The rapid rise in allergic diseases has been linked to urbanization and Westernization. Recent observational studies indicate a significantly lower prevalence of allergic disease in children exposed to farming environments during the ante- and postnatal period. Consumption of unpasteurized and fermented cow's milk have been hypothesized as independent protective factors against allergy. Lack of microbial diversity and low levels of lactic acid producing bacteria (LAB) in infant diets may be predisposing factors to developing atopic eczema, allergic sensitisation and asthma. In South Africa, rural communities with a low prevalence of allergy consume unpasteurized and traditional fermented milk products on a regular basis. The objective of this study was to characterize and compare the microbiome of differently sourced cow's milk samples. Raw, unpasteurized cow's milk was collected from farms in an urban and rural setting, respectively. Another sample, collected from a cow on a rural farm, was left to naturally ferment (amasi) while three different brands of commercially fermented milk samples were obtained from a local retail shop. The variable V3 and V4 regions of the 16S rRNA gene were amplified and diversity and abundance plots were constructed and analyzed. Clear differences in the diversity and abundance of especially LAB in the differently sourced samples were demonstrated. Urban, and rural fresh cow's milk samples were the most diverse, and commercially bought products, the least. The commercially fermented products were similarly dominated by LAB, belonging to the phylum Firmicutes (more than 98% abundance) and the phylum Proteobacteria (less than 2% abundance). The homemade fermented milk (amasi) comprised approximately 50% Firmicutes and approximately 50% Proteobacteria. At the family member level, Leuconostocaceae dominated in all three the commercially bought samples. At the species level, Lactococcus lactis (AB100803) dominated in all the milk products, with less abundance in the fresh cow's milk samples. Lactobacillus paracasei (D79212) and Streptococcus infantis (AY485603) were abundant in amasi and absent in the commercially fermented products. Statistically significant difference between fermented and unfermented cow's milk samples at species level were demonstrated. Lactococcus chungangensis (EF694028), Leuconostococcus mesenteroides (AB023247) and Leuconostococcus pseudomesenteroides (AB023237) were abundant in the commercially fermented products, but absent in amasi. Important pathogens were identified in fresh cow's milk and amasi. We concluded that commercially fermented milk, although of low diversity, may be utilized as a safe allergy protective weaning food in infant diets. The microbiome of homemade amasi is more diverse than commercially fermented products and important allergy protective lactic acid producing organisms were identified in this study. However, the safety of amasi remains a concern. This information can be used in future research to produce important allergy protective ‘starter cultures' and to appropriately shape the gut microbiome early in life.

<p>Contact allergy is one of the most common skin diseases with great social and economical impact. The origin and nature of contact allergens (haptens) capable of inducing T-cell mediated allergic reactions are diverse, ranging from organic molecules to metal ions. Most of the current knowledge on T-cell responses to haptens in humans with contact allergy have been established by studies on the metal ion nickel (Ni), the most common cause of contact allergy, whereas reactivity to the large group of organic haptens has been less studied.</p><p>Haptens are not immunogenic by themselves but must bind carrier molecules prior to their presentation on MHC class I or II molecules and subsequent recognition by T cells. Due to differences in their chemical nature, haptens interact with host molecules by different mechanisms and differences in their solubility can influence their access to different antigen-presenting pathways.</p><p>The aim of the present study was to define immune responses elicited by haptens of different chemical nature including Ni (hydrophilic metal ion), methylisothiazolinones (hydrophilic organic molecule) and parthenolide (lipophilic organic molecule). The immune response displayed by subjects with allergy to these substances, and non-allergic control subjects, was assessed by measuring hapten-induced cytokine production in peripheral blood mononuclear cells (PBMC) with a focus on ELISpot analysis of T-cell type 1 (e.g. IFN-g and IL-2) and type 2 (e.g. IL-4, IL-5 and IL-13) cytokines. For Ni and parthenolide, the phenotype of the hapten-reactive T cells was determined. The allergic status of subjects was defined by clinical history and patch testing. The latter is the established diagnostic method for contact allergy, based on applying various haptens to the subjects’ back and grading the skin reaction after 2-3 days.</p><p>All three haptens elicited a concomitant T-cell type 1 and 2 response in subjects with contact allergy to the corresponding hapten, suggesting the induction of a functionally related cytokine profile, irrespective of the chemical character of the hapten. The cytokine response was related to the degree of the subjects’ patch test reactivity; PBMC from a vast majority of subjects with strong and moderate patch test reactivity displayed detectable cytokine responses to the corresponding haptens, whereas subjects with weak or no (controls) patch test reactivity did not. Despite the similar cytokine profile induced, the phenotype of the reactive T cells was found to differ between haptens with Ni eliciting CD4+ T cells and parthenolide eliciting CD8+ T cells. This difference may be explained by a better ability of a lipophilic hapten to gain access to the MHC class I-restricted antigen-presentation pathway. Moreover, the data suggest that analysis of cytokine responses to haptens may facilitate future development of <i>in vitro</i>-based diagnostics assay for contact allergy.</p><p>Finally, the relationship between the variation over time in patch test reactivity and systemic reactivity to Ni, in terms of cytokine responses to Ni <i>in vitro</i>, was investigated. The degree of patch test reactivity is known to vary over time, in particular in subjects with weak reactivity. Ni-allergic subjects were patch tested three times with three month intervals and PBMC obtained at the same time points were assessed for<i> in vitro</i> reactivity to Ni. The overall reactivity in the patch test and the <i>in vitro</i> test was well correlated confirming that both methods provide a good and comparable estimate of the systemic reactivity to Ni. However, fluctuations in the patch test reactivity over time were not well correlated with variations in the cytokine response elicited <i>in vitro</i> suggesting that other parameters besides changes in the systemic reactivity could significantly contribute to the variation in patch test reaction over time.</p>

Contact allergy is one of the most common skin diseases with great social and economical impact. The origin and nature of contact allergens (haptens) capable of inducing T-cell mediated allergic reactions are diverse, ranging from organic molecules to metal ions. Most of the current knowledge on T-cell responses to haptens in humans with contact allergy have been established by studies on the metal ion nickel (Ni), the most common cause of contact allergy, whereas reactivity to the large group of organic haptens has been less studied. Haptens are not immunogenic by themselves but must bind carrier molecules prior to their presentation on MHC class I or II molecules and subsequent recognition by T cells. Due to differences in their chemical nature, haptens interact with host molecules by different mechanisms and differences in their solubility can influence their access to different antigen-presenting pathways. The aim of the present study was to define immune responses elicited by haptens of different chemical nature including Ni (hydrophilic metal ion), methylisothiazolinones (hydrophilic organic molecule) and parthenolide (lipophilic organic molecule). The immune response displayed by subjects with allergy to these substances, and non-allergic control subjects, was assessed by measuring hapten-induced cytokine production in peripheral blood mononuclear cells (PBMC) with a focus on ELISpot analysis of T-cell type 1 (e.g. IFN-g and IL-2) and type 2 (e.g. IL-4, IL-5 and IL-13) cytokines. For Ni and parthenolide, the phenotype of the hapten-reactive T cells was determined. The allergic status of subjects was defined by clinical history and patch testing. The latter is the established diagnostic method for contact allergy, based on applying various haptens to the subjects’ back and grading the skin reaction after 2-3 days. All three haptens elicited a concomitant T-cell type 1 and 2 response in subjects with contact allergy to the corresponding hapten, suggesting the induction of a functionally related cytokine profile, irrespective of the chemical character of the hapten. The cytokine response was related to the degree of the subjects’ patch test reactivity; PBMC from a vast majority of subjects with strong and moderate patch test reactivity displayed detectable cytokine responses to the corresponding haptens, whereas subjects with weak or no (controls) patch test reactivity did not. Despite the similar cytokine profile induced, the phenotype of the reactive T cells was found to differ between haptens with Ni eliciting CD4+ T cells and parthenolide eliciting CD8+ T cells. This difference may be explained by a better ability of a lipophilic hapten to gain access to the MHC class I-restricted antigen-presentation pathway. Moreover, the data suggest that analysis of cytokine responses to haptens may facilitate future development of in vitro-based diagnostics assay for contact allergy. Finally, the relationship between the variation over time in patch test reactivity and systemic reactivity to Ni, in terms of cytokine responses to Ni in vitro, was investigated. The degree of patch test reactivity is known to vary over time, in particular in subjects with weak reactivity. Ni-allergic subjects were patch tested three times with three month intervals and PBMC obtained at the same time points were assessed for in vitro reactivity to Ni. The overall reactivity in the patch test and the in vitro test was well correlated confirming that both methods provide a good and comparable estimate of the systemic reactivity to Ni. However, fluctuations in the patch test reactivity over time were not well correlated with variations in the cytokine response elicited in vitro suggesting that other parameters besides changes in the systemic reactivity could significantly contribute to the variation in patch test reaction over time.

The work is divided into a theoretical and practical part. The theoretical part of the work is focused on explaining the basic concepts in allergology, types of allergies are presented, their symptoms and treatment. Furthermore, the work describes the types of prevention and the task of a nursing in allergology. In the practical part of the work three goals were set up. The first goal was to determine the role of a nurse in secondary prevention in patients / clients with an allergic disease. The second objective of the research was to determine whether differences exist by nurses in the provision of secondary prevention in patients / clients with an allergic disease at selected sites. The third objective was to determine how nurses prepare patients / clients for the adherence to a treatment regimen associated with their allergic disease. To achieve these objectives a qualitative research method of semi-structured interviews has been selected. The research group consisted of ten nurses, two nurses working in the allergology ambulance at the hospital and four nurses from private ambulances in České Budějovice, two nurses from private ambulances and one from the allergology ambulance at the hospital in Písek, and one nurse from the private allergology ambulance in Strakonice.

The present thesis focuses on Czech allergology and clinical immunology by studying this branch of health care in a geographic variation framework while using methods of spatial econometrics. This has been the first work with such focus. District-level data on care provision and utilization in 2012 are used. It is found that there exist geographical differences between provision and utilization and that the geographical distribution of allergists and clinical immunologists does not correspond to population's needs. Care utilization is modeled using a spatial autoregressive model specification. Based on this model, it is concluded that a shortage of physicians in the majority of districts actually limits care utilization. Also based on the utilization model, there is a discussion about the potential need for policy coordination. Care provision cannot be modeled using explanatory variables that are available, therefore, future data collection is necessary. However, it was found that variables influencing the need for care by patients do not influence care provision per physician. JEL Classification I11, I14, I19 Keywords geographic variation, Czech, allergology, clinical immunology, ACI, spatial model Author's e-mail 18702440@fsv.cuni.cz Supervisor's e-mail michal.paulus@fsv.cuni.cz

Bakgrund: Eksem förekommer hos 10-20% av barn i hela världen. En tredjedel av barnen med eksem har födoämnesallergi. Hos de flesta växer födoämnesallergin bort innan skolåldern. Förbättrat kliniskt omhändertagande och bättre förståelse av hur klinisk tolerans uppkommer är viktiga mål för forskning inom barnmedicin. Studieupplägg: Denna doktorsavhandling baseras på studier av två grupper av barn. Den första är en stor grupp med misstänkt allergi som undersökts med pricktest vid ett tillfälle. Den andra gruppen består av små barn med eksem och misstänkt födoämnesallergi. Barnen påbörjade studien innan två års ålder och har sedan följts över tid till fyra och ett halvt års ålder. Säkerhet vid pricktest: 5908 barn med en medelålder på 6 år och 5 månader, undersöktes med pricktest (SPT). Sju barn (0,12 %) reagerade med generaliserad allergisk reaktion (GAR), och behövde antiallergisk medicinering. Sju barn reagerade vasovagalt (VVR) med svimning eller ”nära-svimning”. Riskfaktorer för GAR var ålder &lt;1 år (RR 6,28) och aktivt eksem (RR 16,98). Risken för VVR var högst hos tonårsflickor och barn/ungdomar undersökta med många allergen (många prickar) samtidigt, oavsett om de var positiva eller inte. Effekt av lokalbehandling och födoämneselimination hos spädbarn med eksem: 123 barn, 52 flickor och 71 pojkar deltog i studien. Åldern varierade mellan 1-24 månader, med en medelålder på 8,4 månader vid studiens början. Kraven för att få delta var eksem och/eller misstänkt födoämnesallergi. Diagnos av eksem gjordes med stöd av Hanifin och Rajkas kriterier. Eksemgrad bedömdes med instrumentet SCORAD. Barnen bedömdes vid två tillfällen med ca sex veckors mellanrum. 62 % av barnen hade positiv pricktest för födoämnen. SCORAD-värdena i gruppen med positiv pricktest var högre än i gruppen med negativ pricktest, barnen som var födoämnessensibiliserade hade alltså svårare eksem. Efter sex veckors behandling; födoämneselimination+ lokalbehandling hos SPTpositiva barn; endast lokalbehandling hos SPT-negativa barn; var det ingen skillnad i eksemens svårighetsgrad mellan de två grupperna. Både födoämnessensibiliserade och icke födoämnessensibiliserade förbättrades signifikant av behandling. En grupp med negativ pricktest, men med påvisade antikroppar mot födoämnen i blodet (analyserade först i efterhand), som behandlades enbart med lokalbehandling förbättrade sina eksem lika mycket som de barn som också ställts på eliminationskost. Antikroppar i blod och saliv i relation till toleransutveckling: Serumnivåer av total- samt ägg- och mjölkspecifika antikroppar av IgE, IgG1 och IgG4 analyserades. I saliv analyserades totalnivåer av sekretoriskt IgA samt specifikt IgA mot mjölk och ägg. Prover togs vid studiens början, efter sex veckor samt vid 4,5 års ålder. Barn som var sensibiliserade mot mjölk och/eller ägg, men som tålde dessa födoämnen vid 4,5 års ålder hade högre IgG4 nivåer och högre IgG4/IgE-kvot vid studiens början, än de barn som ej uppnått tolerans. De högsta IgG4/IgE-kvoterna sågs hos barnen med negativt pricktest men positivt specifikt IgE i blod. Under den första korta observationsperioden på sex veckor sågs ingen påverkan på barnens antikroppsnivåer. Recept/metodutvecklande och resultat av öppna och dubbel-blinda placebokontrollerade födoämnesprovokationer: Efter recept och metodutveckling för födoämnesprovokationer med mjölk och ägg, utfördes 52 provokationer på 39 barn. Fyra barn, alla provocerade blint, reagerade på provokationen. Generella slutsatser: Risken för generaliserade allergiska reaktioner vid pricktest är liten hos barn och tonåringar, men den finns. Riskfaktorer är låg ålder och aktivt eksem. Vasovagala reaktioner är lika vanliga som generaliserade allergiska reaktioner. Lokalbehandling/smörjning ger signifikant förbättring av eksem. Elimination av födoämnen kanske inte är nödvändigt hos eksembarn med sensibilisering för mjölk och ägg under förutsättning att hudvården sköts noga. Höga IgG4/IgE-kvoter av specifika antikroppar mot födoämnen kan vara associerat med snabbare toleransutveckling, och kan stödja idén med fortsatt allergenexponering hos födoämnessensibiliserade barn. Recept på beredningar som väl maskerar komjölk och ägg, vid öppna och blindade födoämnesprovokationer, är en god hjälp vid provokationer av små barn som ofta är misstänksamma mot nya smaker och konsistenser av mat. / Background: Eczema affects at least 20 % of children worldwide, and 1/3 of them also have food allergy. In most children, the food allergy is temporary. Improved clinical management and better understanding of etiological mechanisms underlying the tolerance development are target issues in paediatric research. Study design: The thesis is based on two study groups. The first is a large group of children with suspected allergy investigated with skin prick test in a cross-sectional study. The second group is a cohort of infants with eczema and/or suspected food allergy before 2 years of age, investigated prospectively with follow-up to 4.5 years of age. Safety of skin prick test (SPT): 5908 children with a mean age of 6.4 years (range: 1 month – 18 years) were investigated with SPT. Seven children, i.e. 0.12%, displayed a generalized allergic reaction (GAR), necessitating pharmacological treatment. Seven children showed a vasovagal reaction (VVR). Risk factors for GAR were age &lt; 1 year (RR 6.28) and eczema (RR 16.98). The risk for VVR was highest among female adolescents, and children investigated with multiple skin pricks. The effect of skin care and food elimination on eczema in infants: 123 children, 52 girls and 71 boys, with a mean age of 8.4 months (range: 1-24 months) were recruited due to eczema and/or suspected food allergy. For diagnosis of eczema, the Hanifin and Rajka criteria were used, and for scoring of eczema severity SCORAD. The infants were investigated twice with an interval of 6 weeks. 62% showed positive SPTs. The SCORAD was higher among the sensitized children before treatment compared to not sensitized children. After treatment, i.e. skin care for all and elimination diet for sensitized children, there was no difference regarding eczema severity. Both SPT-positive and SPT-negative children decreased their SCORAD values significantly after treatment. A SPT-negative subgroup, with circulating specific IgE to milk/egg, was only treated with skin care, but these children improved their eczema to the same extent as those also treated with an elimination diet. Serum and salivary antibodies and achievement of tolerance Analyses were performed regarding: serum levels of total and egg- and milk-specific IgE antibodies, IgG1 and IgG4 antibodies to β-lactoglobulin (BLG) and ovalbumin (OVA); and salivary levels of total IgA, total SIgA and salivary IgA antibodies to OVA and BLG. Samples were drawn at inclusion, after 6 weeks of intervention (skin care, elimination diet), and at 4.5 years of age. Children sensitized to egg and/or milk who had developed tolerance at 4 ½ years of age had higher levels of IgG4 antibodies to OVA and BLG and also higher IgG4/IgE ratios on inclusion in the study, than those who remained non-tolerant. The highest IgG4/IgE ratios were found in children with circulating IgE antibodies to egg and/or milk but negative SPT on inclusion. The six-week treatment period did not significantly affect the levels of serum and salivary antibodies. Recipes and outcomes of open and double-blinded food challenges in children: After development of recipes for open and blinded challenge with cow’s milk and egg, 52 challenges were performed in 39 children. 4 children, challenged blindly, had a positive outcome of the challenge. General conclusions: The risk for generalized allergic reactions at SPT is low among children and teenagers, but allergic reactions do occur, and low age and eczema are risk factors. Vasovagal reactions occur as often as allergic reactions. Skin care gives significant improvement of eczema severity. Elimination diet may not be needed in infants with sensitization to milk and/or egg, provided that the skin care is adequate. High ratios of serum IgG4/IgE antibodies to food allergens may be associated with faster achievement of clinical tolerance, and may support the concept of benefit from continuing allergen exposure in sensitized children. Recipes for masking of cow’s milk and egg in open or blinded food challenges may help to accomplish challenges in young children, often suspicious to unfamiliar tastes or textures.

Recently, the pace of growth in the amount of data sources within Life Sciences has increased exponentially until pose a difficult problem to efficiently manage their integration. The data avalanche we are experiencing may be significant for a turning point in science, with a change of orientation from proprietary to publicly available data and a concomitant acceptance of studies based on the latter. To investigate these issues, a Network of Excellence (EMBRACE) was launched with the aim to integrate the major databases and the most popular bioinformatics software tools. The focus of this thesis is therefore to approach the problem of seamlessly integrating varied data sources and/or distributed research tools. In paper I, we have developed a web service to facilitate allergenicity risk assessment, based on allergen descriptors, in order to characterize proteins with the potential for sensitization and cross-reactivity. In paper II, a web service was developed which uses a lightweight protocol to integrate human endogenous retrovirus (ERV) data within a public genome browser. This new data catalogue and many other publicly available sources were integrated and tested in a bioinformatics-rich client application. In paper III, GeneFinder, a distributed tool for genome-wide association studies, was developed and tested. Useful information based on a particular genomic region can be easily retrieved and assessed. Finally, in paper IV, we developed a prototype pipeline to mine the dog genome for endogenous retroviruses and displaying the transcriptional landscape of these retroviral integrations. Moreover, we further characterized a group that until this point was believed to be primate-specific. Our results also revealed that the dog has been very effective in protecting itself from such integrations. This work integrates different applications in the fields of protein allergology, biotechnology, genome association studies and endogenous retroviruses. / EMBRACE NoE EU FP6

Allergic diseases are chronic inflammatory conditions, characterised by eosinophil inflammation systemically and in target organs, where cytotoxic granule proteins are responsible for tissue injury. Allergic rhinitis is known to be a risk factor for the development of asthma, yet not all with rhinitis develop asthma. The overall aim was to investigate the involvement of eosinophils in allergic rhinitis and allergic asthma in vivo and in experimental settings, with a focus on differences between rhinitis and asthma. Birch pollen allergy was used as a model and patients were studied during pollen season and after nasal and bronchial allergen challenge. During pollen season and at baseline, allergic rhinitis and allergic asthma had the same degree of systemic eosinophil inflammation. Despite this, impairment in lung function during season and increased bronchial responsiveness at baseline were more common in the asthmatics. Systemic inflammation was more pronounced after seasonal exposure than after experimental challenge. Allergic rhinitis and allergic asthma had the same degree of eosinophil airway inflammation after bronchial challenge, but only the asthmatics had increased bronchial responsiveness measured as PD20 for birch allergen. Allergen primed eosinophils were investigated in vitro for C3b-induced degranulation after seasonal and experimental challenge. The released amount of eosinophil granule proteins was within the same range for all three allergen challenge models with just minor differences in propensity for degranulation between rhinitics and asthmatics. Signalling through PI3K for degranulation was studied with the specific inhibitor Wortmannin. PI3K signalling for eosinophil degranulation was clearly involved in allergic rhinitis and allergic asthma irrespective of the model for allergen exposure. Asthmatics demonstrated less inhibition of degranulation through PI3K during pollen season, indicating that other pathways contribute to eosinophil degranulation in allergic asthmatics. Conclusion: Allergic rhinitis and allergic asthma present with the same degree of systemic and local eosinophil inflammation. The eosinophils are primed for degranulation equally and follow the same pathway through PI3K for degranulation. Our data indicates that eosinophil inflammation per se is not sufficient for the development of asthma.