The sequencing of several ant genomes within the last six years open new research avenues for understanding not only the genetic basis of social species but also the complex systems such as immune responses in general. Similar to other social insects, ants live in cooperative colonies, often in high densities and with genetically identical or closely related individuals. The contact behaviours and crowd living conditions allow the disease to spread rapidly through colonies. Nevertheless, ants can efficiently combat infections by using diverse and effective immune mechanisms. However, the components of the immune system of carpenter ant Camponotus floridanus and also the factors in bacteria that facilitate infection are not well understood. To form a better view of the immune repository and study the C. floridanus immune responses against the bacteria, experimental data from Illumina sequencing and mass-spectrometry (MS) data of haemolymph in normal and infectious conditions were analysed and integrated with the several bioinformatics approaches. Briefly, the tasks were accomplished in three levels. First, the C. floridanus genome was re-annotated for the improvement of the existing annotation using the computational methods and transcriptomics data. Using the homology based methods, the extensive survey of literature, and mRNA expression profiles, the immune repository of C. floridanus were established. Second, large-scale protein-protein interactions (PPIs) and signalling network of C. floridanus were reconstructed and analysed and further the infection induced functional modules in the networks were detected by mapping of the expression data over the networks. In addition, the interactions of the immune components with the bacteria were identified by reconstructing inter-species PPIs networks and the interactions were validated by literature. Third, the stage-specific MS data of larvae and worker ants were analysed and the differences in the immune response were reported. Concisely, all the three omics levels resulted to multiple findings, for instance, re-annotation and transcriptome profiling resulted in the overall improvement of structural and functional annotation and detection of alternative splicing events, network analysis revealed the differentially expressed topologically important proteins and the active functional modules, MS data analysis revealed the stage specific differences in C. floridanus immune responses against bacterial pathogens. Taken together, starting from re-annotation of C. floridanus genome, this thesis provides a transcriptome and proteome level characterization of ant C. floridanus, particularly focusing on the immune system responses to pathogenic bacteria from a biological and a bioinformatics point of view. This work can serve as a model for the integration of omics data focusing on the immuno-transcriptome of insects. / Das Sequenzieren mehrerer Ameisen Genome innerhalb der letzten 6 Jahre eröffnete neue Forschungswege, um nicht nur die genetische Grundlade sozialer Arten, sondern auch komplexere Systeme wie generelle Immunantworten zu untersuchen. Ähnlich zu anderen sozialen Insekten leben Ameisen in Kolonien, oft mit einer sehr hohen Dichte mit genetisch übereinstimmenden oder nah verwandten Individuen. Das Sozialverhalten und die engen Lebensumstände führen dazu, dass sich Krankheiten in Kolonien schnell ausbreiten können. Dennoch können Ameisen mit der Nutzung ihrer komplexen Immunsystemmechanismen Infektionen effektiv abwehren. Die Zusammensetzung des Immunsystems der Rossameise Camponotus floridanus (C. floridanus) und die Faktoren der Bakterien, welche die Infektionen verursachen sind noch nicht gut untersucht. Um einen besseren Überblick über die verschiedenen Gruppen der Immun- Gene zu bekommen und um die Immunantworten von C. floridanus gegen Bakterien zu untersuchen haben wir experimentelle Daten der Illumina Sequenzierung und der Massenspektrometrie (MS) aus der Hämolymphe unter normalen und unter infizierten Bedingungen analysiert und über verschiedene bioinformatische Ansätzen zusammengefasst. Die Aufgabe wurde in drei Ebenen unterteilt. Zuerst wurde das Genom von C. floridanus neu annotiert, die Verbesserung der existierenden Annotation wurde rechnerisch und mit Transkriptom- Daten erreicht. Mit der Nutzung der auf Homologie- basierenden Methoden, der umfassenden Überprüfung der Literatur und der Nutzung von mRNA Genexpressionsanalysen wurde für C. floridanus dieser Überblick erstellt. Anschließend wurden größere Protein- Protein- Interaktionen (PPI) und Signalnetzwerke von C. floridanus rekonstruiert und analysiert und daraufhin wurden die Infektions-induzierten funktionalen Module im Netzwerk entdeckt und die Expressionsdaten über Netzwerke abgebildet. Zusätzlich wurden die Anteile der Immunantwort bei der Interaktion mit Bakterien mittels der Rekonstruktion von zwischenartlichen PPI Netzwerken identifiziert und diese Interaktionen wurden mit Literaturwerten validiert. In der dritten und letzten Phase wurden Daten der Stadium- spezifischen Massenspektrometrie (MS) von Larven- und Arbeiterameisen analysiert und die Unterschiede in den Immunantworten aufgezeichnet. Zusammengefasst lieferten alle drei Omiks- Ebenen jeweils viele Ergebnisse, zum Beispiel führte die neue Annotation und das Transkription- Profil zu einer generellen Verbesserung der strukturellen und funktionalen Annotation und dem Aufspüren von alternativen Splicing- Ereignissen. Die Netzwerkanalyse deckte die unterschiedlich exprimierten topologisch wichtigen Proteine und die aktiven funktionalen Module auf, die Analyse der MS- Daten erbrachte Ergebnisse über die Stadium- spezifischen Unterschiede in der Immunantwort von C. floridanus gegen bakterielle Pathogene. Rundum, beginnend mit der neuen Annotation des Genoms von C. floridanus stellt diese Arbeit eine Transkriptom- und Protein Charakterisierung der Ameise C. floridanus dar. Besonders lag der Fokus auf die Antworten des Immunsystems auf Pathogene Bakterien aus biologischer- und bioinformatischer Sicht. Diese Arbeit kann als Vorlage für die Integration von Omiks Daten dienen, welche sich auf die Immun- Transkriptome von Insekten fokussieren.

München, Techn. Universiẗat, Diss., 2007.

<p>Probably no group of organisms has been as important as bacteriophages when it comes to the understanding of fundamental biological processes like transcriptional control, DNA replication, site-specific recombination, e.t.c.</p><p>The work presented in this thesis is a contribution towards the complete understanding of these organisms. Two proteins, integrase, and Cox, which are important for the choice of the life mode of bacteriophage P2, are investigated. P2 is a temperate phage, i.e. it can either insert its DNA into the host chromosome (by site-specific recombination) and wait (lysogeny), or it can produce new progeny with the help of the host protein machinery and thereafter lyse the cell (lytic cycle). The integrase protein is necessary for the integration and excision of the phage genome. The Cox protein is involved as a directional factor in the site-specific recombination, where it stimulates excision and inhibits integration. It has been shown that the Cox protein also is important for the choice of the lytic cycle. The choice of life mode is regulated on a transcriptional level, where two mutually exclusive promoters direct whether the lytic cycle (Pe) or lysogeny (Pc) is chosen. The Cox pro-tein has been shown to repress the Pc promoter and thereby making tran-scription from the Pe promoter possible, leading to the lytic cycle. Further, the Cox protein can function as a transcriptional activator on the parasite phage, P4. P4 has gained the ability to adopt the P2 protein machinery to its own purposes.</p><p>In this work the importance of the native size for biologically active integrase and Cox proteins has been determined. Further, structure-function analyses of the two proteins have been performed with focus on the protein-protein interfaces. In addition it is shown that P2 Cox and the P2 relative Wphi Cox changes the DNA topology upon specific binding. From the obtained results a mechanism for P2 Cox-DNA interaction is discussed.</p><p>The results from this thesis can be used in the development of a gene delivery system based on the P2 site-specific recombination system.</p>

<p> </p><p>The regulation of egg temperature requires the transfer of heat from the brood patch. Thus, the brood patch needs the presence of thermo receptors as well as an appropriate vasomotor response. During the incubation an exact detection of the egg’s temperature is essential. So, in this study we attempted to detect the presence and regulation of the expressionof  thermoTRP channels (thermo Transient Receptor Potential channels) (TRPV1, TRPV3, TRPV4, TRPM8 and TRPA1) during egg incubation. Six incubating Jungle fowl hens, and five non incubating jungle fowl hens and one jungle fowl cock were used as main samples and controls. Total RNA was extracted from liver, kidney, heart, blood, White Blood Cell, Dorsal Root Ganglion and skin. The samples from the skin were taken from the brood patch and inter scapular region. PCR investigation showed that different thermo TRP channels were expressed in different tissues. TRPV1, V3, V4 and M8 mRNA were detected in the skin of brood patch. However, V1 and V3 expression in the brood patch skin did not differ between broody and non broody hens. In conclusion, although considerable morphological changes in the skin of brood patch could be seen, the expression of TRPV1 and V3 channels did not change significantly, but this cannot exclude the alteration in the expression of TRP channels in different stages of broodiness or specific parts of skin like AVAs (Arteriovenous anastomosis) which will be the subject for more studies.</p>

<p>Innate immunity has received impressive attention in the past decade owing to the discovery of the Toll like receptors (TLRs) and the NOD-like receptors (NLRs). While the TLRs specialize in fighting microbes at the cell surface, the NLRs complement by detecting and responding to intracellular microbes. Recently, the non-microbe sensing NLR called inflammasomes, have been identified, which senses metabolic stress as well as certain pathogenic microbes and elicits host’s inflammatory response. <strong></strong></p><p>The NLR, NALP3 (formerly known as cryopyrin) forms a large cytoplasmic complex called the ‘inflammasome’ when NALP3, activated by a stimuli, associates with the adaptor proteins ASC and CARD-8. This interaction leads to the activation of pro-inflammatory caspase-1 which subsequently results in the formation of Interleukin (IL)-1β and IL-18. Mutations in the gene encoding NALP3, termed <em>NLRP3</em> can lead to its constitutive activation resulting in an uncontrolled production of IL-1β. These mutations have been implicated in hereditary inflammatory diseases, often grouped under cryopyrin associated periodic syndromes (CAPS).</p><p>This thesis describes a patient with a long history of arthritis and antibiotic resistant fever, but without the typical symptoms of CAPS. The patient was found to be a heterozygous carrier of two common polymorphisms Q705K in <em>NLRP3 </em>and C10X in the <em>CARD-8</em>. Experimental studies showed elevated levels of caspase-1 and IL-1β in the patient, and a total clinical remission was achieved by IL-1β blockade. These two polymorphisms combined, were found to occur in approximately 4% of the control population, suggesting the possibility of a genetic predisposition for inflammation in these individuals. Therefore, a cohort of rheumatoid arthritis (RA) patients, where elevated IL-1β could be one of the reasons behind chronic inflammation, was investigated. We found that carrying the combined polymorphisms resulted in increased RA susceptibility and a more severe disease course. Hypothetically, this subgroup of patients might benefit from IL-1β blockade. Additional studies are warranted to elucidate the functional effects of the two polymorphisms and to determine whether they identify a subgroup of patients that could benefit from IL-1 targeted therapy. Given the structural similarity of NALP3 to other NALPs, the possibility of involvement of the alternative, homologous genes cannot be eliminated.</p>

<p>Flera internationella studier har visat att elever i åldrar som motsvarar Sveriges gymnasienivå har svårt att förstå genetiska begrepp. Den främsta orsaken till detta är begreppens abstrakta karaktär. Syftet med den här studien är att skapa en webbaserad övning som konkretiserar de biomolekylära begreppen associerade med det centrala dogmat. I övningen studeras en människlig gen och dess transkript på nukleotidnivå och tillhörande proteiner på aminosyranivå. Genom att navigera i en publik gendatabas får eleverna följa det genetiska informationsflödet från gen till protein via omoget och moget mRNA. Övningen ger också ett exempel på kopplingen mellan genotyp och fenotyp. En första version av övningen testades på 29 elever varav 22 genomförde ett kunskapstest före och efter övningen och 28 deltog i en enkätundersökning om deras inställning till övningen. Dessutom intervjuades tre biologilärare på gymnasienivå. Övningen modifierades utifrån testresultaten, elevernas svar i enkätundersökningen och lärarnas kommentarer. Framförallt var det proteinets koppling till genen och sambandet mellan genens kodon och proteinets aminosyror som behövde förtydligas i övningen. Den slutliga versionen av övningen är inkluderad i denna uppsats.</p>

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<p>Vargen har varit hatad i alla tider, en symbol för något ont. Den jagar gärna i flock och tar renar och river får. I den här artikelserien undersöks orsaken bakom licensjakten på varg 2010, det vill säga bristen på acceptans, och om det är ett argument för att skjuta 10 procent av vargstammen som idag anses vara akut hotad. Artikelserien ger också svar på varför en vargpopulation som är så inavlad som vår inte kommer klara sig långsiktigt, och vad som krävs för att få en hållbar stam.</p>

<p>Asexual reproduction and polyploidy are relatively rare in animals with chromosomal sex determination and always represent a derived condition. To accomplish asexual reproduction several changes in gene expression are required in the mechanism of oogenesis. Polyploidy increases the cell volume and also gives rise to alterations in general physiology. Nevertheless, there are asexual animals that not only survive but seem to be doing better than their sexual progenitors. This is expressed in the distribution pattern called geographical parthenogenesis. Using molecular phylogeny, I here examine the evolution of Otiorynchid weevils, mainly <i>Otiorhynchus scaber</i> and <i>sulcatus</i> in an attempt to trace the evolutionary history and find out what causes the variation in success of different parthenogens. I also evaluate the contribution of asexuality, hybridity and polyploidy as explanations behind geographical parthenogenesis in insects. I conclude that what is called <i>O. scaber</i> is, in fact, a set of geographical polyploids as polyploidy and not asexuality explains the difference in clonal success. I also argue that <i>O. sulcatus</i> is a recently formed clonal species of non-hybrid origin that may well be a good example of a true general purpose genotype. I find little support for asexuality or a hybrid origin as explanations behind geographical parthenogenesis in insects. Finally, I argue that polyploidy in all eukaryotes should be seen as an opportunity for the species evolution, not as a limitation that ensures the demise of the taxa.</p>

<p>The aurochs Bos primigenius, extinct since 1627, was the wild progenitor of cattle. It is believed that all European cattle originate from one domestication event in the Near East 10 000 years ago. However, it is evident from the archaeological record that the aurochs survived into historic time and spent many years existing alongside domestic cattle. Thus, a question posed is whether aurochsen were locally domesticated or incorporated into early domestic cattle stock.</p><p>In this thesis, genetic techniques are applied to ancient and modern DNA from bovids in order to study questions relating to the origin of early European cattle. DNA from ancient specimens is fragmented and in greatly reduced quantity. Therefore mitochondrial DNA, present in many copies in the living cell, has long been dominating the ancient DNA research field. Analyses of ancient DNA presented in this work are based on both mitochondrial DNA and nuclear DNA, through the study of Single Nuclear Polymorohism (SNPs). A method for typing ancient SNPs was developed and applied to ancient cattle bones.</p><p>Mitochondrial DNA of cattle is structured into five geographically distributed lineages, the dominant lineage in Europe is also found in the Near East where additional lineages are found. This pattern has been attributed to the proposed domestication event in the Near East from where cattle carrying the single lineage were brought to Europe. However, the results presented here show that cattle domestication was more complicated than previously suggested. SNP data from extant cattle and bones from cattle and aurochs point towards a hybridisation event. European cattle appear indeed to have been domesticated in the Near East and brought in to the European continent from there. However, once in Europe, hybridisation with local aurochsen took place. It appears therefore that today’s cattle descend both from both Anatolian and European aurochsen.</p>