Functions and intramolecular interactions of ribosomal RNA in decoding of termination codons

Two regions in the 3$\prime$ domain of 16S rRNA (the RNA of the small ribosomal subunit) have been implicated in decoding of termination codons. Using segment-directed PCR random mutagenesis, I isolated 33 translational suppressor mutations in the 3$\prime$ domain of 16S rRNA. Characterization of the mutations by both genetic and biochemical methods indicated that some of the mutations are defective in UGA-specific peptide chain termination and that others may be defective in peptide chain termination at all termination codons. The studies of the mutations at an internal loop in the non-conserved region of helix 44 also indicated that this structure, in a non-conserved region of 16S rRNA, is involved in both peptide chain termination and assembly of 16S rRNA.^ With a suppressible trpA UAG nonsense mutation, a spontaneously arising translational suppressor mutation was isolated in the rrnB operon cloned into a pBR322-derived plasmid. The mutation caused suppression of UAG at two codon positions in trpA but did not suppress UAA or UGA mutations at the same trpA positions. The specificity of the rRNA suppressor mutation suggests that it may cause a defect in UAG-specific peptide chain termination. The mutation is a single nucleotide deletion (G2484$\Delta$) in helix 89 of 23S rRNA (the large RNA of the large ribosomal subunit). The result indicates a functional interaction between two regions of 23S rRNA. Furthermore, it provides suggestive in vivo evidence for the involvement of the peptidyl-transferase center of 23S rRNA in peptide chain termination. The $\Delta$2484 and A1093/$\Delta$2484 (double) mutations were also observed to alter the decoding specificity of the suppressor tRNA lysT(U70), which has a mutation in its acceptor stem. That result suggests that there is an interaction between the stem-loop region of helix 89 of 23S rRNA and the acceptor stem of tRNA during decoding and that the interaction is important for the decoding specificity of tRNA.^ Using gene manipulation procedures, I have constructed a new expression vector to express and purify the cellular protein factors required for a recently developed, realistic in vitro termination assay. The gene for each protein was cloned into the newly constructed vector in such a way that expression yielded a protein with an N-terminal affinity tag, for specific, rapid purification. The amino terminus was engineered so that, after purification, the unwanted N-terminal tag can be completely removed from the protein by thrombin cleavage, yielding a natural amino acid sequence for each protein. I have cloned the genes for EF-G and all three release factors into this new expression vector and the genes for all the other protein factors into a pCAL-n expression vector. These constructs will allow our laboratory group to quickly and inexpensively purify all the protein factors needed for the new in vitro termination assay. (Abstract shortened by UMI.) ^

Decoding Delay Minimization in Inter-Session Network Coding

Intra-session network coding has been shown to offer significant gains in terms of achievable throughput and delay in settings where one source multicasts data to several clients. In this paper, we consider a more general scenario where multiple sources transmit data to sets of clients over a wireline overlay network. We propose a novel framework for efficient rate allocation in networks where intermediate network nodes have the opportunity to combine packets from different sources using randomized network coding. We formulate the problem as the minimization of the average decoding delay in the client population and solve it with a gradient-based stochastic algorithm. Our optimized inter-session network coding solution is evaluated in different network topologies and is compared with basic intra-session network coding solutions. Our results show the benefits of proper coding decisions and effective rate allocation for lowering the decoding delay when the network is used by concurrent multicast sessions.

Growth Codes: Intermediate Performance Analysis and Application to Video

Growth codes are a subclass of Rateless codes that have found interesting applications in data dissemination problems. Compared to other Rateless and conventional channel codes, Growth codes show improved intermediate performance which is particularly useful in applications where partial data presents some utility. In this paper, we investigate the asymptotic performance of Growth codes using the Wormald method, which was proposed for studying the Peeling Decoder of LDPC and LDGM codes. Compared to previous works, the Wormald differential equations are set on nodes' perspective which enables a numerical solution to the computation of the expected asymptotic decoding performance of Growth codes. Our framework is appropriate for any class of Rateless codes that does not include a precoding step. We further study the performance of Growth codes with moderate and large size codeblocks through simulations and we use the generalized logistic function to model the decoding probability. We then exploit the decoding probability model in an illustrative application of Growth codes to error resilient video transmission. The video transmission problem is cast as a joint source and channel rate allocation problem that is shown to be convex with respect to the channel rate. This illustrative application permits to highlight the main advantage of Growth codes, namely improved performance in the intermediate loss region.

Decoding urban landscapes through the analysis of place names and imaginaries at a local scale.

Toponomastics is increasingly interested in the subjective role of place names in quotidian life. In the frame of Urban Geography, the interest in this matter is currently growing, as the recently change in modes of habitation has urged our discipline to find new ways of exploring the cities. In this context, the study of how name's significance is connected to a urban society constitutes a very interesting approach. We believe in the importance of place names as tools for decoding urban areas and societies at a local-scale. This consideration has been frequently taken into account in the analysis of exonyms, although in their case they are not exempt of political and practical implications that prevail over the tool function. The study of toponomastic processes helps us understanding how the city works, by analyzing the liaison between urban landscape, imaginaries and toponyms which is reflected in the scarcity of some names, in the biased creation of new toponyms and in the pressure exercised over every place name by tourists, residents and local government for changing, maintaining or eliminating them. Our study-case, Toledo, is one of the oldest cities in Spain, full of myths, stories and histories that can only be understood combined with processes of internal evolution of the city linked to the arrival of new residents and the more and more notorious change of its historical landscape. At a local scale, we are willing to decode the information which is contained in its toponyms about its landscape and its society.

Systematic analysis of the decoding delay on MVC decoders

We present a framework for the analysis of the decoding delay and communication latency in Multiview Video Coding. The application of this framework on MVC decoders allows minimizing the overall delay in immersive video-conference systems.

Systematic analysis of the decoding delay in multiview video

We present a framework for the analysis of the decoding delay in multiview video coding (MVC). We show that in real-time applications, an accurate estimation of the decoding delay is essential to achieve a minimum communication latency. As opposed to single-view codecs, the complexity of the multiview prediction structure and the parallel decoding of several views requires a systematic analysis of this decoding delay, which we solve using graph theory and a model of the decoder hardware architecture. Our framework assumes a decoder implementation in general purpose multi-core processors with multi-threading capabilities. For this hardware model, we show that frame processing times depend on the computational load of the decoder and we provide an iterative algorithm to compute jointly frame processing times and decoding delay. Finally, we show that decoding delay analysis can be applied to design decoders with the objective of minimizing the communication latency of the MVC system.

Rate-Adaptive LDPC-based key reconciliation for high performance quantum key distribution

The postprocessing or secret-key distillation process in quantum key distribution (QKD) mainly involves two well-known procedures: information reconciliation and privacy amplification. Information or key reconciliation has been customarily studied in terms of efficiency. During this, some information needs to be disclosed for reconciling discrepancies in the exchanged keys. The leakage of information is lower bounded by a theoretical limit, and is usually parameterized by the reconciliation efficiency (or inefficiency), i.e. the ratio of additional information disclosed over the Shannon limit. Most techniques for reconciling errors in QKD try to optimize this parameter. For instance, the well-known Cascade (probably the most widely used procedure for reconciling errors in QKD) was recently shown to have an average efficiency of 1.05 at the cost of a high interactivity (number of exchanged messages). Modern coding techniques, such as rate-adaptive low-density parity-check (LDPC) codes were also shown to achieve similar efficiency values exchanging only one message, or even better values with few interactivity and shorter block-length codes.

Efficient information reconciliation for Continuous-Variable QKD using Non-Binary Low-Density Parity-Check Codes

We present here an information reconciliation method and demonstrate for the first time that it can achieve efficiencies close to 0.98. This method is based on the belief propagation decoding of non-binary LDPC codes over finite (Galois) fields. In particular, for convenience and faster decoding we only consider power-of-two Galois fields.

Decoding temporally encoded sensory input by cortical oscillations and thalamic phase comparators

The temporally encoded information obtained by vibrissal touch could be decoded “passively,” involving only input-driven elements, or “actively,” utilizing intrinsically driven oscillators. A previous study suggested that the trigeminal somatosensory system of rats does not obey the bottom-up order of activation predicted by passive decoding. Thus, we have tested whether this system obeys the predictions of active decoding. We have studied cortical single units in the somatosensory cortices of anesthetized rats and guinea pigs and found that about a quarter of them exhibit clear spontaneous oscillations, many of them around whisking frequencies (≈10 Hz). The frequencies of these oscillations could be controlled locally by glutamate. These oscillations could be forced to track the frequency of induced rhythmic whisker movements at a stable, frequency-dependent, phase difference. During these stimulations, the response intensities of multiunits at the thalamic recipient layers of the cortex decreased, and their latencies increased, with increasing input frequency. These observations are consistent with thalamocortical loops implementing phase-locked loops, circuits that are most efficient in decoding temporally encoded information like that obtained by active vibrissal touch. According to this model, and consistent with our results, populations of thalamic “relay” neurons function as phase “comparators” that compare cortical timing expectations with the actual input timing and represent the difference by their population output rate.

Glu-tRNAGln amidotransferase: A novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation

The three genes, gatC, gatA, and gatB, which constitute the transcriptional unit of the Bacillus subtilis glutamyl-tRNAGln amidotransferase have been cloned. Expression of this transcriptional unit results in the production of a heterotrimeric protein that has been purified to homogeneity. The enzyme furnishes a means for formation of correctly charged Gln-tRNAGln through the transamidation of misacylated Glu-tRNAGln, functionally replacing the lack of glutaminyl-tRNA synthetase activity in Gram-positive eubacteria, cyanobacteria, Archaea, and organelles. Disruption of this operon is lethal. This demonstrates that transamidation is the only pathway to Gln-tRNAGln in B. subtilis and that glutamyl-tRNAGln amidotransferase is a novel and essential component of the translational apparatus.

Nonlinearity in genetic decoding: Homologous DNA replicase genes use alternatives of transcriptional slippage or translational frameshifting

The τ and γ subunits of DNA polymerase III are both encoded by a single gene in Escherichia coli and Thermus thermophilus. γ is two-thirds the size of τ and shares virtually all its amino acid sequence with τ. E. coli and T. thermophilus have evolved very different mechanisms for setting the approximate 1:1 ratio between τ and γ. Both mechanisms put ribosomes into alternate reading frames so that stop codons in the new frame serve to make the smaller γ protein. In E. coli, ≈50% of initiating ribosomes translate the dnaX mRNA conventionally to give τ, but the other 50% shift into the −1 reading frame at a specific site (A AAA AAG) in the mRNA to produce γ. In T. thermophilus ribosomal frameshifting is not required: the dnaX mRNA is a heterogeneous population of molecules with different numbers of A residues arising from transcriptional slippage on a run of nine T residues in the DNA template. Translation of the subpopulation containing nine As (or +/− multiples of three As) yields τ. The rest of the population of mRNAs (containing nine +/− nonmultiples of three As) puts ribosomes into the alternate reading frames to produce the γ protein(s). It is surprising that two rather similar dnaX sequences in E. coli and T. thermophilus lead to very different mechanisms of expression.

Sequential decoding,

Includes bibliography.

Optimized Decoding for Auditory Attention Detection

Thesis (Master's)--University of Washington, 2016-06