Although autism spectrum disorder (ASD), which remains incurable, is an idiopathic disorder, it has been associated with an assortment of both environmental and genetic factors for pathogenesis despite the fact that the exact pathogenic factors of ASD remain undetermined. One such environmental factor with a potential impact on ASD development is air pollution via early stage exposure to airborne particles, i.e., particulate matter (PM) with 2.5 or 10 microns diameters (PM2.5 or PM10). While a number of studies have identified the impact air pollutants has on ASD, this thesis investigates the potential roles of the particle concentration, timing of exposure, and chemical type of particle have on inducing ASD. The central rationale is that exposure to small particles, including but not limited to PM2.5 and PM10, in high concentrations during development may be associated with an increase in the rates of ASD. To examine this possibility, published literature has been analytically reviewed to assess the impacts of PM2.5 and PM10 on the brain and mechanisms through which the particles act to influence brain cells. In particular, there is a strong association between small particle exposure, especially during 2nd and 3rd trimester of pregnancy, and autism spectrum disorder prevalence. Overall, the data suggest that PM-triggered oxidative stress and neuroinflammation in the developing brain may be partially responsible for the pathophysiological onset of ASD. However, additional investigations are needed in order to determine whether early life exposure to PM2.5 and PM10 can be specifically linked ASD-like brain pathology, behavioral evolvement, and ASD onset. Furthermore, the exact mechanisms underlying the ASD pathogenic effect of airborne particles have to be uncovered before effective preventive and therapeutic interventions can be devised.

Learning to read accurately and efficiently relies on proficiency in earlier-developing communication skills, which includes processing and producing speech. It remains unknown to what extent differences in speech production and underlying neural mechanisms for speech production may be related to variability in the development of skilled reading and in reading outcomes. This thesis presents a series of studies which leverage the large scale, open-source longitudinal dataset from the Adolescent Brain and Cognitive Development (ABCD) Study to characterize functionally-defined cortical networks for speech in school-age children and investigate the relationship between speech network connectivity and reading skill development. The first study demonstrates the feasibility of using a task-based adult atlas of cortical speech regions to define functional networks for speech production in task-free pediatric functional MRI data. Resting-state subnetworks in our school-age sample (9–10 years old) broadly align with those established in the task-based atlas, demonstrating the potential for examining speech networks in large-scale datasets that have collected resting-state MRI data. The second study models single-word reading skill in relation to the mean connectivity of functional speech networks and finds that stronger intrinsic connectivity of subnetworks containing higher-level associative regions is initially predictive of single-word reading skill, but that the effect is no longer significant when controlling for nonverbal IQ and vocabulary skill. The third study compares the mean connectivity of functional speech networks with single-word reading outcomes two years later and observes that good readers had significantly stronger connectivity in the higher-order subnetwork surrounding (though not containing) the core sensorimotor regions for speech, compared to poor readers. All together, these findings provide justification for further study in this area and leave open the possibility for functional neural correlates of speech production to inform mechanisms of reading development.

<p>Appropriate social behaviour depends on the wiring together of relevant sensory and cognitive neural circuits during development and is impaired in Autism Spectrum Disorder (ASD). A functional variant of the <em>MET</em> gene at rs1858830 confers risk for ASD and a basic mechanistic hypothesis relating <em>MET</em> gene function to ASD has been proposed: Decreased MET protein expression during development increases the risk of ASD-relevant circuit miswiring. In the human, robust MET is localized to the posterior cingulate, inferior temporal, posterior parietal, and visual cortices, including face-processing regions. This pattern is consistent with the importance of vision in the social milieu of primates, suggesting a conserved developmental function of the MET receptor in facilitating the neural connectivity that allows for appropriate social behaviour. This study investigates the down-stream influence of the <em>MET</em> C allele at rs1858830 on morphological characteristics of brain regions involved in social processing of audiovisual information. We used an imaging-genetics approach to characterize neuroimaging intermediate phenotypes associated of the <em>MET</em> C allele in individuals with ASD (n= 14) and neurotypical controls. Audiovisual stimuli were presented in an emotion-matching task intended to engage diffuse networks of brain regions involved in cross-modal perceptual integration. We present modest evidence of an enhanced penetrance of the <em>MET </em>C risk allele in individuals with ASD, reflecting a mechanism whereby a common variant that is not disorder-causing in and of itself has a larger effect on network function in individuals with ASD compared to neurotypical individuals. Subtle differences between ASD and TD individuals were revealed when the cohort was stratified by <em>MET</em> risk genotype, demonstrating the potential power for an imaging-genetic approach to resolve phenotypic heterogeneity in ASD. Definition of neuroimaging intermediate phenotypes may prove to be a sensitive means of parsing out ASD subgroups, and could ultimately lead to the development of tailored therapeutic interventions.</p> / Master of Science (MSc)

No description available.

<p>Genes encoding homeodomain leucine zipper, HDZip, transcription factors constitute a large gene family in <i>Arabidopsis thaliana</i>. In this thesis the isolation and characterization of four HDZip genes (<i>ATHB3</i>, -<i>13</i>, -<i>20</i> and -23) is described. These genes are similar in sequence and form a distinct subclass within the HDZip gene family. Since the genes cause similar alterations in cotyledon shape when expressed constitutively, we refer to the members of this subclass as <i>pointed cotyledon</i> HDZip genes. </p><p>To determine the biological functions of the genes, the phenotypes of plants constitutively expressing the genes have been analysed. Each of the genes specifically inhibits lateral cell expansion in cotyledons and leaves and thereby causes them to be abnormally narrow. Detailed expression analysis shows that only <i>ATHB23</i> is expressed in the entire leaf and cotyledon from early stages of development while <i>ATHB20</i> is predominantly expressed in the root cortex. <i>ATHB13</i> is expressed in basal parts of mature leaves and floral organs and <i>ATHB3</i> in root and stem cortex. The ATHB13 protein acts within a signalling pathway that mediates a response to sucrose that specifically regulates the expression of specific sugar-regulated genes. <i>ATHB3</i> specifically inhibits primary root development without affecting the development of secondary roots when constitutively expressed. </p><p>Reduced expression of <i>ATHB3</i> by antisense suppression results in increased expression of <i>ATHB13</i>, indicating that ATHB3 acts as a repressor of <i>ATHB13</i> expression in the wild type.</p><p>This thesis also reports the isolation of seven new genes of HDZip class I and reviews available functional information on the genes in this class. One conclusion is that HDZip I proteins that are closely related phylogenetically are also functionally related, in most cases. Seven different mutations in HDZip I genes were also identified. The lack of phenotypic deviations from wild type of these mutants suggests that these HDZip proteins act in a redundant fashion in the plant.</p>

<p>Strict control of gene expression is essential during development and in response to physiological stimuli. This thesis describes the functional characterisation of the gene regulatory mechanisms controlling the expression of the potent human growth factor Platelet Derived Growth Factor B gene, in a cell type specific context and in response to low oxygen tension. In addition, analysis of hypoxia in neuroblastoma indicates a role during tumour differentiation. </p><p>Initally, a promoter-specific enhancer system controlling the expression of PDGF-B was characterised in placentally derived choriocarcinoma cells. The specificity of this enhancer promoter interaction was shown to be dependent on specific sequence elements identified in both the promoter and enhancer regions. It was then shown that the activity of the PDGF-B promoter is controlled via modulation of histone acetylation status in a cell type specific manner and furthermore, that one role of its enhancer could be to regulate transcription via alterations in acetylation status at the promoter. </p><p>PDGF-B expression was then shown to be controlled by hypoxia in a biphasic manner in bladder carcinoma cells. An initial induction was followed by repression of transcription following chronic hypoxia. The biphasic response was shown to be dependent on glucose levels and uniquely amongst hypoxia regulated genes studied so far, PDGF-B expression was shown to be repressed by low glucose. </p><p>Finally, detailed <i>in vivo</i> and <i>in vitro</i> analysis revealed that the major form of differentiation in childhood neuroblastoma is towards chromaffin-like rather than ganglionic lineages. This type of differentiation did not correlate with disease progression but was suggested to be dependent on tumour hypoxia, since chromaffin differentiation markers co-localised with markers of tumour hypoxia in both clinical samples and xenogenic tumours. </p><p>In conclusion, the work presented in this thesis has identified several novel, highly specific gene regulatory mechanisms that are involved in development, the response to physiological stimuli and in disease progression.</p>

<p>This work is focused on the molecular genetic basis for morphological change in evolution. Genes belonging to the MADS-box gene family, which includes members, that determine angiosperm floral organ identity, were isolated and characterised from two non-angiosperm plants; Norway spruce (<i>Picea abies</i>) and the club moss (<i>Lycopodium annotinum</i>).</p><p>The exon/intron organisation of the isolated genes was determined, and its significance as an independent test of the position of a gene within the gene family tree evaluatad. identity genes were identified. One Norway spruce gene, <i>DAL2</i>, is an ortholog to</p><p>Norway spruce genes that are closely related to the angiosperm floral organ angiosperm C-class MADS-box genes that specify stamen and carpel identity. The expression of <i>DAL2</i> in male and female cones suggests that orthologous genes in conifers and argiosperms determine the identities of pollen- and seed-bearing structures. Constitutive expression of <i>DAL2</i> in the angiosperm Arabidopsis resulted in homeotic conversions very similar to those resulting from constiutive expression of the Arabidopsis C-class gene.</p><p>Angiosperm B-class MADS-box genes determine petal and stamen identity. The isolated Norway spruce B-class orthologs: <i>DAL11, DAL12</i>, and <i>DAL13</i> are expressed in the developing male cones exclusively, suggesting a conserved function of B-class related genes in the determination of pollen forming organs among seed plants.</p><p>No orthologs to the floral organ identity genes couId be isolated from the club moss, suggesting that the origin of these gene classes may be coupled to the origin of the pollen and the seed.</p><p>The club moss MADS-box genes, <i>LAMB2, LAMB4</i> and <i>LAMB6</i>, conform structurally to plant type MADS-box genes, whereas <i>LAMB1</i> is divergent in details. The genes <i>LAMB3</i> and <i>LAMB5 </i>encode shorter proteins.</p><p><i>LAMB1</i> expression is restricted to reproductive structures, whereas <i>LAMB2</i>, <i>LAMB4, LAMB5</i> and <i>LAMB6</i> are broadly expressed. The implications from these expression patterns on the ancestral function of plant type MADS-box genes are discussed. </p>

<p>The molecular mechanisms of the immune system in shrimp, <i>Penaeus monodon</i>, are completely unknown, despite its economic importance as an aquaculture species, especially in Asia and Latin America. The genes and their gene products involved in the prophenoloxidase activating system, which is considered to be a non-self recognition and defence system in many invertebrates, have been isolated and characterised in shrimp. These include a zymogen of this cascade, prophenoloxidase (proPO); a cell adhesion protein, peroxinectin and a pattern recognition protein, β-1,3-glucan binding protein (GBP). All proteins are synthesised in shrimp hemocytes, not in the hepatopancreas. The shrimp proPO cDNA clone has 3,002 bp and contains an open reading frame of 2,121 bp encoding a putative polypeptide of 688 amino acids, with a molecular mass of 78.7 kDa. Comparison of amino acids sequences showed that this shrimp proPO was more closely to that of another crustacean, the freshwater crayfish, <i>Pacifastacus leniusculus</i>, than to insect proPOs. </p><p>Upon activation of the proPO system in shrimp, a cell adhesion activity in the hemolymph is generated. Inhibition of adhesion by an antiserum against the crayfish cell adhesion protein, peroxinectin, revealed that the cell adhesion activity detected in shrimp hemolymph might result from a peroxinectin in shrimp. Indeed, a cDNA clone which encoded shrimp peroxinectin was isolated with an open reading frame of 2,337 bp encoding a putative protein of 778 amino acids including a signal peptide. Two putative integrin-binding motifs (RGD and KGD) are present suggesting that integrin is involved in the adhesion activity. The peroxinectin transcript was slightly reduced in shrimp injected with a β-1,3-glucan or laminarin. </p><p>Also found in shrimp hemolymph was a 31 kDa-GBP that could bind to β-1,3-glucan polymers such as curdlan and zymosan, but not to LPS. The cDNA sequence of shrimp GBP showed high similarity to that of crayfish LGBP, other insect recognition proteins as well as bacterial and sea urchin glucanases. Shrimp injected with an insoluble β-1,3-glucan, curdlan or heat-killled <i>Vibrio harveyi</i> did not show any significant changes in relevant mRNA levels. </p><p>An attempt to knock out the LGBP expression by its exogeneous dsRNA was done in a proliferating blood cell culture from the hematopoietic tissue of crayfish. We found that the expression of endogeneous LGBP mRNA could be substantially inhibited by incubation of dsRNA-LGBP in the cell culture. The effect is quick, specific, and also affects the cell behaviours.</p>

<p>Cyanobacteria belonging to the genus <i>Nostoc</i> have the capacity to form symbiotic associations with a wide range of organisms. Diversity, specificity and cellular modifications of the symbiosis between <i>Nostoc</i> and fungi in the formation of lichens were investigated in this thesis.</p><p>The use of the tRNA^LeuUAA intron as a genetic marker for the subgeneric identification of Nostoc in complex field material was developed. Lichens belonging to the genera <i>Peltigera</i> and <i>Nephroma</i> show limited variability in their <i>Nostoc</i> symbionts. The <i>in situ</i> symbiont consists of a single strainn rather than a community of different <i>Nostocs</i>, and single thalli consistently contained the same symbiont. Patterns in symbiont identity were found in geographically remote populations and the lichen species, rather than growth locality, was shown to be important for the identity of the <i>Nostoc</i> symbiont. Examination of a <i>P. aphthosa</i> photosymbiodeme revealed that one <i>Nostoc</i> has the capacity to perform the physiological roles found in both bipartite and tripartite lichens. The symbiotic association between bryophytes and <i>Nostoc</i> on the other hand exhibited a much greater variation of <i>Nostoc</i> symbionts.</p><p>Evolutionary patterns in the tRNA^LeuUAA intron were analyzed and it was shown that sequence variation was caused by several processes other than random mutations. Such evolutionary processes in genetic markers are crucial to consider, especially if phylogenetic reconstructions are attempted.</p><p>Protein profiles of symbiotic and free living <i>Nostoc</i> were analyzed using 2-dimensional gel electrophoresis. One of the major proteins in the extracts from freshly isolated symbionts was partially sequenced and shown to contain a fasciclin domain. The corresponding ORF in <i>N. punctiforme</i> was homologous to symbiotically induced genes found in different symbiotic systems. </p><p>This thesis gives new perspectives on lichens and pr for further exaovides a platform for further examiniations using tools provided by modern biology.</p>

<p>Species of the genus <i>Rickettsia</i> are obligate intracellular parasites of the a-proteobacterial subdivision. It has been suggested that obligate intracellular bacteria have evolved from free-living bacteria with much larger genome sizes. Transitions to intracellular growth habitats are normally associated with radical genomic alterations, particularly genome rearrangements and gene losses.</p><p>This thesis presents a comparative study of evolutionary processes such as gene rearrangements, deletions and duplications in a variety of <i>Rickettsia</i> species. The results show that early intrachromosomal recombination events mediated by duplicated genes and short repeats have resulted in deletions as well as rearrangements. For example, an exceptional organization of the elongation factor genes was found in all species examined, suggesting that this rearrangement event occurred at the early stage of the evolution of <i>Rickettsia</i>. Likewise, it was found that a repetitive element, the so-called <i>Rickettsia</i> Palindromic Element (RPE) flourished prior to species divergence in <i>Rickettsia</i>. Finally, a phylogenetic analysis shows that the duplication events that gave rise to the five genes encoding ATP/ADP transporters occurred long before the divergence of the two major groups of <i>Rickettsia</i>. Taken together, this suggests that <i>Rickettsia</i> have been intracellular parasites for an extensive period of time.</p><p>A detailed analysis of the patterns of nucleotide changes in genes and intergenic regions among the different species provides evidence for a gradual accumulation of short deletions. This suggests that different distributions of genes and repeated sequences in modern <i>Rickettsia</i> species reflect species-specific differences in rates of deterioration rather than variation in rates of intra-genomic sequence proliferation. </p>