Recent Genome Wide Association Studies (GWAS) have identified a series of single nucleotide polymorphism (SNP)s that are associated with Alzheimer’s disease (AD). One of the SNPs, rs3851179 (G/A), is near the gene phosphatidylinositol-binding clathrin assembly protein (PICALM). To evaluate whether this SNP is associated with PICALM expression, we quantified PICALM mRNA in 56 brain cDNA samples. Using linear regression analysis, we analyzed PICALM expression relative to rs3851179, AD status, and cell type specific markers. An association was detected between rs3851179 and PICALM, microvessel mRNA, glial fibrillary acidic protein (GFAP) mRNA, and synaptophysin (SYN) mRNA. To gain clarity into other possible SNP mechanisms, we searched brain cDNA for PICALM splice variants. We identified several PICALM splice variants involving exons 13-19. To identify and gain an estimation of relative abundance of splice variants, we PCR-amplified across exons 13-20 in cDNA from six individuals, three rs3851179 GG individuals and three rs3851179 AA individuals. Sequencing the cloned isoforms we found that PICALM lacking exon 13 (delta 13) is the most abundant isoform. Other isoforms detected included deletion of exon 18-19. We targeted the latter part of the gene, exon 17-20, to investigate unequal allelic expression using next generation sequencing. Individuals heterozygous for rs76719109 (n= 35), located in exon 17, were used to study the abundance of G/T allele in cDNA and genomic DNA. When we analyzed the T:G allelic ratio, the variant lacking exons 18 and 19 showed unequal allelic expression (p-value < 0.001) in a subset of individuals. One individual was an outlier, showing overall unequal allelic expression, which maybe be harboring a rare mutation capable of modifying PICALM expression. The PICALM intronic SNP rs588076 was associated with delta 18-19 isoform splicing (p-value < 0.001). In conclusion, this study gained a greater insight into the role of AD genetics in PICALM expression and splicing.

To gain a better understanding of contaminating bacteria in bioethanol industry, we profiled the bacterial community structure in corn-based bioethanol fermentations and evaluated its correlation to environmental variables. Twenty-three batches of corn-mash sample were collected from six bioethanol facilities. The V4 region of the collective bacterial 16S rRNA genes was analyzed by Illumina Miseq sequencing to investigate the bacterial community structure. Non-metric multidimensional scaling (NMDS) ordination plots were constructed to visualize bacterial community structure groupings among different samples, as well as the effects of multiple environmental variables on community structure variation. Our results suggest that bacterial community structure is facility-specific, although there are two core bacterial phyla, Firmicutes and Proteobacteria. Feedstock, facility, and fermentation technology may explain the difference in community structure between different facilities. Lactic acid, the most important environmental variable that influences bacterial community structure grouping, could be utilized as an indicator of bacterial contamination. We also identified genes responsible for the multiple antibiotic-resistance phenotype of an Enterobacter cloacae strain isolated from a bioethanol fermentation facility. We performed PCR assays and revealed the presence of canonical genes encoding resistance to penicillin and erythromycin. However, a gene encoding resistance to virginiamycin was not detected.

Syftet med studien var att jämföra skattad hanteringsförmåga och hälsorelateradlivskvalitet hos närstående till personer med kronisk hjärtsvikt och stroke. Ett annat syfte var också att studera om samband fanns mellan hanteringsförmågaoch hälsorelaterad livskvalitet.  Metod: En komparativ och korrelativdesign med kvantitativ ansats användes. För att mäta hanteringsförmåga ochhälsorelaterad livskvalitet användes Jalowiec Coping Scale (JCS) och Shortform- 36 (SF- 36). Urvalsgruppen för studien var närstående till patienter med kronisk hjärtsvikt och stroke (n = 46). Resultatet visade att båda närstående grupperna använde mer optimistisk-, självtillit och konfrontativ stil. Närstående till patienter med stroke skattar sitt psykiska välbefinnande högre än närstående till patienter med kronisk hjärtsvikt(p=0,024). Det framkom flera låga och moderata negativa statistiska signifikanta samband mellan hälsorelaterad livskvalitet och hanteringsförmåga. De psykiska skalorna (SF-36) hade fler statistiska samband med coping stilar(JCS) än de fysiska skalorna. Konklusionen visade att närstående till patienter med kronisk hjärtsvikt skattar sin hälsorelaterade livskvalitet lägre på den psykiska välbefinnande än närstående till patienter med stroke.  Generellt var att lägre användning av copingstilar hade mer samband med högre skattad hälsorelaterad livskvalitet. / The aims of the study were to compare handling ability and health-related quality of life in next of kin to patients with chronic heart failure and stroke, as well as study correlations between handling ability and health-related quality of life. Method: A comparative and correlative design with quantitative approach was used. To measure handling ability and health-related quality Jalowiec Coping Scale (JCS) and Short Form-36 (SF-36) were used. The study group was next of kin to patients with chronic heart failure and stroke (n = 46). The results showed that both groups use most optimistic, self- reliant and confrontative coping styles. Next of kin to patients with stroke estimated mental health significantly higher than next of kin to patients with chronic heart failure (p = 0.024). There were several significant negative low-and moderate correlations between health-related quality of life and handling ability. In SF-36, the mental scales were more significantly associated with coping strategies (JCS) than the physical scales. Conclusions: Next of kin to patients with chronic heart failure rated health-related quality of life lower in the scale mental health than next of patients with stroke. Lower use of coping styles were more associated with higher health- related quality of life. / Att leva med långvarig ohälsa- hanteringsförmåga/resurser och upplevd livskvalitet

As we gain increased understanding of genetic disorders and gene regulation more focus has turned towards complex interactions. Combinations of genes or gene and environmental factors have been suggested to explain the missing heritability behind complex diseases. Furthermore, gene activation and splicing seem to be governed by a complex machinery of histone modification (HM), transcription factor (TF), and DNA sequence signals. This thesis aimed to apply and develop multivariate machine learning methods for use on such biological problems. Monte Carlo feature selection was combined with rule-based classification to identify interactions between HMs and to study the interplay of factors with importance for asthma and allergy. Firstly, publicly available ChIP-seq data (Paper I) for 38 HMs was studied. We trained a classifier for predicting exon inclusion levels based on the HMs signals. We identified HMs important for splicing and illustrated that splicing could be predicted from the HM patterns. Next, we applied a similar methodology on data from two large birth cohorts describing asthma and allergy in children (Paper II). We identified genetic and environmental factors with importance for allergic diseases which confirmed earlier results and found candidate gene-gene and gene-environment interactions. In order to interpret and present the classifiers we developed Ciruvis, a web-based tool for network visualization of classification rules (Paper III). We applied Ciruvis on classifiers trained on both simulated and real data and compared our tool to another methodology for interaction detection using classification. Finally, we continued the earlier study on epigenetics by analyzing HM and TF signals in genes with or without evidence of bidirectional transcription (Paper IV). We identified several HMs and TFs with different signals between unidirectional and bidirectional genes. Among these, the CTCF TF was shown to have a well-positioned peak 60-80 bp upstream of the transcription start site in unidirectional genes.

In xDSL technology, high-speed data are transferred between the central office and the customers, or between two or more central offices using unshielded telephone lines. A major impairment that hinders the increase in data-rate through the twisted-pair line is nearend crosstalk (NEXT) between the adjacent twisted pairs. DSL systems with overlapping transmit and receive spectra are susceptible to NEXT which significantly increases the interference noise in the received signal and also reduces the reliability and availablity of the system. One way to cancel the NEXT in the received signal is to deploy adaptive filters. However, if adaptive filters are deployed to cancel every possible NEXT signal from the other twisted pairs, the computational complexity increases in proportion to N2 where N is the number of twisted pairs in the bundle and, therefore, it becomes prohibitive even for small values of N. In this dissertation, four new methods for NEXT reduction are proposed. The methods aim at reducing computational complexity while maintaining speed and performance. In Chapter 3 an efficient NEXT cancellation system is proposed. The new system first detects the NEXT signals present in the received signal and then assigns adaptive filters to cancel the most significant NEXT signals detected. The detection process uses a fast and efficient algorithm that estimates the crosscorrelation between the transmitted and received signal. By subtracting the adaptive filter estimates of the NEXT signals that have been detected and assigned adaptive filters for cancellation, the magnitude of smaller NEXT signals can be estimated more accurately during the NEXT detection stage. The new system offers an overall computational complexity of order N. This represents a large reduction in the computational effort relative to that in previous NEXT cancellation system which offer computational complexities of order N2. In Chapter 4, the NEXT cancellation system proposed in Chapter 3 is implemented using frequency-domain least-mean-square (FDLMS) adaptive filters to cancel the NEXT signals. Several schemes for assigning the adaptive filter step sizes are explored. It has been found that by making the step sizes proportional to the magnitude of the NEXT signals during the initial phases of adaptation and then making them all equal during the later phases, the convergence rate can be significantly improved. And by returning after convergence to step sizes that are proportional to the magnitudes of the NEXT signals, a much better tracking performance is achieved. In Chapter 5, a new technique that reduces the computational complexity in adaptive filters for NEXT cancellation is proposed. In this technique, the filter length of each adaptive filter is adjusted according to the strength of the NEXT signal. Since the NEXT signals from the other twisted pairs are typically of different magnitudes, using such a technique leads to a significant reduction in the total number of filter taps when compared with fixedlength adaptive filters. The NEXT cancellation is started by using adaptive filters with minimum filter lengths. As the adaptation progresses, the filter length of each adaptive filter is adjusted according to the magnitude of the NEXT signal. Upon convergence, another algorithm is deployed which readjusts the filter lengths of those adaptive filters that are too long or too short. Chapter 6 deals with another new method to mitigate NEXT based on a wavelet denoising technique. In xDSL systems, the received signal typically has greater power in the lower end of the frequency spectrum whereas the NEXT signal has greater power in the higher end. The wavelet technique takes advantage of the difference between the power spectrum of the received signal and that of the NEXT to mitigate the crosstalk noise. In addition, the method has a low computational complexity which makes it fast, efficient, and well suited for high data-rate applications.

Conifer seed-infesting chalcids of the genus Megastigmus (Hymenoptera: Torymidae) are important forest pests. At least one species, M. spermotrophus Wachtl, has been shown to be able to manipulate the seed development of its host, Douglas-fir (Pseudotsuga menziesii) in remarkable ways, such as redirecting unfertilized ovules that would normally abort. The mechanism of host manipulation is currently unknown. Microbial associates and venoms are two potential mechanisms of host manipulation. Microbial associates are emerging as an important player in insect-plant interactions. There is also evidence that venoms may be important in gall-induction by phytophagous wasps. PCR and 16S rRNA pyrosequencing was used to characterize the microbial associates of Megastigmus and transcriptomic sequencing was used to identify putative venoms that were highly expressed in female M. spermotrophus. The common inherited bacterial symbionts Wolbachia and Rickettsia were found to be prevalent among several populations of Megastigmus spp. screened using a targeted PCR approach. A member of the Betaproteobacteria, Ralstonia, was identified as the dominant microbial associate of M. spermotrophus using 16S rRNA pyrosequencing. The transcriptome of M. spermotrophus was assembled de novo and three putative venoms were identified as highly expressed in females. One of these putative venoms, Aspartylglucosaminidase, (AGA) appears to have originated through gene duplication within the Hymenoptera and has been identified as a major venom component of two divergent parasitoid wasps. AGA was identified as a promising candidate for further investigation as a potential mechanism of early host manipulation by M. spermotrophus. / Graduate / 0353 / 0410 / 0715 / apaulson@shaw.ca

With the convergence of the wireless networks and the Internet and the booming demand for multimedia applications, the next-generation (beyond the third generation, or B3G) wireless systems are expected to be all IP-based and provide real-time and non-real-time mobile services anywhere and anytime. Powerful and efficient mobility support is thus the key enabler to fulfil such an attractive vision by supporting various mobility scenarios. This thesis contributes to this interesting while challenging topic. After a literature review on mobility support architectures and protocols, the thesis starts presenting our contributions with a generic multi-layer mobility support framework, which provides a general approach to meet the challenges of handling comprehensive mobility issues. The cross-layer design methodology is introduced to coordinate the protocol layers for optimised system design. Particularly, a flexible and efficient cross-layer signalling scheme is proposed for interlayer interactions. The proposed generic framework is then narrowed down with several fundamental building blocks identified to be focused on as follows. As widely adopted, we assume that the IP-based access networks are organised into administrative domains, which are inter-connected through a global IP-based wired core network. For a mobile user who roams from one domain to another, macro (inter-domain) mobility management should be in place for global location tracking and effective handoff support for both real-time and non-real-lime applications. Mobile IP (MIP) and the Session Initiation Protocol (SIP) are being adopted as the two dominant standard-based macro-mobility architectures, each of which has mobility entities and messages in its own right. The work explores the joint optimisations and interactions of MIP and SIP when utilising the complementary power of both protocols. Two distinctive integrated MIP-SIP architectures are designed and evaluated, compared with their hybrid alternatives and other approaches. The overall analytical and simulation results shown significant performance improvements in terms of cost-efficiency, among other metrics. Subsequently, for the micro (intra-domain) mobility scenario where a mobile user moves across IP subnets within a domain, a micro mobility management architecture is needed to support fast handoffs and constrain signalling messaging loads incurred by intra-domain movements within the domain. The Hierarchical MIPv6 (HMIPv6) and the Fast Handovers for MIPv6 (FMIPv6) protocols are selected to fulfil the design requirements. The work proposes enhancements to these protocols and combines them in an optimised way. resulting in notably improved performances in contrast to a number of alternative approaches.

Advances in DNA sequencing revolutionized the field of genomics over the last 5 years. New sequencing instruments make it possible to rapidly generate large amounts of sequence data at substantially lower cost. These high-throughput sequencing technologies (e.g. Roche 454 FLX, Life Technology SOLiD, Dover Polonator, Helicos HeliScope and Illumina Genome Analyzer) make whole genome sequencing and resequencing, transcript sequencing as well as quantification of gene expression, DNA-protein interactions and DNA methylation feasible at an unanticipated scale. In the field of evolutionary genomics, high-throughput sequencing permitted studies of whole genomes from ancient specimens of different hominin groups. Further, it allowed large-scale population genetics studies of present-day humans as well as different types of sequence-based comparative genomics studies in primates. Such comparisons of humans with closely related apes and hominins are important not only to better understand human origins and the biological background of what sets humans apart from other organisms, but also for understanding the molecular basis for diseases and disorders, particularly those that affect uniquely human traits, such as speech disorders, autism or schizophrenia. However, while the cost and time required to create comparative data sets have been greatly reduced, the error profiles and limitations of the new platforms differ significantly from those of previous approaches. This requires a specific experimental design in order to circumvent these issues, or to handle them during data analysis. During the course of my PhD, I analyzed and improved current protocols and algorithms for next generation sequencing data, taking into account the specific characteristics of these new sequencing technologies. The presented approaches and algorithms were applied in different projects and are widely used within the department of Evolutionary Genetics at the Max Planck Institute of Evolutionary Anthropology. In this thesis, I will present selected analyses from the whole genome shotgun sequencing of two ancient hominins and the quantification of gene expression from short-sequence tags in five tissues from three primates.

Sexual selection has long been a working explanation for the elaboration of appreciable traits in plants and animals, but the idea that it is an equally potent agent of change at the level of individual molecules is relatively recent. Indications that genes associated with reproductive biology evolve especially rapidly planted this notion, but many details about the genomics of sex remain elusive. Numerous studies have characterized rapid sequence and expression divergence of sex-related molecules, but few if any have demonstrated convincingly that these patterns exist as a result of sexual selection. This dissertation describes several genome-scale studies related to reproduction and the sexes in teleost fishes, a group of animals underexploited in regard to this topic. Using commercial microarrays I measured the extent of sexually dimorphic gene expression in the zebrafish, Danio rerio. Sex-biased patterns of gene expression in this species are similar to those described in other animals. A number of genes expressed at high levels in ovaries and testes relative to the body were identified as a product of the study, and these data may be useful for future studies of reproductive genes in Danio fishes. In a second study, the recent advent of high throughput cDNA pyrosequencing was leveraged to characterize the relationships between tissue-, sex-, and species-specific expression patterns of genes and rates of sequence evolution in swordtail fishes (Xiphophorus). I discovered ample evidence for expression biases of all three types, and a generally positive but idiosyncratic relationship between the magnitude of expression bias and rates of protein-coding sequence evolution. Pyrosequencing of cDNA was also used to explore the possibility that postcopulatory sexual selection drives the rapid evolution of male pregnancy genes, a novel class of reproductive molecules unique to syngnathid fishes (seahorses and pipefishes). Genes differentially expressed in the male brooding tissues as a function of pregnancy status evolve more rapidly at the amino acid level than genes exhibiting static expression. Brooding tissue genes expressed during male pregnancy have evolved especially rapidly in polyandrous lineages, a finding that supports the hypothesized relationship between postcopulatory sexual selection and the adaptive evolution of reproductive molecules.

Comparative genomics provides a tool to investigate large biological datasets, i.e. genomic datasets. In my thesis I focused on inferring patterns of selection in coding and non-coding regions of avian genomes. Until recently, large comparative studies on selection were mainly restricted to model species with sequenced genomes. This limitation has been overcome with advances in sequencing technologies and it is now possible to gather large genomic data sets for non-model species.  Next-generation sequencing data was used to study patterns of nucleotide substitutions and from this we inferred how selection has acted in the genomes of 10 non-model bird species. In general, we found evidence for a negative correlation between neutral substitution rate and chromosome size in birds. In a follow up study, we investigated two closely related bird species, to study expression levels in different tissues and pattern of selection. We found that between 2% and 18% of all genes were differentially expressed between the two species. We showed that non-coding regions adjacent to genes are under evolutionary constraint in birds, which suggests that noncoding DNA plays an important functional role in the genome. Regions downstream to genes (3’) showed particularly high level of constraint. The level of constraint in these regions was not correlated to the length of untranslated regions, which suggests that other causes play also a role in sequence conservation. We compared the rate of nonsynonymous substitutions to the rate of synonymous substitutions in order to infer levels of selection in protein-coding sequences. Synonymous substitutions are often assumed to evolve neutrally. We studied synonymous substitutions by estimating constraint on 4-fold degenerate sites of avian genes and found significant evolutionary constraint on this category of sites (between 24% and 43%). These results call for a reappraisal of synonymous substitution rates being used as neutral standards in molecular evolutionary analysis (e.g. the dN/dS ratio to infer positive selection). Finally, the problem of sequencing errors in next-generation sequencing data was investigated. We developed a program that removes erroneous bases from the reads. We showed that low coverage sequencing projects and large genome sequencing projects will especially gain from trimming erroneous reads.