Peanut allergy is a public health concern which affects a significant proportion of the population. Accidental exposure to peanut can cause severe and fatal reactions in peanut allergic individuals and currently their only safeguard is to practise careful avoidance. Identification and protection of at-risk members of the allergic population is critical in managing this life-threatening condition. This thesis produces key data to enable this. A prospective study was performed on 60 peanut allergic participants to determine thresholds of reactivity to peanut using oral challenges with incrementally increasing amounts of peanut protein. Following a double-blind placebo-controlled peanut challenge, participants received three further peanut challenges, two with co-factors: sleep deprivation and exercise, and one without. Severity was measured using a numerical scale derived from symptoms and serum tryptase was measured at each challenge. A total of 187 challenges were performed. Findings were that the median amount of peanut protein which induces a reaction in 10% of the population (ED10) was 12.3mg (95% CI 7.3,20.4) equivalently this suggests that 90% of the allergic population will not react to doses below this level. Both sleep deprivation and exercise have a significant effect on lowering reaction threshold (ED10), by 5 times and 2.5 times respectively. Separately there is a reduction in threshold with successive challenges. Co-factors also significantly increased symptom severity during challenge reactions. In particular sleep deprivation significantly increased the severity of gastrointestinal symptoms suggesting that a stressful stimulus may affect intestinal permeability. Evidence was provided for the importance of asthma as a risk factor which increased the severity of respiratory symptoms during reaction. Using a novel visual analogue scale for measuring the participant’s perception of severity, a poor correlation was observed between the participant’s perception of the reaction and the overall numerical severity score, suggesting that participants misperceive severe symptoms. This thesis provides the first data showing that symptom patterns in repeated challenges show a high degree of homogeneity within individuals, but importantly that this symptom homogeneity is also observed across individuals. Lastly the utility of serum tryptase in identifying food allergic reactions has been disputed previously. This thesis provides evidence of its value and identifies a rise cut-off of 30% as being diagnostic of a food allergic reaction, but cautions that acute levels must be compared with baseline as this rise may occur within the normal range.

<p>The development of a multicellular organism is programmed by complex patterns of gene expression. In eukaryotic cells, genes are packaged by histone proteins into chromatin. Chromatin regulators often function as transcription co-factors. </p><p>In this study, we have investigated the function of four co-factors, dAda2b, Reptin, Ebi and Brakeless during development of the fruit fly<i> Drosophila</i> <i>melanogaster</i>. dAda2b and Reptin belong to histone acetyl transferase (HAT) complexes, a SAGA-like complex and the Tip60 complex, respectively. We generated <i>dAda2b </i>mutants and found that lack of dAda2b strongly affects global histone acetylation and viability. We further propose that Ada2 may be involved in DNA repair. Our studies revealed new roles of Reptin and other Tip60 complex components in Polycomb Group mediated repression and heterochromatin formation, thereby promoting generation of silent chromatin.</p><p>During embryogenesis, transcriptional repressors establish localized and tissue-specific patterns of gene expression. In this thesis, we identified two novel co-repressors in the early embryo, Ebi and Brakeless. Ebi genetically and physically interacts with the Snail repressor. The Ebi-interaction motif in the Snail protein is essential for Snail function<i> in</i> <i>vivo</i> and is evolutionarily conserved in insects. We further demonstrated that Ebi associates with histone deacetylase 3 (HDAC3) and that histone deacetylation is part of the mechanism by which Snail mediates transcriptional repression. </p><p>We isolated Brakeless in a genetic screen for novel regulators of gene expression during embryogenesis. We found that mutation of <i>brakeless</i> impairs function of the Tailless repressor. Brakeless associates with Atrophin, another Tailless corepressor, and they function together in Tailless-mediated repression. </p><p>In summary, transcription co-factors, including chromatin regulators, are selectively required in distinct processes during development.</p>

The development of a multicellular organism is programmed by complex patterns of gene expression. In eukaryotic cells, genes are packaged by histone proteins into chromatin. Chromatin regulators often function as transcription co-factors. In this study, we have investigated the function of four co-factors, dAda2b, Reptin, Ebi and Brakeless during development of the fruit fly Drosophila melanogaster. dAda2b and Reptin belong to histone acetyl transferase (HAT) complexes, a SAGA-like complex and the Tip60 complex, respectively. We generated dAda2b mutants and found that lack of dAda2b strongly affects global histone acetylation and viability. We further propose that Ada2 may be involved in DNA repair. Our studies revealed new roles of Reptin and other Tip60 complex components in Polycomb Group mediated repression and heterochromatin formation, thereby promoting generation of silent chromatin. During embryogenesis, transcriptional repressors establish localized and tissue-specific patterns of gene expression. In this thesis, we identified two novel co-repressors in the early embryo, Ebi and Brakeless. Ebi genetically and physically interacts with the Snail repressor. The Ebi-interaction motif in the Snail protein is essential for Snail function in vivo and is evolutionarily conserved in insects. We further demonstrated that Ebi associates with histone deacetylase 3 (HDAC3) and that histone deacetylation is part of the mechanism by which Snail mediates transcriptional repression. We isolated Brakeless in a genetic screen for novel regulators of gene expression during embryogenesis. We found that mutation of brakeless impairs function of the Tailless repressor. Brakeless associates with Atrophin, another Tailless corepressor, and they function together in Tailless-mediated repression. In summary, transcription co-factors, including chromatin regulators, are selectively required in distinct processes during development.

Purpose of Review: Interactions between microorganisms can alter subsequent disease outcomes. Human papilloma virus (HPV) and Chlamydia trachomatis (CT) establish human genital co-infections, and CT infection is a co-factor for HPV-induced cervical cancer. This review focuses upon (i) data indicating that clinically significant interactions occur and (ii) proposed mechanisms underlying these outcomes. Recent Findings: Epidemiological surveys indicate that (i) simultaneous HPV/CT genital co-infections are common; (ii) CT co-infection accelerates HPV-induced cytopathology; and (iii) HPV infection facilitates CT infection. Single-infection studies suggest specific molecular mechanisms by which co-infection alters clinical outcomes, including (i) HPV E6/E7 protein modification of host cell pathways enhances CT replication or immune evasion and (ii) CT-mediated host cell or neutrophil dysfunctions promote HPV-mediated neoplasia. Summary: There are multiple avenues for future dissection of HPV/CT interactions. Moreover, the known and potential health consequences of co-infection highlight the need for improving current HPV vaccines and developing an effective CT vaccine.

Transkription är stokastisk, där utbrottsmässiga episoder av RNA-transkription genererar RNA-molekyler. Trots att detta är en kärndel av eukaryotiskt liv, är lite känt om hur DNA-bindande transkriptionsfaktorer och transkriptionella kofaktorer formar gen-specifik transkriptionell utbrottskinetik. Syftet med detta examensarbete var att tyda rollerna hos kofaktorerna Med14 och P300/CBP inom transkriptionell utbrottskinetik. För detta ändamål användes Auxin inducible degron systemet för snabb nedbrytning av Med14 eller P300/CBP-proteiner i HCT116-celler, följt av Smart-seq3xpress single cell-RNA-sekvensering. Ett särskild fokus i denna avhandling var även att utvärdera förmågan att härleda direkta  genuttrycksförändringar genom analys av introniska reads – detta då introner ko-transkriptionellt splitsas och dess nyttjande skulle fånga effekter av mycket närliggande transkription. Resultaten visar en tidsberoende minskning av introniskt innehåll och en nedreglering av genuttryck för majoriteten av generna i de behandlade cellinjerna, medan opåverkade kontroller inte visar sådana trender. Utbrottskinetikresultaten indikerar att det inte finns någon korrelation mellan P300/CBP-pertuberade cellers geners ursprungliga utbrottsstorlek och några trender i genuttryckets relativa förändring, medan detsamma kan sägas för Med14-pertuberade cellers geners utbrottsfrekvens. Svaga trender från P300/CBP-påverkade cellers utbrottskinetik och uttrycksändring kan antyda att deras utbrottsfrekvens och inte utbrottsstorlek har påverkats. Resultaten antyder att perturbationen var framgångsrik och att P300/CBP inte påverkar utbrottsstorlek samt att Med14 kan reglera utbrottsfrekvensen för alla påverkade gener i lika hög grad. Vidare forskning behövs inom utbrottskinetikdata för att utöka vår förståelse av denna studies implikationer gällande Med14:s och P300/CBP:s reglerande roller på transkriptionella utbrott. / Transcription is stochastic with episodes of RNA transcription generating bursts of RNA molecules. Despite being a core part of eukaryotic life, little is known about how DNA-binding transcription factors and transcriptional co-factors shape gene-specific transcriptional bursting kinetics. The aim of this thesis was to decipher the roles of the co-factors Med14 and P300/CBP in transcriptional burst kinetics. To this end, the Auxin inducible degron system was used for rapid Med14 or P300/CBP protein degradation in HCT116 cells, followed by Smart-seq3xpress single-cell RNA-sequencing. A particular focus of this thesis was to evaluate the abilities to infer direct gene expression changes by analysis of intronic reads – since introns are co-transcriptionally spliced and would capture very recent transcription. Results show a time dependent decrease of intronic contents and a downregulation in gene expression for a majority of genes in the perturbed cell lines, while unperturbed controls show no such trends. Bursting kinetics results indicate that there is no correlation between P300/CBP perturbed cells’ gene’s original bursting size and any trends in gene expression fold change while the same can be said for Med14 perturbed cell’s gene’s burst frequency. Weak trends from P300/CBP perturbed cells’ bursting kinetics and expression fold change could imply that their bursting frequency and not bursting size has been affected. The results imply that the perturbation was successful and that P300/CBP does not affect bursting size as well as that Med14 could regulate bursting frequency for all affected genes to an equal degree. Further research is needed into the bursting kinetics data to expand our understanding of this study’s implications regarding regulatory roles of Med14 and P300/CBP on transcriptional bursting.