Ureaplasma diversum- ja Mycoplasma bovigenitalium -sukuelintartunnat suomalaisissa lypsykarjoissa ja sonneissa

Summary: Ureaplasma diversum and Mycoplasma bovigenitalium genital tract infections in Finnish dairy herds and bulls

Quantitative proteomics in the characterization of T helper lymphocyte differentiation

The term proteome is used to define the complete set of proteins expressed in cells or tissues of an organism at a certain timepoint. Respectively, proteomics is used to describe the methods, which are used to study such proteomes. These methods include chromatographic and electrophoretic techniques for protein or peptide fractionation, mass spectrometry for their identification, and use of computational methods to assist the complicated data analysis. A primary aim in this Ph.D. thesis was to set-up, optimize, and develop proteomics methods for analysing proteins extracted from T-helper (Th) lymphocytes. First, high-throughput LC-MS/MS and ICAT labeling methods were set-up and optimized for analysing the microsomal fraction proteins extracted from Th lymphocytes. Later, iTRAQ method was optimized to study cytokine regulated protein expression in the nuclei of Th lymphocytes. High-throughput LC-MS/MS analyses, like ICAT and iTRAQ, produce large quantities of data and robust software and data analysis pipelines are needed. Therefore, different software programs used for analysing such data were evaluated. Moreover, a pre-filtering algorithm was developed to classify good-quality and bad-quality spectra prior to the database searches. Th-lymphocytes can differentiate into Th1 or Th2 cells based on surrounding antigens, co-stimulatory molecules, and cytokines. Both subsets have individual cytokine secretion profiles and specific functions. Th1 cells participate in the cellular immunity against intracellular pathogens, while Th2 cells have important role in the humoral immunity against extracellular parasites. An abnormal response of Th1 and Th2 cells and imbalance between the subsets are charasteristic of several diseases. Th1 specific reactions and cytokines have been detected in autoimmune diseases, while Th2 specific response and cytokine profile is common in allergy and asthma. In this Ph. D. thesis mass spectrometry-based proteomics was used to study the effects of Th1 and Th2 promoting cytokines IL-12 and IL-4 on the proteome of Th lymphocytes. Characterization of microsomal fraction proteome extracted from IL-12 treated lymphobasts and IL-4 stimulated cord blood CD4+ cells resulted in finding of cytokine regulated proteins. Galectin-1 and CD7 were down-regulated in IL-12 treated cells, while IL-4 stimulation decreased the expression of STAT1, MXA, GIMAP1, and GIMAP4. Interestingly, the transcription of both GIMAP genes was up-regulated in Th1 polarized cells and down-regulated in Th2 promoting conditions.

Mitotic regulation by Polo-like kinase 1 and the Chromosomal Passenger Complex

During mitosis, the duplicated genome must be accurately divided between two daughter cells. Polo-like kinase 1 (Plk1) and Aurora B kinase, together with its binding partners Incenp, Survivin and Borealin (chromosomal passenger complex, CPC), have key roles in coordinating mitotic events. The accuracy of cell division is safeguarded by a signaling cascade termed the mitotic spindle checkpoint (SC), which ensures that chromosomes are not physically separated before correct bipolar attachments have been formed between kinetochores and spindle microtubules (MT). An inhibitory “wait anaphase” signal, which delays chromosome separation (anaphase onset), is created at individual kinetochores and broadcasted throughout the cell in response to lack of kinetochore-microtubule (kMT) attachment or proper interkinetochore tension. It is believed that the fast turnover of SC molecules at kinetochores contributes to the cell’s ability to produce this signal and enables rapid responses to changing cellular conditions. Kinetochores that lack MT attachment and tension express a certain phosphoepitope called the 3F3/2 phosphoepitope, which has been linked to SC signaling. In the experimental part, we investigated the regulation of the 3F3/2 phosphoepitope, analyzed whether CPC molecules turn over at centromeres, and dissected the mitotic roles of the CPC using a microinjection technique that allowed precise temporal control over its function. We found that the kinetochore 3F3/2 phosphoepitope is created by Plk1, and that CPC proteins exhibit constant exchange at centromeres. Moreover, we found that CPC function is necessary in the regulation of chromatid movements and spindle morphology in anaphase. In summary, we identified new functions of key mitotic regulators Plk1 and CPC, and provided insighs into the coordination of mitotic events.

Kroppen som bärare av hälsa och lidande

The overall aim of this study is to seek new knowledge and deeper understanding of the body as a phenomenon from a caring science point of view. By means of a hermeneutic definition, the body is studied on a contextual as well as an ontological level in order to create a deeper understanding for human beings in relation to health and suffering. The study focuses of the body as a perspective of human beings. It is important for the knowledge growth in caring science to create a deeper understanding for the body, thus making it possible to understand patients in nursing care. The overall methodology is a hermeneutic definition which covers a contextual and an ontological concept definition. In the three empirical studies, Giorgi’s phenomenological method was used. The first empirical study comprises twelve students’ statements about experiences of their body in different situatons in life. The second study is composed of interviews with fifteen patients who had been afflicted by illness and been subjected to surgical treatment. In the third empirical study, ten patients who had been cared for in perioperative nursing care were interviewed. In the data analysis, the essential meaning of the body as a phenomenon is described, along with its variations and nuances. In the ontological determination of the body, an etymologic and semantic analysis is carried out, as well as a qualitative analysis of ideas, where the material is comprised of chosen texts on the body from different perspectives. In the concluding analysis the results were synthesized. The result of the first empirical study shows that a body is expressive and manifests movement in its striving for dignity. The body harbours language and inherent powers to cope with the unexpected, as well as feelings of anxiety, fear and powerlessness. The second study shows that the body is experienced as mysterious when it is afflicted by illness, but it is also found mysterious as an opponent to man and life. A battle is fought between the illness that breaks down the body, and human beings fighting to keep their unity whole. The body appears as a prison and a host for a threatening illness. The body bears a feeling of powerlessness when it is changed by illness and suffering. In a care and treatment context, the body is objectified by the patient and the caregiver. It is the illness that forces the patient to sacrifice parts of the body in order to once again become whole in the unity. The third study shows that the patient in a perioperative nursing context delivers him-/herself over to the hands of the caregiver, who defends and protects body and life. The patient experiences a sense of well-being when the caretaker receives him/her and protects the body from dangers. Suffering is alleviated when the patients are allowed to talk about what has happened in their body. The result of the semantic analysis shows that the body as a concept is described as bending around the human soul and spirit. Linguistically, dimensions like corporeal, shape, totality, unity and mortal clay, are described. Different ideas about the body described it as: a material animate part of man, active and demanding, something that perceives its surrounding world and as a subjective body of senses, thoughts and language. Ideas about the body also describe it as a biological and physiological, living organism, submitted to the laws of nature, a passive apparatus and a socially constructed gender. The results of the different studies were synthesized and reflected against a caring science perspective. The research has created a deeper understanding for the body as a material abode and as an entity of body, soul and spirit.

DPS-Like Peroxide Resistance Protein: Structural and Functional Studies on a Versatile Nanocontainer

Oxidative stress is a constant threat to almost all organisms. It damages a number of biomolecules and leads to the disruption of many crucial cellular functions. It is caused by reactive oxygen species (ROS), such as hydrogen peroxide (H2O₂), superoxide (•O₂ -), and hydroxyl radical (•OH). The most harmful of these compounds is •OH, which is only formed in cells in the presence of redox-cycling transition metals, such as iron and copper. Bacteria have developed a number of mechanisms to cope with ROS. One of the most widespread means employed by bacteria is the DNA-binding proteins from starved cells (Dps). Dps proteins protect the cells by binding and oxidizing Fe2+, thus greatly reducing the production of •OH. The oxidized iron is stored inside the protein as an iron core. In addition, Dps proteins bind directly to DNA forming a protective coating that shields DNA from harmful agents. Moreover, Dps proteins have been found to elicit other protective functions in cells and to participate in bacterial virulence. Dps proteins are of special importance to Streptococci owing to the lack of catalase in this genus of bacteria.This study was focused on structural and functional characterization of streptococcal Dpslike peroxide resistance (Dpr) proteins. Initially, crystal structures of Streptococcus pyogenes Dpr were determined. The data confirmed the presence of a di-metal ferroxidase center (FOC) in Dpr proteins and revealed the presence of a novel N-terminal helix as well as a surface metal-binding site. The crystal structures of Streptococcus suis Dpr complexed with transition metals demonstrated the metal specificity of the FOC. Solution binding studies also indicated the presence of a di-metal FOC. These results suggested a possible role for Dpr in the detoxification of various metals. Iron was found to mineralize inside the protein as ferrihydrite based on X-ray absorption spectroscopy data. The iron core was found to exhibit clear superparamagnetic behaviour using magnetic and Mössbauer measurements. The results from this study are expected to further increase our understanding on the binding, oxidation, and mineralization of iron and other metals in Dpr proteins. In particular, the structural and magnetic properties of the iron core can form a basis for potential new applications in nanotechnology. From the streptococcal viewpoint, the results would help in understanding better the complicated picture of bacterial pathogenesis. Dpr proteins may also provide a novel target for drug design due to their tight involvement in bacterial virulence.

Feeling vs. Being like a Domestic Goddess: Cookbooks and Lifestyle Choices

Tämä pro gradu -tutkielma tarkastelee, miten keittokirjat muovaavat pääasiassa naispuolista lukijakuntaansa. Tärkein kysymys, johon tutkielmassa on etsitty vastausta on, että onko naisilla, menneiden sukupolvien taisteltua vuosikymmeniä tasa-arvon puolesta, oikeus valita viettää aikaa keittiössä ja oikeasti nauttiakin siitä. Kahtena päälähteenä tutkielmassa on käytetty brittiläisen Nigella Lawsonin keittokirjoja How to Eat ja How to be a Domestic Goddess. Näiden kirjojen analysoinnin ja muiden lähteiden avulla tutkielmassa on käsitelty ruuanlaiton ja leipomisen nautittavuutta ja sitä onko se ylipäätään sallittua vai syntistä. Lawson on julkaissut urallaan sitten vuoden 1998 yhteensä yhdeksän keittokirjaa, joiden lisäksi kirjojen tueksi on tehty useita televisiosarjoja. How to Eat on yleispätevä opas hyvän ruuan nautintoihin ja periaatteisiin, How to be a Domestic Goddess taas sisältää lähinnä leivontareseptejä. Nämä kaksi kirjaa ovat Lawsonin ensimmäiset keittokirjat. Nigella Lawsonin keittokirjat eivät ole vain reseptikokelmia eivätkä reseptit vain aineisosalistoja ja valmistusohjeita. Lawsonin kirjoja voi lukea kirjallisuutena eikä vain reseptien takia. Lawson viittaa usein naisen asemaan ja yrittää vakuuttaa lukijoitaan ruuanlaiton ja leipomisen nautittavuudesta.

Food webs in the era of molecular revolution – Like resolving the Gordian knot with a tricorder

Living nature consists of countless organisms, which are classified into millions of species. These species interact in many ways; for example predators when foraging on their prey, insect larvae consuming plants, and pathogenic bacteria drifting into humans. In addition, abiotic nature has a great initiative impact on life through many factors (including sunlight, ambient temperature, and water. In my thesis, I have studied interactions among different life forms in multifaceted ways. The webs of these interactions are commonly referred to as food webs, describing feeding relationships between species or energy transfer from one trophic level to another. These ecological interactions – whether they occur between species, between individuals, or between microorganisms within an individual – are among the greatest forces affecting natural communities. Relationships are tightly related to biological diversity, that is, species richness and abundances. A species is called a node in food web vocabulary, and its interactions to other species are called links. Generally, Artic food webs are considered to be loosely linked, simple structures. This conception roots into early modern food webs, where insects and other arthropods, for example, were clumped under one node. However, it has been shown that arthropods form the greatest part of diversity and biomass both in the tropics and in Arctic areas. Earlier challenges of revealing the role of insects and microorganisms in interactions webs have become possible with the help of recent advances in molecular techniques. In the first chapter, I studied the prey diversity of a common bat, Myotis daubentonii, in southwestern Finland. My results proved M. daubentonii being a versatile predator whose diet mainly consists of aquatic insects, such as chironomid midges. In the second chapter, I expanded the view to changes in seasonal and individual-based variation in the diet of M. daubentonii including the relationship between available and observed prey. I found out that chironomids remain the major prey group even though their abundance decreases in proportion to other insect groups. Diet varied a lot between individuals, although the differences were not statistically significant. The third chapter took the study to a large network in Greenland. I showed that Artic food webs are very complex when arthropods are taken into account. In the fourth chapter, I examined the bacterial flora of M. daubentonii and surveyed the zoonotic potential of these bacteria. I found Bartonella bacteria, of which one was described as a new species named after the locality of discovery. I have shown in my thesis that Myotis daubentonii as a predator links many insect species as well as terrestrial and aquatic environments. Moreover, I have exposed that Arctic food webs are complex structures comprising of many densely linked species. Finally, I demonstrated that the bacterial flora of bats includes several previously unknown species, some of which could possibly turn in to zoonosis. To summarize, molecular methods have untied several knots in biological research. I hope that this kind of increasing knowledge of the surrounding nature makes us further value all the life forms on earth.