Interleukin-4 induced leukocyte differentiation

Monocytes, macrophages and dendritic cells (DCs) are important mediators of innate immune system, whereas T lymphocytes are the effector cells of adaptive immune responses. DCs play a crucial role in bridging innate and adaptive immunity. Naïve CD4+ Th progenitors (Thp) differentiate to functionally distinct effector T cell subsets including Th1, Th2 and Th17 cells, which while being responsible for specific immune functions have also been implicated in pathological responses, such as autoimmunity, asthma and allergy. The main objective of this thesis is to dissect the signalling networks involved in the IL-4 induced differentiation of two important leukocyte subtypes, Th2 cells and DCs. Gene expression profiling lead to identification of over 200 genes which are differentially expressed during cytokine induced differentiation of human monocytes to DCs or macrophages and which are likely to be essential for the proper biological functions of these cell types. Transcriptome analysis demonstrated the dynamic regulation of gene expression by IL-12 and IL-4 during the initiation of Th cell differentiation, which was partly counteracted by an immunosuppressive cytokine, TGFβ, present in the culture media. Results from RNAi mediated gene knockdown experiments and global gene expression analysis elucidated that SATB1 regulates multiple genes important for Th cell polarization or function as well as may compete with GATA3 for the reciprocal regulation of IL-5 transcription. In conclusion, the results obtained have extended our system-level understanding of the immune cell differentiation processes and provide an excellent basis for the further functional studies which could lead to development of improved therapeutic approaches for a range of immunological conditions.

Chemical profiling of six samples of Brazilian propolis

Six samples of Brazilian propolis from Minas Gerais and Paraná states were analyzed to identify the constituents (GC/MS and HPLC/MS) and to determine their contents (HPLC and external standardization). All samples contained characteristic constituents of green propolis, but the samples from Minas Gerais had higher contents of prenylated phenylpropanoids and caffeoylquinic acids. Kaempferide and two other flavonoids were among the major constituents of the samples from Minas Gerais. Luteolin 5-O-methyl ether was detected only in samples from Paraná. Baccharis dracunculifolia was a source of resins for all samples analyzed, but the samples from Paraná had more complex plant origin.

Molecular profiling of human endometrium and endometriosis

Endometriosis is a common hormone-dependent gynecological disease leading to severe menstrual and/or chronic pelvic pain with or without subfertility. The disease is defined by the presence of endometrium-like tissue outside the uterine cavity, primarily on the pelvic peritoneum, ovaries and infiltrating organs of the peritoneal cavity. The current tools for diagnosis and treatment of endometriosis need to be improved to ensure reliable diagnosis and effective treatment. In addition, endometriosis is associated with increased risk of ovarian cancer and, therefore, the differential diagnosis between the benign and malignant ovarian cysts is of importance. The long-term objective of the present study was to support the discovery of novel tools for diagnosis and treatment of endometriosis. This was approached by exploiting genome-wide expression analysis of endometriosis specimens. A novel expression profiling -based classification of endometriosis indicated specific subgroups of lesions partially consistent with the clinical appearance, but partially according to unknown factors. The peritoneum of women with endometriosis appeared to be altered in comparison to that of healthy control subjects, suggesting a novel aspect on the pathogenesis of the disease. The evaluation of action and metabolism of sex hormones in endometrium and endometriosis tissue indicated a novel role of androgens in regulation of the tissues. In addition, an enzyme involved in androgen and neurosteroid metabolism, hydroxysteroid (17beta) dehydrogenase 6, was found to be highly up-regulated in endometriosis tissue as compared to healthy endometrium. The enzyme may have a role in the pathogenesis of endometriosis or in the endometriosis associated pain generation. Finally, a new diagnostic biomarker, HE4, was discovered distinguishing patients with ovarian endometriotic cysts from those with malignant ovarian cancer. The information acquired in this study enables deeper understanding of endometriosis and facilitates the development of improved diagnostic tools and more specific treatments of the disease

Profiling the Value of Industrial Maintenance Services

Industrial maintenance can be executed internally, acquired from the original equipment manufacturer or outsourced to a service provider, and this concludes in many different kind of business relationships. To maximize the total value in a maintenance business relationship it is important to know what the partner values. The value of maintenance services can be considered to consist of value elements and the perceived total value for the customer and the service provider is the sum of these value elements. The specific objectives of this thesis are to identify the most important value elements for the maintenance service customer and provider and also to recognize where the value elements differ. The study was executed as a statistical analysis using the survey method. The data has been collected by an online survey sent to 345 maintenance service professionals in Finland. In the survey, four different types of value elements were considered: the customer’s high critical and low critical items and the service provider’s core and support service. The most valued elements by the respondents were reliability, safety at work, environmental safety, and operator knowledge. The least valued elements were asset management factors and access to markets. Statistically significant differences in value elements between service types were also found. As a managerial implication a value gap profile is presented. This Master’s Thesis is part of the MaiSeMa (Industrial Maintenance Services in a Renewing Business Network: Identify, Model and Manage Value) research project where network decision models are created to identify, model and manage the value of maintenance services.

What can digital transcript profiling reveal about human cancers?

Important biological and clinical features of malignancy are reflected in its transcript pattern. Recent advances in gene expression technology and informatics have provided a powerful new means to obtain and interpret these expression patterns. A comprehensive approach to expression profiling is serial analysis of gene expression (SAGE), which provides digital information on transcript levels. SAGE works by counting transcripts and storing these digital values electronically, providing absolute gene expression levels that make historical comparisons possible. SAGE produces a comprehensive profile of gene expression and can be used to search for candidate tumor markers or antigens in a limited number of samples. The Cancer Genome Anatomy Project has created a SAGE database of human gene expression levels for many different tumors and normal reference tissues and provides online tools for viewing, comparing, and downloading expression profiles. Digital expression profiling using SAGE and informatics have been useful for identifying genes that have a role in tumor invasion and other aspects of tumor progression.

The biological effects of high-pressure gas on the yeast transcriptome

The aim of the present study was to examine the feasibility of DNA microarray technology in an attempt to construct an evaluation system for determining gas toxicity using high-pressure conditions, as it is well known that pressure increases the concentration of a gas. As a first step, we used yeast (Saccharomyces cerevisiae) as the indicator organism and analyzed the mRNA expression profiles after exposure of yeast cells to nitrogen gas. Nitrogen gas was selected as a negative control since this gas has low toxicity. Yeast DNA microarray analysis revealed induction of genes whose products were localized to the membranes, and of genes that are involved in or contribute to energy production. Furthermore, we found that nitrogen gas significantly affected the transport system in the cells. Interestingly, nitrogen gas also resulted in induction of cold-shock responsive genes. These results suggest the possibility of applying yeast DNA microarray to gas bioassays up to 40 MPa. We therefore think that "bioassays" are ideal for use in environmental control and protection studies.

Gene expression profiling of clinical stages II and III breast cancer

Clinical stage (CS) is an established indicator of breast cancer outcome. In the present study, a cDNA microarray platform containing 692 genes was used to identify molecular differences between CSII and CSIII disease. Tumor samples were collected from patients with CSII or CSIII breast cancer, and normal breast tissue was collected from women without invasive cancer. Seventy-eight genes were deregulated in CSIII tumors and 22 in CSII tumors when compared to normal tissue, and 20 of them were differentially expressed in both CSII and CSIII tumors. In addition, 58 genes were specifically altered in CSIII and expression of 6 of them was tested by real time RT-PCR in another cohort of patients with CSII or CSIII breast cancer and in women without cancer. Among these genes, MAX, KRT15 and S100A14, but not APOBEC3G or KRT19, were differentially expressed on both CSIII and CSII tumors as compared to normal tissue. Increased HMOX1 levels were detected only in CSIII tumors and may represent a molecular marker of this stage. A clear difference in gene expression pattern occurs at the normal-to-cancer transition; however, most of the differentially expressed genes are deregulated in tumors of both CS (II and III) compared to normal breast tissue.

Serum metabolic profiling of human gastric cancer based on gas chromatography/mass spectrometry

Research on molecular mechanisms of carcinogenesis plays an important role in diagnosing and treating gastric cancer. Metabolic profiling may offer the opportunity to understand the molecular mechanism of carcinogenesis and help to non-invasively identify the potential biomarkers for the early diagnosis of human gastric cancer. The aims of this study were to explore the underlying metabolic mechanisms of gastric cancer and to identify biomarkers associated with morbidity. Gas chromatography/mass spectrometry (GC/MS) was used to analyze the serum metabolites of 30 Chinese gastric cancer patients and 30 healthy controls. Diagnostic models for gastric cancer were constructed using orthogonal partial least squares discriminant analysis (OPLS-DA). Acquired metabolomic data were analyzed by the nonparametric Wilcoxon test to find serum metabolic biomarkers for gastric cancer. The OPLS-DA model showed adequate discrimination between cancer and non-cancer cohorts while the model failed to discriminate different pathological stages (I-IV) of gastric cancer patients. A total of 44 endogenous metabolites such as amino acids, organic acids, carbohydrates, fatty acids, and steroids were detected, of which 18 differential metabolites were identified with significant differences. A total of 13 variables were obtained for their greatest contribution in the discriminating OPLS-DA model [variable importance in the projection (VIP) value >1.0], among which 11 metabolites were identified using both VIP values (VIP >1) and the Wilcoxon test. These metabolites potentially revealed perturbations of glycolysis and of amino acid, fatty acid, cholesterol, and nucleotide metabolism of gastric cancer patients. These results suggest that gastric cancer serum metabolic profiling has great potential in detecting this disease and helping to understand its metabolic mechanisms.

Whole transcriptome organisation in the dehydrated supraoptic nucleus

The supraoptic nucleus (SON) is part of the central osmotic circuitry that synthesises the hormone vasopressin (Avp) and transports it to terminals in the posterior lobe of the pituitary. Following osmotic stress such as dehydration, this tissue undergoes morphological, electrical and transcriptional changes to facilitate the appropriate regulation and release of Avp into the circulation where it conserves water at the level of the kidney. Here, the organisation of the whole transcriptome following dehydration is modelled to fit Zipf's law, a natural power law that holds true for all natural languages, that states if the frequency of word usage is plotted against its rank, then the log linear regression of this is -1. We have applied this model to our previously published euhydrated and dehydrated SON data to observe this trend and how it changes following dehydration. In accordance with other studies, our whole transcriptome data fit well with this model in the euhydrated SON microarrays, but interestingly, fit better in the dehydrated arrays. This trend was observed in a subset of differentially regulated genes and also following network reconstruction using a third-party database that mines public data. We make use of language as a metaphor that helps us philosophise about the role of the whole transcriptome in providing a suitable environment for the delivery of Avp following a survival threat like dehydration.

Gene expression profiling analysis of lung adenocarcinoma

The present study screened potential genes related to lung adenocarcinoma, with the aim of further understanding disease pathogenesis. The GSE2514 dataset including 20 lung adenocarcinoma and 19 adjacent normal tissue samples from 10 patients with lung adenocarcinoma aged 45-73 years was downloaded from Gene Expression Omnibus. Differentially expressed genes (DEGs) between the two groups were screened using the t-test. Potential gene functions were predicted using functional and pathway enrichment analysis, and protein-protein interaction (PPI) networks obtained from the STRING database were constructed with Cytoscape. Module analysis of PPI networks was performed through MCODE in Cytoscape. In total, 535 upregulated and 465 downregulated DEGs were identified. These included ATP5D, UQCRC2, UQCR11 and genes encoding nicotinamide adenine dinucleotide (NADH), which are mainly associated with mitochondrial ATP synthesis coupled electron transport, and which were enriched in the oxidative phosphorylation pathway. Other DEGs were associated with DNA replication (PRIM1, MCM3, and RNASEH2A), cell surface receptor-linked signal transduction and the enzyme-linked receptor protein signaling pathway (MAPK1, STAT3, RAF1, and JAK1), and regulation of the cytoskeleton and phosphatidylinositol signaling system (PIP5K1B, PIP5K1C, and PIP4K2B). Our findings suggest that DEGs encoding subunits of NADH, PRIM1, MCM3, MAPK1, STAT3, RAF1, and JAK1 might be associated with the development of lung adenocarcinoma.

Characterisation of Cladonia rangiferina transcriptome and genome, and the effects of dehydration and rehydration on its gene expression

Lichens are symbiotic organisms, which consist of the fungal partner and the photosynthetic partner, which can be either an alga or a cyanobacterium. In some lichen species the symbiosis is tripartite, where the relationship includes both an alga and a cyanobacterium alongside the primary symbiont, fungus. The lichen symbiosis is an evolutionarily old adaptation to life on land and many extant fungal species have evolved from lichenised ancestors. Lichens inhabit a wide range of habitats and are capable of living in harsh environments and on nutrient poor substrates, such as bare rocks, often enduring frequent cycles of drying and wetting. Most lichen species are desiccation tolerant, and they can survive long periods of dehydration, but can rapidly resume photosynthesis upon rehydration. The molecular mechanisms behind lichen desiccation tolerance are still largely uncharacterised and little information is available for any lichen species at the genomic or transcriptomic level. The emergence of the high-throughput next generation sequencing (NGS) technologies and the subsequent decrease in the cost of sequencing new genomes and transcriptomes has enabled non-model organism research on the whole genome level. In this doctoral work the transcriptome and genome of the grey reindeer lichen, Cladonia rangiferina, were sequenced, de novo assembled and characterised using NGS and traditional expressed sequence tag (EST) technologies. RNA extraction methods were optimised to improve the yield and quality of RNA extracted from lichen tissue. The effects of rehydration and desiccation on C. rangiferina gene expression on whole transcriptome level were studied and the most differentially expressed genes were identified. The secondary metabolites present in C. rangiferina decreased the quality – integrity, optical characteristics and utility for sensitive molecular biological applications – of the extracted RNA requiring an optimised RNA extraction method for isolating sufficient quantities of high-quality RNA from lichen tissue in a time- and cost-efficient manner. The de novo assembly of the transcriptome of C. rangiferina was used to produce a set of contiguous unigene sequences that were used to investigate the biological functions and pathways active in a hydrated lichen thallus. The de novo assembly of the genome yielded an assembly containing mostly genes derived from the fungal partner. The assembly was of sufficient quality, in size similar to other lichen-forming fungal genomes and included most of the core eukaryotic genes. Differences in gene expression were detected in all studied stages of desiccation and rehydration, but the largest changes occurred during the early stages of rehydration. The most differentially expressed genes did not have any annotations, making them potentially lichen-specific genes, but several genes known to participate in environmental stress tolerance in other organisms were also identified as differentially expressed.

Perception of privacy in smartphone applications: profiling users based on personality types.

This document is focused on studying privacy perception and personality traits of users in the context of smartphone application privacy. It is divided into two parts. The first part presents an in depth systematic literature review of the existing academic writings available on the topic of relation between privacy perception and personality traits. Demographics, methodologies and other useful insight is extracted and the available literature is divided into broader group of topics bringing the five main areas of research to light and highlighting the current research trends in the field along with pinpointing the research gap of interest to the author. The second part of the thesis uses the results from the literature review to administer an empirical study to investigate the current privacy perception of users and the correlation between personality traits and privacy perception in smartphone applications. Big five personality test is used as the measure for personality traits whereas three sub-variables are used to measure privacy perception i.e. perceived privacy awareness, perceived threat to privacy and willingness to trade privacy. According to the study openness to experience is the most dominant trait having a strong correlation with two privacy sub-variables whereas emotional stability doesn’t show any correlation with privacy perception. Empirical study also explores other findings as preferred privacy sources and application installation preferences that provide further insight about users and might be useful in future.

De novo transcriptome assembly and annotation of the isopod Idotea balthica

The Baltic Sea is a unique environment that contains unique genetic populations. In order to study these populations on a genetic level basic molecular research is needed. The aim of this thesis was to provide a basic genetic resource for population genomic studies by de novo assembling a transcriptome for the Baltic Sea isopod Idotea balthica. RNA was extracted from a whole single adult male isopod and sequenced using Illumina (125bp PE) RNA-Seq. The reads were preprocessed using FASTQC for quality control, TRIMMOMATIC for trimming, and RCORRECTOR for error correction. The preprocessed reads were then assembled with TRINITY, a de Bruijn graph-based assembler, using different k-mer sizes. The different assemblies were combined and clustered using CD-HIT. The assemblies were evaluated using TRANSRATE for quality and filtering, BUSCO for completeness, and TRANSDECODER for annotation potential. The 25-mer assembly was annotated using PANNZER (protein annotation with z-score) and BLASTX. The 25-mer assembly represents the best first draft assembly since it contains the most information. However, this assembly shows high levels of polymorphism, which currently cannot be differentiated as paralogs or allelic variants. Furthermore, this assembly is incomplete, which could be improved by sampling additional developmental stages.

Cardiovascular health risk profiling of Niagara Region grade 9 students : implications for elementary curriculum /

The purpose of this study was to determine if Ontario's health and physical education curriculum contributes sufficiently to ensure the health of our children and young adults. To determine the curriculum effect, the health risk profile of Niagara Region's grade 9 students was compared to Canada's adolescent population. All subjects completed a "Heart Health Lifestyle" survey and were measured for height, weight, percent body fat, blood pressure, and total cholesterol and performed the 20-metre shuttle run test as part of their physical and health education classes. The Niagara Region grade 9 population had a healthy risk profile. Aerobic power was inversely related, and cholesterol levels were positively associated to body mass index and percent body fat in the whole group analysis. These results indicate that physical education can offer unique and essential aspects allowing individuals a means to learn and control body movements and keep physically fit while providing protection against modern disease. Ontario's health and physical education curriculum does contribute to the health of our children and adolescents; however, there is a need to implement a stronger mandate for daily vigorous physical activity.

Metabolic, biochemical and molecular profiling of Catharanthus roseus flower cultivars and transformed hairy roots for monoterpenoid indole alkaloid accumulation /

Catharanthlls rosellS (L.) G Don is a commercially significant flower species and in addition is the only source of the monoterpenoid indole alkaloids (MIA) vinblastine and vincristine, which are key pharmaceutical compounds that are used to combat a number of different cancers. Therefore, procurement of the antineoplastic agents is difficult but essential procedure. Alternatively, CatharanthllS tissue cultures have been investigated as a source of these agents; however they do not produce vindoline, which is an obligate precursor to vinblastine and vincristine. The interest in developing high MIA cultivars of Catharantlws rosellS has prompted metabolic profiling studies to determine the variability of MIA accumulation of existing flowering cultivars, with particular focus on the vindoline component ofthe pathway. Metabolic profiling studies that used high performance liquid chromatography of MIAs from seedlings and young leaf extracts from 50 different flowering cultivars showed that, except for a single low vindoline cultivar (Vinca Mediterranean DP Orchid), they all accumulate similar levels of MIAs. Further enzymatic studies with extracts from young leaves and from developing seedlings showed that the low vindoline cultivar has a IO-fold lower tabersonine-16-hydroxylase activity than those of CatharanthllS rosellS cv Little Delicata. Additionally, studies aimed at metabolic engineering ofvindoline bios}l1thesis in Catharanthus rosellS hairy root cultures have been performed by expressing the last step in vindoline biosynthesis [Dcacetylvindoline-4-0- acetyltransferase (DAT)]. Enzymatic profiling studies with transformed hairy roots have confirmed that over-expressing DAT leads to lines with high levels of O-acetyltransferase activity when compared to non-expressing hairy roots. One particular DA T over111 expressing hairy root culture (line 7) contained 200 times the OAT activity than leaves of control lines. Additional MIA analyses revealed that DAT over-expressing hairy roots have an altered alkaloid profile with significant variation in the accumulation of h6rhammericine. Further analysis of transformed hairy root line 7 suggests a correlation between the expression of OAT activity and h6rhammericine accumulation with root maturation. These studies show that metabolic and selective enzymatic profiling can enhance our ability to search for relevant MIA pathway mutants and that genetic engineering with appropriate pathway genes shows promise as a tool to modify the MIA profile of Catharanthus roseus.