investigated. No APP duplications were identified in 141 Swedish and Finnish early-onset AD patients, implying that this is not a common disease mechanism in the Scandinavian population. In the fourth study, genes with altered mRNA levels in the brain of a transgenic AD mouse model (tgAPP-ArcSwe) were identified using microarray analysis. Differentially expressed genes were further analyzed in AD brain. Two genes from the Wnt signaling pathway, TCF7L2 and MYC, had significantly increased mRNA levels in both transgenic mice and in AD brains, implicating cell differentiation and possibly neurogenesis in AD.