Noncommutative Quantum Field Theories and UV/IR Mixing

Our present-day understanding of fundamental constituents of matter and their interactions is based on the Standard Model of particle physics, which relies on quantum gauge field theories. On the other hand, the large scale dynamical behaviour of spacetime is understood via the general theory of relativity of Einstein. The merging of these two complementary aspects of nature, quantum and gravity, is one of the greatest goals of modern fundamental physics, the achievement of which would help us understand the short-distance structure of spacetime, thus shedding light on the events in the singular states of general relativity, such as black holes and the Big Bang, where our current models of nature break down. The formulation of quantum field theories in noncommutative spacetime is an attempt to realize the idea of nonlocality at short distances, which our present understanding of these different aspects of Nature suggests, and consequently to find testable hints of the underlying quantum behaviour of spacetime. The formulation of noncommutative theories encounters various unprecedented problems, which derive from their peculiar inherent nonlocality. Arguably the most serious of these is the so-called UV/IR mixing, which makes the derivation of observable predictions especially hard by causing new tedious divergencies, to which our previous well-developed renormalization methods for quantum field theories do not apply. In the thesis I review the basic mathematical concepts of noncommutative spacetime, different formulations of quantum field theories in the context, and the theoretical understanding of UV/IR mixing. In particular, I put forward new results to be published, which show that also the theory of quantum electrodynamics in noncommutative spacetime defined via Seiberg-Witten map suffers from UV/IR mixing. Finally, I review some of the most promising ways to overcome the problem. The final solution remains a challenge for the future.

The genome packaging machinery of dsDNA bacteriophage PRD1

Viral genomes are encapsidated within protective protein shells. This encapsidation can be achieved either by a co-condensation reaction of the nucleic acid and coat proteins, or by first forming empty viral particles which are subsequently packaged with nucleic acid, the latter mechanism being typical for many dsDNA bacteriophages. Bacteriophage PRD1 is an icosahedral, non-tailed dsDNA virus that has an internal lipid membrane, the hallmark of the Tectiviridae family. Although PRD1 has been known to assemble empty particles into which the genome is subsequently packaged, the mechanism for this has been unknown, and there has been no evidence for a separate packaging vertex, similar to the portal structures used for packaging in the tailed bacteriophages and herpesviruses. In this study, a unique DNA packaging vertex was identified for PRD1, containing the packaging ATPase P9, packaging factor P6 and two small membrane proteins, P20 and P22, extending the packaging vertex to the internal membrane. Lack of small membrane protein P20 was shown to totally abolish packaging, making it an essential part of the PRD1 packaging mechanism. The minor capsid proteins P6 was shown to be an important packaging factor, its absence leading to greatly reduced packaging efficiency. An in vitro DNA packaging mechanism consisting of recombinant packaging ATPase P9, empty procapsids and mutant PRD1 DNA with a LacZ-insert was developed for the analysis of PRD1 packaging, the first such system ever for a virus containing an internal membrane. A new tectiviral sequence, a linear plasmid called pBClin15, was identified in Bacillus cereus, providing material for sequence analysis of the tectiviruses. Analysis of PRD1 P9 and other putative tectiviral ATPase sequences revealed several conserved sequence motifs, among them a new tectiviral packaging ATPase motif. Mutagenesis studies on PRD1 P9 were used to confirm the significance of the motifs. P9-type putative ATPase sequences carrying a similar sequence motif were identified in several other membrane containing dsDNA viruses of bacterial, archaeal and eukaryotic hosts, suggesting that these viruses may have similar packaging mechanisms. Interestingly, almost the same set of viruses that were found to have similar putative packaging ATPases had earlier been found to share similar coat protein folds and capsid structures, and a common origin for these viruses had been suggested. The finding in this study of similar packaging proteins further supports the idea that these viruses are descendants of a common ancestor.