Gene Regulation in The Human Immune System. Gene Expression Signatures of Th2 Cell Differentiation, Type 1 Diabetes, and Intrauterine Immune Adaptation

The human immune system is constantly interacting with the surrounding stimuli and microorganisms. However, when directed against self or harmless antigens, these vital defense mechanisms can cause great damage. In addition, the understanding the underlying mechanism of several human diseases caused by aberrant immune cell functions, for instance type 1 diabetes and allergies, remains far from being complete. In this Ph.D. study these questions were addressed using genome-wide transcriptomic analyses. Asthma and allergies are characterized by a hyperactive response of the T helper 2 (Th2) immune cells. In this study, the target genes of the STAT6 transcription factor in naïve human T cells were identified with RNAi for the first time. STAT6 was shown to act as a central activator of the genes expression upon IL-4 signaling, with both direct and indirect effects on Th2 cell transcriptome. The core transcription factor network induced by IL-4 was identified from a kinetic analysis of the transcriptome. Type 1 diabetes is an autoimmune disease influenced by both the genetic susceptibility of an individual and the disease-triggering environmental factors. To improve understanding of the autoimmune processes driving pathogenesis in the prediabetic phase in humans, a unique series of prospective whole-blood RNA samples collected from HLA-susceptible children in the Finnish Type 1 Diabetes Prediction and Prevention (DIPP) study was studied. Changes in different timewindows of the pathogenesis process were identified, and especially the type 1 interferon response was activated early and throughout the preclinical T1D. The hygiene hypothesis states that allergic diseases, and lately also autoimmune diseases, could be prevented by infections and other microbial contacts acquired in early childhood, or even prenatally. To study the effects of the standard of hygiene on the development of neonatal immune system, cord blood samples from children born in Finland (high standard of living), Estonia (rapid economic growth) and Russian Karelia (low standard of living) were compared. Children born in Russian Karelia deviated from Finnish and Estonian children in many aspects of the neonatal immune system, which was developmentally more mature in Karelia, resembling that of older infants. The results of this thesis offer significant new information on the regulatory networks associated with immune-mediated diseases in human. The results will facilitate understanding and further research on the role of the identified target genes and mechanisms driving the allergic inflammation and type 1 diabetes, hopefully leading to a new era of drug development.

Linguistic models for decision support

Linguistic modelling is a rather new branch of mathematics that is still undergoing rapid development. It is closely related to fuzzy set theory and fuzzy logic, but knowledge and experience from other fields of mathematics, as well as other fields of science including linguistics and behavioral sciences, is also necessary to build appropriate mathematical models. This topic has received considerable attention as it provides tools for mathematical representation of the most common means of human communication - natural language. Adding a natural language level to mathematical models can provide an interface between the mathematical representation of the modelled system and the user of the model - one that is sufficiently easy to use and understand, but yet conveys all the information necessary to avoid misinterpretations. It is, however, not a trivial task and the link between the linguistic and computational level of such models has to be established and maintained properly during the whole modelling process. In this thesis, we focus on the relationship between the linguistic and the mathematical level of decision support models. We discuss several important issues concerning the mathematical representation of meaning of linguistic expressions, their transformation into the language of mathematics and the retranslation of mathematical outputs back into natural language. In the first part of the thesis, our view of the linguistic modelling for decision support is presented and the main guidelines for building linguistic models for real-life decision support that are the basis of our modeling methodology are outlined. From the theoretical point of view, the issues of representation of meaning of linguistic terms, computations with these representations and the retranslation process back into the linguistic level (linguistic approximation) are studied in this part of the thesis. We focus on the reasonability of operations with the meanings of linguistic terms, the correspondence of the linguistic and mathematical level of the models and on proper presentation of appropriate outputs. We also discuss several issues concerning the ethical aspects of decision support - particularly the loss of meaning due to the transformation of mathematical outputs into natural language and the issue or responsibility for the final decisions. In the second part several case studies of real-life problems are presented. These provide background and necessary context and motivation for the mathematical results and models presented in this part. A linguistic decision support model for disaster management is presented here – formulated as a fuzzy linear programming problem and a heuristic solution to it is proposed. Uncertainty of outputs, expert knowledge concerning disaster response practice and the necessity of obtaining outputs that are easy to interpret (and available in very short time) are reflected in the design of the model. Saaty’s analytic hierarchy process (AHP) is considered in two case studies - first in the context of the evaluation of works of art, where a weak consistency condition is introduced and an adaptation of AHP for large matrices of preference intensities is presented. The second AHP case-study deals with the fuzzified version of AHP and its use for evaluation purposes – particularly the integration of peer-review into the evaluation of R&D outputs is considered. In the context of HR management, we present a fuzzy rule based evaluation model (academic faculty evaluation is considered) constructed to provide outputs that do not require linguistic approximation and are easily transformed into graphical information. This is achieved by designing a specific form of fuzzy inference. Finally the last case study is from the area of humanities - psychological diagnostics is considered and a linguistic fuzzy model for the interpretation of outputs of multidimensional questionnaires is suggested. The issue of the quality of data in mathematical classification models is also studied here. A modification of the receiver operating characteristics (ROC) method is presented to reflect variable quality of data instances in the validation set during classifier performance assessment. Twelve publications on which the author participated are appended as a third part of this thesis. These summarize the mathematical results and provide a closer insight into the issues of the practicalapplications that are considered in the second part of the thesis.

Translation, adaptation and validation of the Roland-Morris questionnaire - Brazil Roland-Morris

The purpose of the present study was to translate the Roland-Morris (RM) questionnaire into Brazilian-Portuguese and adapt and validate it. First 3 English teachers independently translated the original questionnaire into Brazilian-Portuguese and a consensus version was generated. Later, 3 other translators, blind to the original questionnaire, performed a back translation. This version was then compared with the original English questionnaire. Discrepancies were discussed and solved by a panel of 3 rheumatologists and the final Brazilian version was established (Brazil-RM). This version was then pretested on 30 chronic low back pain patients consecutively selected from the spine disorders outpatient clinic. In addition to the traditional clinical outcome measures, the Brazil-RM, a 6-point pain scale (from no pain to unbearable pain), and its numerical pain rating scale (PS) (0 to 5) and a visual analog scale (VAS) (0 to 10) were administered twice by one interviewer (1 week apart) and once by one independent interviewer. Spearman's correlation coefficient (SCC) and intraclass correlation coefficient (ICC) were computed to assess test-retest and interobserver reliability. Cross-sectional construct validity was evaluated using the SCC. In the pretesting session, all questions were well understood by the patients. The mean time of questionnaire administration was 4 min and 53 s. The SCC and ICC were 0.88 (P<0.01) and 0.94, respectively, for the test-retest reliability and 0.86 (P<0.01) and 0.95, respectively, for interobserver reliability. The correlation coefficient was 0.80 (P<0.01) between the PS and Brazil-RM score and 0.79 (P<0.01) between the VAS and Brazil-RM score. We conclude that the Brazil-RM was successfully translated and adapted for application to Brazilian patients, with satisfactory reliability and cross-sectional construct validity.

Pupil size following dark adaptation in patients with retinitis pigmentosa

According to the equivalent light hypothesis, molecular defects in the photoreceptor lead to a continuous activation of the photoreceptor cascade in a manner equivalent to real light. The consequences in diseases such as retinitis pigmentosa (RP) are as disruptive to the cells as real light. Two forms of the equivalent light hypothesis can be distinguished: strong - mutations in rhodopsin or other cascade proteins in some forms of RP continuously excite the visual phototransduction cascade; weak - disruption of outer segments in all patients with RP eliminates circulating dark current and blocks neurotransmitter release in a manner similar to real light. Both forms of the equivalent light hypothesis predict that pupils of patients with RP will be constricted like those of normal subjects in the light. The purpose of this study was to test the equivalent light hypothesis by determining whether steady-state pupil diameter following full dark adaptation is abnormally small in any of a sample of patients with RP. Thirty-five patients with RP and 15 normal subjects were tested. Direct steady-state pupillometric measures were obtained from one eye in a full-field dome after 45 min of dark adaptation by videotaping the pupil with an infrared camera. Mean pupil diameter in the dark was comparable (t = -0.15, P = 0.88) between patients with RP (6.85 ± 0.58 mm) and normal subjects (6.82 ± 0.76 mm). The results of the present study are clearly counter to the prediction of the second (weaker) form of the equivalent light hypothesis.

Effects of physical activity and fitness on the psychological wellbeing of young men and working adults: associations with stress, mental resources, overweight and workability

Background: A positive association has been suggested to exist between physical activity and psychological wellbeing. However, the association between physical fitness, especially muscle fitness and psychological wellbeing, has not yet been fully elucidated. Aims: The objective of the present thesis was to assess the relationship between physical activity and physical fitness with stress symptoms, mental resources and workability among young men and working adults. Subjects and methods: Volunteers of young men (n=831, mean age 25-y (±4.0)), underwent a cardiorespiratory (CRF) and muscle fitness (MFI) test and completed leisure time physical activity (LTPA) and Occupational Stress Questionnaires (OSQ). The participants were divided into tertiles according to LTPA, CRF and MFI. A 12-month exercise intervention evaluated 371 working adults (exercise group, n=338, mean age 45-y (±8.8)); control group, n=33, mean age 41-y (±6.9)).The exercise group underwent a 12-month exercise program followed by a 12-month follow-up. The OSQ, Workability Index (WAI) and CRF were evaluated at baseline and at 4, 8, 12 and 24 months. Results: Physically inactive subjects reported more stress and less available mental resources than the subjects who reported high physical activity levels. Improved physical fitness was associated with less stress and more mental resources among normal weight men, but not in overweight men. After a 12-month exercise intervention, employees in the exercise group increased their physical activity, improved workability, decreased stress symptoms and improved their physical fitness and mental resources. After the follow-up year, workability and stress were improved compared to baseline. Conclusions: In this thesis, good physical fitness was associated with improved psychological wellbeing among young men and working adults.

Paul and death : a study in psychological coping

The present investigation looks into the attitudes toward death in Paul’s authentic letters, and puts them in relation to modern theories of psychological coping. Drawing on psychologically-oriented hermeneutic theory, and theories about psychological coping in particular, I argue that each case of psychological coping must be understood in its historical situation as strategies emanating from a specific person’s subjective appraisal (cf. Pargament, Lazarus and Folkman). Paul’s letters frequently refer to persecution and violent death. To aid in psychological coping is often integral to the purpose of the letters, which makes the perspective of psychological coping akin to their genre. In the course of a tentatively assumed chronological order of 1 Thessalonians, Galatians, 1 Corinthians, 2 Corinthians, Romans, Philippians, and Philemon, Paul moves from the perception of Jesus dying for the faithful to the understanding of dying with Jesus. His coping strategies concerning death are gradually transformed from conservative and deferring coping styles, to a more self-directing coping style, to collaborative and transformative coping styles, and finally to a new sense of deferring coping style in prison. The last case of deferring coping carries the traits of generosity and flexibility even in the face of death, which is in contrast to his previous letters. Through his correspondence, we see Paul’s attitude toward death transformed from denial to reaction, to processing, to acceptance (cf. Lindemann, Kübler-Ross, Bowlby, Parkes, among others). His strategies also shift in accordance with these understandings. Denial is accompanied by diversion, threat by aggression, processing by rumination, and acceptance by joy. The study shows the hermeneutic benefits of reading Paul’s letters as the rhetorically framed expressions of a person in a particular historical situation. The letters open small windows through which we can glimpse the coping process of a person of antiquity. In adopting the method of psychological exegesis, the study shows that the variety of attitudes toward death in Paul’s letters makes sense from the perspective of psychological coping. The psychological aspect of these letters is an underexamined richness that can extend into areas of contemporary individual and group identity, and from there to public policy and ethics.

Cultural adaptation and validation of the "Kidney Disease and Quality of Life - Short Form (KDQOL-SF™ 1.3)" in Brazil

The objective of the present study was to translate the Kidney Disease Quality of Life - Short Form (KDQOL-SF™1.3) questionnaire into Portuguese to adapt it culturally and validate it for the Brazilian population. The KDQOL-SF was translated into Portuguese and back-translated twice into English. Patient difficulties in understanding the questionnaire were evaluated by a panel of experts and solved. Measurement properties such as reliability and validity were determined by applying the questionnaire to 94 end-stage renal disease patients on chronic dialysis. The Nottingham Health Profile Questionnaire, the Karnofsky Performance Scale and the Kidney Disease Questionnaire were administered to test validity. Some activities included in the original instrument were considered to be incompatible with the activities usually performed by the Brazilian population and were replaced. The mean scores for the 19 components of the KDQOL-SF questionnaire in Portuguese ranged from 22 to 91. The components "Social support" and "Dialysis staff encouragement" had the highest scores (86.7 and 90.8, respectively). The test-retest reliability and the inter-observer reliability of the instrument were evaluated by the intraclass correlation coefficient. The coefficients for both reliability tests were statistically significant for all scales of the KDQOL-SF (P < 0.001), ranging from 0.492 to 0.936 for test-retest reliability and from 0.337 to 0.994 for inter-observer reliability. The Cronbach's alpha coefficient was higher than 0.80 for most of components. The Portuguese version of the KDQOL-SF questionnaire proved to be valid and reliable for the evaluation of quality of life of Brazilian patients with end-stage renal disease on chronic dialysis.

Translation into Brazilian Portuguese, cultural adaptation and evaluation of the reliability of the Disabilities of the Arm, Shoulder and Hand Questionnaire

The objective of the present study was to translate, adapt and validate a Brazilian Portuguese version of the Disabilities of the Arm, Shoulder and Hand (DASH) Questionnaire. The study was carried out in two steps. The first was to translate the DASH into Portuguese and to perform cultural adaptation and the second involved the determination of the reliability and validity of the DASH for the Brazilian population. For this purpose, 65 rheumatoid arthritis patients of either sex (according to the classification criteria of the American College of Rheumatology), ranging in age from 18 to 60 years and presenting no other diseases involving the upper limbs, were interviewed. The patients were selected consecutively at the rheumatology outpatient clinic of UNIFESP. The following results were obtained: in the first step (translation and cultural adaptation), all patients answered the questions. In the second step, Spearman's correlation coefficients for interobserver evaluation ranged from 0.762 to 0.995, values considered to be highly reliable. In addition, intraclass correlation coefficients ranged from 0.97 to 0.99, also highly reliable values. Spearman's correlation coefficients and the intraclass correlation coefficients obtained during intra-observer evaluation ranged from 0.731 to 0.937 and from 0.90 to 0.96, respectively, being highly reliable values. The Ritchie Index showed a weak correlation with Brazilian DASH scores, while the visual analog scale of pain showed a good correlation with DASH score. We conclude that the Portuguese version of the DASH is a reliable instrument.

Effect of psychological stress on the L-arginine-nitric oxide pathway and semen quality

It has been reported that mental stress causes abnormality of spermiogram parameters. We investigated the effect of psychological stress on the L-arginine-nitric oxide (NO) pathway. Semen samples were collected from 29 healthy fourth semester medical students just before (stress) and 3 months after (non-stress) the final examinations. Psychological stress was measured by the State Anxiety Inventory questionnaire. After standard semen analysis, arginase activity and NO concentration were measured spectrophotometrically in the seminal plasma. Measurements were made in duplicate. During the stress period, sperm concentration (41.28 ± 3.70 vs 77.62 ± 7.13 x 10(6)/mL), rapid progressive motility of spermatozoa (8.79 ± 1.66 vs 20.86 ± 1.63%) and seminal plasma arginase activity (0.12 ± 0.01 vs 0.22 ± 0.01 U/mL) were significantly lower than in the non-stress situation, whereas seminal plasma NO (17.28 ± 0.56 vs 10.02 ± 0.49 µmol/L) was higher compared to the non-stress period (P < 0.001 for all). During stress there was a negative correlation between NO concentration and sperm concentration, the percentage of rapid progressive motility and arginase activity (r = -0.622, P < 0.01; r = -0.425, P < 0.05 and r = -0.445, P < 0.05, respectively). These results indicate that psychological stress causes an increase of NO level and a decrease of arginase activity in the L-arginine-NO pathway. Furthermore, poor sperm quality may be due to excessive production of NO under psychological stress. In the light of these results, we suggest that the arginine-NO pathway, together with arginase and NO synthase, are involved in semen quality under stress conditions.

Plant-Herbivore Interaction in a Fragmented Landscape: Local Adaptation and Inbreeding

Reciprocal selection between interacting species is a major driver of biodiversity at both the genetic and the species level. This reciprocal selection, or coevolution, has led to the diversification of two highly diverse and abundant groups of organisms, flowering plants and their insect herbivores. In heterogeneous environments, the outcome of coevolved species interactions is influenced by the surrounding community and/or the abiotic environment. The process of adaptation allows species to adapt to their local conditions and to local populations of interacting species. However, adaptation can be disrupted or slowed down by an absence of genetic variation or by increased inbreeding, together with the following inbreeding depression, both of which are common in small and isolated populations that occur in fragmented environments. I studied the interaction between a long-lived plant Vincetoxicum hirundinaria and its specialist herbivore Abrostola asclepiadis in the southwestern archipelago of Finland. I focused on mutual local adaptation of plants and herbivores, which is a demonstration of reciprocal selection between species, a prerequisite for coevolution. I then proceeded to investigate the processes that could potentially hamper local adaptation, or species interaction in general, when the population size is small. I did this by examining how inbreeding of both plants and herbivores affects traits that are important for interaction, as well as among-population variation in the effects of inbreeding. In addition to bi-parental inbreeding, in plants inbreeding can arise from self-fertilization which has important implications for mating system evolution. I found that local adaptation of the plant to its herbivores varied among populations. Local adaptation of the herbivore varied among populations and years, being weaker in populations that were most connected. Inbreeding caused inbreeding depression in both plants and herbivores. In some populations inbreeding depression in herbivore biomass was stronger in herbivores feeding on inbred plants than in those feeding on outbred ones. For plants it was the other way around: inbreeding depression in anti-herbivore resistance decreased when the herbivores were inbred. Underlying some of the among-population variation in the effects of inbreeding is variation in plant phenolic compounds. However, variation in the modification of phenolic compounds in the digestive tract of the herbivore did not explain the inbreeding depression in herbivore biomass. Finally, adult herbivores had a preference for outbred host plants for egg deposition, and herbivore inbreeding had a positive effect on egg survival when the eggs were exposed to predators and parasitoids. These results suggest that plants and herbivores indeed exert reciprocal selection, as demonstrated by the significant local adaptation of V. hirundinaria and A. asclepiadis to one another. The most significant cause of disruption of the local adaptation of herbivore populations was population connectivity, and thus probably gene flow. In plants local adaptation tended to increase with increasing genetic variation. Whether or not inbreeding depression occurred varied according to the life-history stage of the herbivore and/or the plant trait in question. In addition, the effects of inbreeding strongly depended on the population. Taken together, inbreeding modified plant-herbivore interactions at several different levels, and can thus affect the strength of reciprocal selection between species. Thus inbreeding has the potential to affect the outcome of coevolution.

Psychological stress alters the ultrastructure and increases IL-1β and TNF-α in mandibular condylar cartilage

Psychological factors can be correlated with temporomandibular disorders (TMDs), but the mechanisms are unknown. In the present study, we examined the microstructural changes and expression of proinflammatory cytokines in mandibular condylar cartilage of the temporomandibular joint (TMJ) in a psychological stress animal model. Male Sprague-Dawley rats (8 weeks old, 210 ± 10 g) were randomly divided into 3 groups: psychological stress (PS, N = 48), foot shock (FS, N = 24), and control (N = 48). After inducing psychological stress using a communication box with the FS rats for 1, 3, or 5 weeks, PS rats were sacrificed and compared to their matched control littermates, which received no stress and were killed at the same times as the PS rats. Body and adrenal gland weight were measured and corticosterone and adrenocorticotropic hormone levels were determined by radioimmunoassay. After hematoxylin-eosin staining for histological observation, the ultrastructure of the TMJ was examined by scanning electron microscopy. Transcription and protein levels of interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α) were evaluated by ELISA and semi-quantitative RT-PCR. The PS group showed a significantly higher adrenal gland weight after 3 weeks of stress and higher hormone levels at weeks 1, 3, and 5. Histopathological changes and thinning cartilage were apparent at weeks 3 and 5. In the PS group, TNF-α increased at 1, 3, and 5 weeks and IL-1β increased significantly after 1 and 3 weeks of stress, and then decreased to normal levels by 5 weeks. Psychological stress increased plasma hormone levels and RT-PCR indicated increased IL-1β and TNF-α expression in the TMJ in a time-dependent manner. These results suggest that cytokine up-regulation was accompanied by stress-induced cartilage degeneration in the mandibular condyle. The proinflammatory cytokines play a potential role in initiating the cartilage destruction that eventually leads to the TMDs.

Psychological well-being of the parents and child development, behavior, and quality of life in very low birth weight infants

The parents of premature infants, especially the mothers, are at increased risk for distress. Infants born prematurely are at risk for developmental problems. The aim of this study was to investigate whether the psychological well-being of both parents is associated with child development in very low birth weight (VLBW, ≤1500g) children. The burden of prematurity-related morbidity to the children and to the family was also assessed. A cohort of 201 VLBW infants born during 2001–2006 in the Turku University Hospital, Finland, and their parents were studied (I–IV). One study included a control group (n=166) of full-term infants (IV). The psychological well-being of the parents was evaluated by assessments of depressive symptoms, parenting stress, the sense of coherence and general family functioning. Cognitive, behavioral, and socio-emotional development, and the health-related quality of life (HRQoL) of the children were determined when the children were 2 to 8 years old. The psychological well-being of the parents was associated with the cognitive, behavioral and social development of the VLBW children. The VLBW infants with prematurity-related morbidities had a poorer HRQoL and the general functioning of the family was inferior compared to the control children and their families. 64.5% of the VLBW children survived without morbidities. Most of the VLBW children did not have significant behavior problems (93%), had normal social skills (63%), had no emotional problems (64%), and had no problems in executive functioning (62%). Only 3% of the surviving VLBW infants had significant cognitive delay. In conclusion, the depressive symptoms and stress of the parents can be risk factors for disadvantageous child development, while a strong sense of coherence can be protective. Parents of the premature children with developmental delays might also experience more depressive symptoms and stress than other parents. Prematurity-related morbidities were a burden to the VLBW child as well as to the family.