Efficient delivery of scalable media streaming over lossy networks

Recent years have witnessed a rapid growth in the demand for streaming video over the Internet, exposing challenges in coping with heterogeneous device capabilities and varying network throughput. When we couple this rise in streaming with the growing number of portable devices (smart phones, tablets, laptops) we see an ever-increasing demand for high-definition videos online while on the move. Wireless networks are inherently characterised by restricted shared bandwidth and relatively high error loss rates, thus presenting a challenge for the efficient delivery of high quality video. Additionally, mobile devices can support/demand a range of video resolutions and qualities. This demand for mobile streaming highlights the need for adaptive video streaming schemes that can adjust to available bandwidth and heterogeneity, and can provide us with graceful changes in video quality, all while respecting our viewing satisfaction. In this context the use of well-known scalable media streaming techniques, commonly known as scalable coding, is an attractive solution and the focus of this thesis. In this thesis we investigate the transmission of existing scalable video models over a lossy network and determine how the variation in viewable quality is affected by packet loss. This work focuses on leveraging the benefits of scalable media, while reducing the effects of data loss on achievable video quality. The overall approach is focused on the strategic packetisation of the underlying scalable video and how to best utilise error resiliency to maximise viewable quality. In particular, we examine the manner in which scalable video is packetised for transmission over lossy networks and propose new techniques that reduce the impact of packet loss on scalable video by selectively choosing how to packetise the data and which data to transmit. We also exploit redundancy techniques, such as error resiliency, to enhance the stream quality by ensuring a smooth play-out with fewer changes in achievable video quality. The contributions of this thesis are in the creation of new segmentation and encapsulation techniques which increase the viewable quality of existing scalable models by fragmenting and re-allocating the video sub-streams based on user requirements, available bandwidth and variations in loss rates. We offer new packetisation techniques which reduce the effects of packet loss on viewable quality by leveraging the increase in the number of frames per group of pictures (GOP) and by providing equality of data in every packet transmitted per GOP. These provide novel mechanisms for packetizing and error resiliency, as well as providing new applications for existing techniques such as Interleaving and Priority Encoded Transmission. We also introduce three new scalable coding models, which offer a balance between transmission cost and the consistency of viewable quality.

Ribosomal frameshifting and transcriptional slippage: from genetic steganography and cryptography to adventitious use

Genetic decoding is not ‘frozen’ as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational ‘correction’ of problem or ‘savior’ indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5′ or 3′ of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3′ from the shift site. Transcriptional realignment at slippage-prone sequences also generates productively utilized products encoded trans-frame with respect to the genomic sequence. This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression.

A non-classical LysR-type transcriptional regulator PA2206 is required for an effective oxidative stress response in Pseudomonas aeruginosa

LysR-type transcriptional regulators (LTTRs) are emerging as key circuit components in regulating microbial stress responses and are implicated in modulating oxidative stress in the human opportunistic pathogen Pseudomonas aeruginosa. The oxidative stress response encapsulates several strategies to overcome the deleterious effects of reactive oxygen species. However, many of the regulatory components and associated molecular mechanisms underpinning this key adaptive response remain to be characterised. Comparative analysis of publically available transcriptomic datasets led to the identification of a novel LTTR, PA2206, whose expression was altered in response to a range of host signals in addition to oxidative stress. PA2206 was found to be required for tolerance to H2O2 in vitro and lethality in vivo in the Zebrafish embryo model of infection. Transcriptomic analysis in the presence of H2O2 showed that PA2206 altered the expression of 58 genes, including a large repertoire of oxidative stress and iron responsive genes, independent of the master regulator of oxidative stress, OxyR. Contrary to the classic mechanism of LysR regulation, PA2206 did not autoregulate its own expression and did not influence expression of adjacent or divergently transcribed genes. The PA2214-15 operon was identified as a direct target of PA2206 with truncated promoter fragments revealing binding to the 5'-ATTGCCTGGGGTTAT-3' LysR box adjacent to the predicted -35 region. PA2206 also interacted with the pvdS promoter suggesting a global dimension to the PA2206 regulon, and suggests PA2206 is an important regulatory component of P. aeruginosa adaptation during oxidative stress.