Physical and Genetic Analysis of the CUP1 Tandem Array in the Yeast Saccharomyces cerevisiae

The genomes of many strains of baker’s yeast, Saccharomyces cerevisiae, contain multiple repeats of the copper-binding protein Cup1. Cup1 is a member of the metallothionein family, and is found in a tandem array on chromosome VIII. In this thesis, I describe studies that characterized these tandem arrays and their mechanism of formation across diverse strains of yeast. I show that CUP1 arrays are an illuminating model system for observing recombination in eukaryotes, and describe insights derived from these observations.

In our first study, we analyzed 101 natural isolates of S. cerevisiae in order to examine the diversity of CUP1-containing repeats across different strains. We identified five distinct classes of repeats that contain CUP1. We also showed that some strains have only a single copy of CUP1. By comparing the sequences of all the strains, we were able to elucidate the mechanism of formation of the CUP1 tandem arrays, which involved unequal non-homologous recombination events starting from a strain that had only a single CUP1 gene. Our observation of CUP1 repeat formation allows more general insights about the formation of tandem repeats from single-copy genes in eukaryotes, which is one of the most important mechanisms by which organisms evolve.

In our second study, we delved deeper into our mechanistic investigations by measuring the relative rates of inter-homolog and intra-/inter-sister chromatid recombination in CUP1 tandem arrays. We used a diploid strain that is heterozygous both for insertion of a selectable marker (URA3) inside the tandem array, and also for markers at either end of the array. The intra-/inter-sister chromatid recombination rate turned out to be more than ten-fold greater than the inter-homolog rate. Moreover, we found that loss of the proteins Rad51 and Rad52, which are required for most inter-homolog recombination, did not greatly reduce recombination in the CUP1 tandem repeats. Additionally, we investigated the effects of elevated copper levels on the rate of each type of recombination at the CUP1 locus. Both types of recombination are increased at high concentrations of copper (as is known to be the case for CUP1 transcription). Furthermore, the inter-homolog recombination rate at the CUP1 locus is higher than the average over the genome during mitosis, but is lower than the average during meiosis.

The research described in Chapter 2 is published in 2014.

Time-resolved dosimetric verification of respiratory-gated radiotherapy exposures using a high-resolution 2D ionisation chamber array

The aim of this work was to track and verify the delivery of respiratory-gated irradiations, performed with three versions of TrueBeam linac, using a novel phantom arrangement that combined the OCTAVIUS® SRS 1000 array with a moving platform. The platform was programmed to generate sinusoidal motion of the array. This motion was tracked using the real-time position management (RPM) system and four amplitude gating options were employed to interrupt MV beam delivery when the platform was not located within set limits. Time-resolved spatial information extracted from analysis of x-ray fluences measured by the array was compared to the programmed motion of the platform and to the trace recorded by the RPM system during the delivery of the x-ray field. Temporal data recorded by the phantom and the RPM system were validated against trajectory log files, recorded by the linac during the irradiation, as well as oscilloscope waveforms recorded from the linac target signal. Gamma analysis was employed to compare time-integrated 2D x-ray dose fluences with theoretical fluences derived from the probability density function for each of the gating settings applied, where gamma criteria of 2%/2 mm, 1%/1 mm and 0.5%/0.5 mm were used to evaluate the limitations of the RPM system. Excellent agreement was observed in the analysis of spatial information extracted from the SRS 1000 array measurements. Comparisons of the average platform position with the expected position indicated absolute deviations of  <0.5 mm for all four gating settings. Differences were observed when comparing time-resolved beam-on data stored in the RPM files and trajectory logs to the true target signal waveforms. Trajectory log files underestimated the cycle time between consecutive beam-on windows by 10.0  ±  0.8 ms. All measured fluences achieved 100% pass-rates using gamma criteria of 2%/2 mm and 50% of the fluences achieved pass-rates  >90% when criteria of 0.5%/0.5 mm were used. Results using this novel phantom arrangement indicate that the RPM system is capable of accurately gating x-ray exposure during the delivery of a fixed-field treatment beam.

A Synthesis-free Directional Modulation Transmitter using Retrodirective Array

By modification of the classical retrodirective arrays (RDAs) architecture a directional modulation (DM) transmitter can be realized without the need for synthesis. Importantly, through analytical analysis and exemplar simulations, it is proved that, besides the conventional DM application scenario, i.e., secure transmission to one legitimate receiver located along one spatial direction in free space, the proposed synthesis-free DM transmitter should also perform well for systems where there are more than one legitimate receivers positioned along different directions in free space, and where one or more legitimate receivers exist in a multipath environment. None of these have ever been achieved before using synthesis-free DM arrangements.

Broadband Dual-Polarized Antenna with High Port Isolation and Polarization Purity

This paper presents a novel high symmetry balun which significantly improves the performance of dipole-based dual-polarized antennas. The new balun structure provides enhanced differential capability leading to high performance in terms of port-to-port isolation and far-field cross polarization. An example antenna using this balun is proposed. The simulated results show 53.5% of fractional bandwidth within the band 1.71−2.96 GHz (VSWR<1.5) and port-to-port isolation >59 dB. The radiation characteristic shows around 9 dBi of gain and far-field cross polarization <−48 dBi over the entire bandwidth. The detailed balun functioning and full antenna measurements will be presented during the conference. Performance comparison with similar structures will be also provided.

Characterising the TP53-deleted subgroup of chronic lymphocytic leukemia: an analysis of additional cytogenetic abnormalities detected by interphase fluorescence in situ hybridisation and array-based comparative genomic hybridisation.

Deletion of the TP53 gene on chromosome 17p13.1 is the prognostic factor associated with the shortest survival in CLL. We used array-based comparative genomic hybridisation (arrayCGH) to identify additional DNA copy number changes in peripheral blood samples from 74 LRF CLL4 trial patients, 37 with >or=5% and 37 without TP53-deleted cells. ArrayCGH reliably detected deletions on 17p, including the TP53 locus, in cases with >or=50%TP53-deleted cells detected by fluorescence in situ hybridisation, plus seven additional cases with deleted regions on 17p excluding TP53. Losses on chromosomal regions 18p and/or 20p were found exclusively in cases with >or=5%TP53-deleted cells (por=5%TP53-deleted cases (p=0.02). In particular, amplification of 2p and deletion of 6q were both more frequent. Cases with >20%TP53-deleted cells had the worst prognosis in the LRF CLL4 trial.

Secure Transmission in Cooperative Relaying Networks with Multiple Antennas

We investigate the secrecy performance of dualhop amplify-and-forward (AF) multi-antenna relaying systems over Rayleigh fading channels, by taking into account the direct link between the source and destination. In order to exploit the available direct link and the multiple antennas for secrecy improvement, different linear processing schemes at the relay and different diversity combining techniques at the destination are proposed, namely, 1) Zero-forcing/Maximal ratio combining (ZF/MRC), 2) ZF/Selection combining (ZF/SC), 3) Maximal ratio transmission/MRC (MRT/MRC) and 4) MRT/Selection combining (MRT/SC). For all these schemes, we present new closed-form approximations for the secrecy outage probability. Moreover, we investigate a benchmark scheme, i.e., cooperative jamming/ZF (CJ/ZF), where the secrecy outage probability is obtained in exact closed-form. In addition, we present asymptotic secrecy outage expressions for all the proposed schemes in the high signal-to-noise ratio (SNR) regime, in order to characterize key design parameters, such as secrecy diversity order and secrecy array gain. The outcomes of this paper can be summarized as follows: a) MRT/MRC and MRT/SC achieve a full diversity order of M + 1, ZF/MRC and ZF/SC achieve a diversity order of M, while CJ/ZF only achieves unit diversity order, where M is the number of antennas at the relay. b) ZF/MRC (ZF/SC) outperforms the corresponding MRT/MRC (MRT/SC) in the low SNR regime, while becomes inferior to the corresponding MRT/MRC (MRT/SC) in the high SNR. c) All of the proposed schemes tend to outperform the CJ/ZF with moderate number of antennas, and linear processing schemes with MRC attain better performance than those with SC.

Secure Transmission in Spectrum Sharing MIMO Networks with Generalized Antenna Selection over Nakagami-m Channels

In this paper, we investigate the secrecy outage performance of spectrum sharing multiple-input multiple-output networks using generalized transmit antenna selection with maximal ratio combining over Nakagami-m channels. In particular, the outdated channel state information is considered at the process of antenna selection due to feedback delay. Considering a practical passive eavesdropper scenario, we derive the exact and asymptotic closed-form expressions of secrecy outage probability, which enable us to evaluate the secrecy performance with high efficiency and present a new design insight into the impact of key parameters on the secrecy performance. In addition, the analytical results demonstrate that the achievable secrecy diversity order is only determined by the parameters of the secondary network, while other parameters related to primary or eavesdropper’s channels have a significantly impact on the secrecy coding gain. 

Enhanced durability of Li-O2 batteries employing vertically standing Ti nanowire array supported cathodes

Ti nanowire arrays vertically standing on Ti foam prepared by a facile corrosion method were used as self-supported Li-O₂ battery cathodes. The batteries exhibited enhanced durability at high rate current densities (e.g. cycling 640 times at 5 A g^-1).

Secure Wireless Key Establishment Using Retrodirective Array

In this paper a new method of establishing secret keys for wireless communications is proposed. A retrodirective array (RDA) that is configured to receive and re-transmit at different frequencies is utilized as a relay node. Specifically the analogue RDA is able to respond in ‘real-time’, reducing the required number of time slots for key establishment to two, compared with at least three in previous relay key generation schemes. More importantly, in the proposed architecture equivalent reciprocal wireless channels between legitimate keying nodes can be randomly updated within one channel coherence time period, leading to greatly increased key generation rates (KGRs) in slow fading environment. The secrecy performance of this RDA assisted key generation system is evaluated and it is shown that it outperforms previous relay key generation systems.

Multipair massive MIMO full-duplex relaying with MRC/MRT processing

We consider a multipair relay channel, where multiple sources communicate with multiple destinations with the help of a full-duplex (FD) relay station (RS). All sources and destinations have a single antenna, while the RS is equipped with massive arrays. We assume that the RS estimates the channels by using training sequences transmitted from sources and destinations. Then, it uses maximum-ratio combining/maximum-ratio transmission (MRC/MRT) to process the signals. To significantly reduce the loop interference (LI) effect, we propose two massive MIMO processing techniques: i) using a massive receive antenna array; or ii) using a massive transmit antenna array together with very low transmit power at the RS. We derive an exact achievable rate in closed-form and evaluate the system spectral efficiency. We show that, by doubling the number of antennas at the RS, the transmit power of each source and of the RS can be reduced by 1.5 dB if the pilot power is equal to the signal power and by 3 dB if the pilot power is kept fixed, while maintaining a given quality-of-service. Furthermore, we compare FD and half-duplex (HD) modes and show that FD improves significantly the performance when the LI level is low.

Physical Layer Security with Threshold-Based Multiuser Scheduling in Multi-antenna Wireless Networks

In this paper, we consider a multiuser downlink wiretap network consisting of one base station (BS) equipped with AA antennas, NB single-antenna legitimate users, and NE single-antenna eavesdroppers over Nakagami-m fading channels. In particular, we introduce a joint secure transmission scheme that adopts transmit antenna selection (TAS) at the BS and explores threshold-based selection diversity (tSD) scheduling over legitimate users to achieve a good secrecy performance while maintaining low implementation complexity. More specifically, in an effort to quantify the secrecy performance of the considered system, two practical scenarios are investigated, i.e., Scenario I: the eavesdropper’s channel state information (CSI) is unavailable at the BS, and Scenario II: the eavesdropper’s CSI is available at the BS. For Scenario I, novel exact closed-form expressions of the secrecy outage probability are derived, which are valid for general networks with an arbitrary number of legitimate users, antenna configurations, number of eavesdroppers, and the switched threshold. For Scenario II, we take into account the ergodic secrecy rate as the principle performance metric, and derive novel closed-form expressions of the exact ergodic secrecy rate. Additionally, we also provide simple and asymptotic expressions for secrecy outage probability and ergodic secrecy rate under two distinct cases, i.e., Case I: the legitimate user is located close to the BS, and Case II: both the legitimate user and eavesdropper are located close to the BS. Our important findings reveal that the secrecy diversity order is AAmA and the slope of secrecy rate is one under Case I, while the secrecy diversity order and the slope of secrecy rate collapse to zero under Case II, where the secrecy performance floor occurs. Finally, when the switched threshold is carefully selected, the considered scheduling scheme outperforms other well known existing schemes in terms of the secrecy performance and complexity tradeoff