The redoxomics of PTEN: walking a fine line between damage and signaling:mass spectrometry-based approaches to study the effect of oxidation on PTEN function, structure, and protein-protein interactions

The research described in this PhD thesis focuses on proteomics approaches to study the effect of oxidation on the modification status and protein-protein interactions of PTEN, a redox-sensitive phosphatase involved in a number of cellular processes including metabolism, apoptosis, cell proliferation, and survival. While direct evidence of a redox regulation of PTEN and its downstream signaling has been reported, the effect of cellular oxidative stress or direct PTEN oxidation on PTEN structure and interactome is still poorly defined. In a first study, GST-tagged PTEN was directly oxidized over a range of hypochlorous acid (HOCl) concentration, assayed for phosphatase activity, and oxidative post-translational modifications (oxPTMs) were quantified using LC-MS/MS-based label-free methods. In a second study, GSTtagged PTEN was prepared in a reduced and reversibly H2O2-oxidized form, immobilized on a resin support and incubated with HCT116 cell lysate to capture PTEN interacting proteins, which were analyzed by LC-MS/MS and comparatively quantified using label-free methods. In parallel experiments, HCT116 cells transfected with a GFP-tagged PTEN were treated with H2O2 and PTENinteracting proteins immunoprecipitated using standard methods. Several high abundance HOCl-induced oxPTMs were mapped, including those taking place at amino acids known to be important for PTEN phosphatase activity and protein-protein interactions, such as Met35, Tyr155, Tyr240 and Tyr315. A PTEN redox interactome was also characterized, which identified a number of PTEN-interacting proteins that vary with the reversible inactivation of PTEN caused by H2O2 oxidation. These included new PTEN interactors as well as the redox proteins peroxiredoxin-1 (Prdx1) and thioredoxin (Trx), which are known to be involved in the recycling of PTEN active site following H2O2-induced reversible inactivation. The results suggest that the oxidative modification of PTEN causes functional alterations in PTEN structure and interactome, with fundamental implications for the PTEN signaling role in many cellular processes, such as those involved in the pathophysiology of disease and ageing.

Adaptive electrical signal post-processing in optical communications systems

Improving bit error rates in optical communication systems is a difficult and important problem. The error correction must take place at high speed and be extremely accurate. We show the feasibility of using hardware implementable machine learning techniques. This may enable some error correction at the speed required.

Adaptive electrical signal post-processing in optical communications systems

Improving bit error rates in optical communication systems is a difficult and important problem. The error correction must take place at high speed and be extremely accurate. We show the feasibility of using hardware implementable machine learning techniques. This may enable some error correction at the speed required.

Differential patterns of activity and functional connectivity in emotion processing neural circuitry to angry and happy faces in adolescents with and without suicide attempt

Background - Neural substrates of emotion dysregulation in adolescent suicide attempters remain unexamined. Method - We used functional magnetic resonance imaging to measure neural activity to neutral, mild or intense (i.e. 0%, 50% or 100% intensity) emotion face morphs in two separate emotion-processing runs (angry and happy) in three adolescent groups: (1) history of suicide attempt and depression (ATT, n = 14); (2) history of depression alone (NAT, n = 15); and (3) healthy controls (HC, n = 15). Post-hoc analyses were conducted on interactions from 3 group × 3 condition (intensities) whole-brain analyses (p < 0.05, corrected) for each emotion run. Results - To 50% intensity angry faces, ATT showed significantly greater activity than NAT in anterior cingulate gyral–dorsolateral prefrontal cortical attentional control circuitry, primary sensory and temporal cortices; and significantly greater activity than HC in the primary sensory cortex, while NAT had significantly lower activity than HC in the anterior cingulate gyrus and ventromedial prefrontal cortex. To neutral faces during the angry emotion-processing run, ATT had significantly lower activity than NAT in the fusiform gyrus. ATT also showed significantly lower activity than HC to 100% intensity happy faces in the primary sensory cortex, and to neutral faces in the happy run in the anterior cingulate and left medial frontal gyri (all p < 0.006,corrected). Psychophysiological interaction analyses revealed significantly reduced anterior cingulate gyral–insula functional connectivity to 50% intensity angry faces in ATT v. NAT or HC. Conclusions - Elevated activity in attention control circuitry, and reduced anterior cingulate gyral–insula functional connectivity, to 50% intensity angry faces in ATT than other groups suggest that ATT may show inefficient recruitment of attentional control neural circuitry when regulating attention to mild intensity angry faces, which may represent a potential biological marker for suicide risk.

An investigation into the effects of processing instruction on the acquisition of English relative clauses by Syrian learners

The purpose of this research was to investigate the effects of Processing Instruction (VanPatten, 1996, 2007), as an input-based model for teaching second language grammar, on Syrian learners’ processing abilities. The present research investigated the effects of Processing Instruction on the acquisition of English relative clauses by Syrian learners in the form of a quasi-experimental design. Three separate groups were involved in the research (Processing Instruction, Traditional Instruction and a Control Group). For assessment, a pre-test, a direct post-test and a delayed post-test were used as main tools for eliciting data. A questionnaire was also distributed to participants in the Processing Instruction group to give them the opportunity to give feedback in relation to the treatment they received in comparison with the Traditional Instruction they are used to. Four hypotheses were formulated on the possible effectivity of Processing Instruction on Syrian learners’ linguistic system. It was hypothesised that Processing Instruction would improve learners’ processing abilities leading to an improvement in learners’ linguistic system. This was expected to lead to a better performance when it comes to the comprehension and production of English relative clauses. The main source of data was analysed statistically using the ANOVA test. Cohen’s d calculations were also used to support the ANOVA test. Cohen’s d showed the magnitude of effects of the three treatments. Results of the analysis showed that both Processing Instruction and Traditional Instruction groups had improved after treatment. However, the Processing Instruction Group significantly outperformed the other two groups in the comprehension of relative clauses. The analysis concluded that Processing Instruction is a useful tool for instructing relative clauses to Syrian learners. This was enhanced by participants’ responses to the questionnaire as they were in favour of Processing Instruction, rather than Traditional Instruction. This research has theoretical and pedagogical implications. Theoretically, the study showed support for the Input hypothesis. That is, it was shown that Processing Instruction had a positive effect on input processing as it affected learners’ linguistic system. This was reflected in learners’ performance where learners were able to produce a structure which they had not been asked to produce. Pedagogically, the present research showed that Processing Instruction is a useful tool for teaching English grammar in the context where the experiment was carried out, as it had a large effect on learners’ performance.

Target consolidation under high temporal processing demands as revealed by MEG

We investigated the nature of resource limitations during visual target processing by imposing high temporal processing demands on the cognitive system. This was achieved by embedding target stimuli into rapid-serial-visual-presentation-streams (RSVP). In RSVP streams, it is difficult to report the second of two targets (T2) if the second follows the first (T1) within 500 ms. This effect is known as the attentional blink (AB). For the AB to occur, it is essential that T1 is followed by a mask, as without such a stimulus, the AB is significantly attenuated. Usually, it is thought that T1 processing is delayed by the mask, which in turn delays T2 processing, increasing the likelihood for T2 failures (AB). Predictions regarding amplitudes and latencies of cortical responses (M300, the magnetic counterpart to the P300) to targets were tested by investigating the neurophysiological effects of the post-T1 item (mask) by means of magnetoencephalography (MEG). Cortical M300 responses to targets drawn from prefrontal sources – areas associated with working memory – revealed accelerated T1 yet delayed T2 processing with an intervening mask. The explanation we are proposing assumes that “protection” of ongoing T1 processing necessitated by the occurrence of the mask suppresses other activation patterns, which boosts T1 yet also hinders further processing. Our data shed light on the mechanisms employed by the human brain for ensuring visual target processing under high temporal processing demands, which is hypothesized to occur at the expense of subsequently presented information.

Advances in characterisation, calibration and data processing speed of optical coherence tomography systems

This thesis describes advances in the characterisation, calibration and data processing of optical coherence tomography (OCT) systems. Femtosecond (fs) laser inscription was used for producing OCT-phantoms. Transparent materials are generally inert to infra-red radiations, but with fs lasers material modification occurs via non-linear processes when the highly focused light source interacts with the materials. This modification is confined to the focal volume and is highly reproducible. In order to select the best inscription parameters, combination of different inscription parameters were tested, using three fs laser systems, with different operating properties, on a variety of materials. This facilitated the understanding of the key characteristics of the produced structures with the aim of producing viable OCT-phantoms. Finally, OCT-phantoms were successfully designed and fabricated in fused silica. The use of these phantoms to characterise many properties (resolution, distortion, sensitivity decay, scan linearity) of an OCT system was demonstrated. Quantitative methods were developed to support the characterisation of an OCT system collecting images from phantoms and also to improve the quality of the OCT images. Characterisation methods include the measurement of the spatially variant resolution (point spread function (PSF) and modulation transfer function (MTF)), sensitivity and distortion. Processing of OCT data is a computer intensive process. Standard central processing unit (CPU) based processing might take several minutes to a few hours to process acquired data, thus data processing is a significant bottleneck. An alternative choice is to use expensive hardware-based processing such as field programmable gate arrays (FPGAs). However, recently graphics processing unit (GPU) based data processing methods have been developed to minimize this data processing and rendering time. These processing techniques include standard-processing methods which includes a set of algorithms to process the raw data (interference) obtained by the detector and generate A-scans. The work presented here describes accelerated data processing and post processing techniques for OCT systems. The GPU based processing developed, during the PhD, was later implemented into a custom built Fourier domain optical coherence tomography (FD-OCT) system. This system currently processes and renders data in real time. Processing throughput of this system is currently limited by the camera capture rate. OCTphantoms have been heavily used for the qualitative characterization and adjustment/ fine tuning of the operating conditions of OCT system. Currently, investigations are under way to characterize OCT systems using our phantoms. The work presented in this thesis demonstrate several novel techniques of fabricating OCT-phantoms and accelerating OCT data processing using GPUs. In the process of developing phantoms and quantitative methods, a thorough understanding and practical knowledge of OCT and fs laser processing systems was developed. This understanding leads to several novel pieces of research that are not only relevant to OCT but have broader importance. For example, extensive understanding of the properties of fs inscribed structures will be useful in other photonic application such as making of phase mask, wave guides and microfluidic channels. Acceleration of data processing with GPUs is also useful in other fields.