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.

Directional wave measurements using the Offshore Sensing Sailbuoy, link to MATLAB file

An autonomous vessel, the Offshore Sensing Sailbuoy, was used for wave measurements near the Ekofisk oil platform complex in the North Sea (56.5 N, 3.2 E, operated by ConocoPhilllips) from 6 to 20 November 2015. Being 100% wind propelled, the Sailbuoy has two-way communication via the Iridium network and has the capability for missions of six months or more. It has previously been deployed in the Arctic, Norwegian Sea and the Gulf of Mexico, but this was the first real test for wave measurements. During the campaign it held position about 20km northeast of Ekofisk (on the lee side) during rough conditions. Mean wind speed measured at Ekofisk during the campaign was near 9.8m/s, with a maximum of 20.4m/s, with wind mostly from south and south west. A Datawell MOSE G1000 GPS based 2Hz wave sensor was mounted on the Sailbuoy. Mean significant wave height (Hs 1hr) measured was 3m, whereas maximum Hs was 6m. Mean wave period was 7.7s, while maximum wave height, Hmax, was 12.6m. These measurements have been compared with non-directional Waverider observations at the Ekofisk complex. Mean Hs at Ekofisk was 3.1m, while maximum Hs was 6.5m. Nevertheless, the correlation between the two measurements was high (97%). Spectra comparison was also good, except for low Hs (~1m), where the motion of the vessel seemed to influence the measurements. Nevertheless, the Sailbuoy performed well during this campaign, and results suggests that it is a suitable platform for wave measurements in rather rough sea conditions.

Potential temperature in Espartel Sill (Strait of Gibraltar), from 2004-09-30 to 2016-03-02 at 344 meters depth, link to raw data in MATLAB format

Potential temperature measured with a SBE37 at 35.862ºN, 5.97ºW at 344 meters Depth. Data expand from September the 30th, 2004 to March the 2nd, 2016. Original measurement frequency was 30 minutes, the data presented here is a subsampling that extract the coldest temperature found each 12 hours. The time vector corresponds with the moment in which this minimun temperature is observed.

Dual-band Filtenna Array for WLAN Applications

This paper presents the design and results of a dual-band antenna array integrated with bandpass filters for WLAN applications. The array is fed with a single 50 Ω port and consists of two radiating elements; thereby having a 1x2 array structure. The two bands of the antenna array correspond to the two WLAN bands of 2.4 GHz and 5.8 GHz. A standalone array has first been designed. Other than the two fundamental resonant frequencies, the standalone array exhibits spurious harmonics at various other frequencies. For the suppression of these harmonics, the array has been integrated with two bandpass filters, centered at 2.4 GHz and 5.8 GHz. The resulting filtenna array was simulated, fabricated and measured. Obtained simulation and measurement results agree well with each other and have been presented to validate the accuracy of the proposed structure. Measured return loss of the structure shows dual-bands at 2.4 GHz and 5.8 GHz of more than 30 dB each and also a successful suppression of the spurious harmonics of the antenna array has been achieved. Radiation patterns have also been simulated and measured and both results shown. The gain and efficiency have also been presented; with the values being 6.7 dBi and 70% for the 2.4 GHz band and 7.4 dBi and 81% for the 5.8 GHz band respectively.

Robust indoor speaker recognition in a network of audio and video sensors

Situational awareness is achieved naturally by the human senses of sight and hearing in combination. Automatic scene understanding aims at replicating this human ability using microphones and cameras in cooperation. In this paper, audio and video signals are fused and integrated at different levels of semantic abstractions. We detect and track a speaker who is relatively unconstrained, i.e., free to move indoors within an area larger than the comparable reported work, which is usually limited to round table meetings. The system is relatively simple: consisting of just 4 microphone pairs and a single camera. Results show that the overall multimodal tracker is more reliable than single modality systems, tolerating large occlusions and cross-talk. System evaluation is performed on both single and multi-modality tracking. The performance improvement given by the audio–video integration and fusion is quantified in terms of tracking precision and accuracy as well as speaker diarisation error rate and precision–recall (recognition). Improvements vs. the closest works are evaluated: 56% sound source localisation computational cost over an audio only system, 8% speaker diarisation error rate over an audio only speaker recognition unit and 36% on the precision–recall metric over an audio–video dominant speaker recognition method.

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.