Growth of bainitic ferrite and carbon partitioning during the early stages of bainite transformation in a 2 mass% silicon steel studied by in situ neutron diffraction, TEM and APT

In situ neutron diffraction, transmission electron microscopy (TEM) and atom probe tomography (APT) have been used to study the early stages of bainite transformation in a 2 mass% Si nano-bainitic steel. It was observed that carbon redistribution between the bainitic ferrite and retained austenite at the early stages of the bainite transformation at low isothermal holding occurred in the following sequence: (i) formation of bainitic ferrite nuclei within carbon-depleted regions immediately after the beginning of isothermal treatment; (ii) carbon partitioning immediately after the formation of bainitic ferrite nuclei but substantial carbon diffusion only after 33 min of bainite isothermal holding; (iii) formation of the carbon-enriched remaining austenite in the vicinity of bainitic laths at the beginning of the transformation; (iv) segregation of carbon to the dislocations near the austenite/ferrite interface; and (v) homogeneous redistribution of carbon within the remaining austenite with the progress of the transformation and with the formation of bainitic ferrite colonies. Bainitic ferrite nucleated at internal defects or bainite/austenite interfaces as well as at the prior austenite grain boundary. Bainitic ferrite has been observed in the form of an individual layer, a colony of layers and a layer with sideplates at the early stages of transformation.

Biochemical characterization of Aprataxin, the protein deficient in Ataxia with Oculomotor Apraxia type 1

Neurodegenerative disorders are heterogenous in nature and include a range of ataxias with oculomotor apraxia, which are characterised by a wide variety of neurological and ophthalmological features. This family includes recessive and dominant disorders. A subfamily of autosomal recessive cerebellar ataxias are characterised by defects in the cellular response to DNA damage. These include the well characterised disorders Ataxia-Telangiectasia (A-T) and Ataxia-Telangiectasia Like Disorder (A-TLD) as well as the recently identified diseases Spinocerebellar ataxia with axonal neuropathy Type 1 (SCAN1), Ataxia with Oculomotor Apraxia Type 2 (AOA2), as well as the subject of this thesis, Ataxia with Oculomotor Apraxia Type 1 (AOA1). AOA1 is caused by mutations in the APTX gene, which is located at chromosomal locus 9p13. This gene codes for the 342 amino acid protein Aprataxin. Mutations in APTX cause destabilization of Aprataxin, thus AOA1 is a result of Aprataxin deficiency. Aprataxin has three functional domains, an N-terminal Forkhead Associated (FHA) phosphoprotein interaction domain, a central Histidine Triad (HIT) nucleotide hydrolase domain and a C-terminal C2H2 zinc finger. Aprataxins FHA domain has homology to FHA domain of the DNA repair protein 5’ polynucleotide kinase 3’ phosphatase (PNKP). PNKP interacts with a range of DNA repair proteins via its FHA domain and plays a critical role in processing damaged DNA termini. The presence of this domain with a nucleotide hydrolase domain and a DNA binding motif implicated that Aprataxin may be involved in DNA repair and that AOA1 may be caused by a DNA repair deficit. This was substantiated by the interaction of Aprataxin with proteins involved in the repair of both single and double strand DNA breaks (XRay Cross-Complementing 1, XRCC4 and Poly-ADP Ribose Polymerase-1) and the hypersensitivity of AOA1 patient cell lines to single and double strand break inducing agents. At the commencement of this study little was known about the in vitro and in vivo properties of Aprataxin. Initially this study focused on generation of recombinant Aprataxin proteins to facilitate examination of the in vitro properties of Aprataxin. Using recombinant Aprataxin proteins I found that Aprataxin binds to double stranded DNA. Consistent with a role for Aprataxin as a DNA repair enzyme, this binding is not sequence specific. I also report that the HIT domain of Aprataxin hydrolyses adenosine derivatives and interestingly found that this activity is competitively inhibited by DNA. This provided initial evidence that DNA binds to the HIT domain of Aprataxin. The interaction of DNA with the nucleotide hydrolase domain of Aprataxin provided initial evidence that Aprataxin may be a DNA-processing factor. Following these studies, Aprataxin was found to hydrolyse 5’adenylated DNA, which can be generated by unscheduled ligation at DNA breaks with non-standard termini. I found that cell extracts from AOA1 patients do not have DNA-adenylate hydrolase activity indicating that Aprataxin is the only DNA-adenylate hydrolase in mammalian cells. I further characterised this activity by examining the contribution of the zinc finger and FHA domains to DNA-adenylate hydrolysis by the HIT domain. I found that deletion of the zinc finger ablated the activity of the HIT domain against adenylated DNA, indicating that the zinc finger may be required for the formation of a stable enzyme-substrate complex. Deletion of the FHA domain stimulated DNA-adenylate hydrolysis, which indicated that the activity of the HIT domain may be regulated by the FHA domain. Given that the FHA domain is involved in protein-protein interactions I propose that the activity of Aprataxins HIT domain may be regulated by proteins which interact with its FHA domain. We examined this possibility by measuring the DNA-adenylate hydrolase activity of extracts from cells deficient for the Aprataxin-interacting DNA repair proteins XRCC1 and PARP-1. XRCC1 deficiency did not affect Aprataxin activity but I found that Aprataxin is destabilized in the absence of PARP-1, resulting in a deficiency of DNA-adenylate hydrolase activity in PARP-1 knockout cells. This implies a critical role for PARP-1 in the stabilization of Aprataxin. Conversely I found that PARP-1 is destabilized in the absence of Aprataxin. PARP-1 is a central player in a number of DNA repair mechanisms and this implies that not only do AOA1 cells lack Aprataxin, they may also have defects in PARP-1 dependant cellular functions. Based on this I identified a defect in a PARP-1 dependant DNA repair mechanism in AOA1 cells. Additionally, I identified elevated levels of oxidized DNA in AOA1 cells, which is indicative of a defect in Base Excision Repair (BER). I attribute this to the reduced level of the BER protein Apurinic Endonuclease 1 (APE1) I identified in Aprataxin deficient cells. This study has identified and characterised multiple DNA repair defects in AOA1 cells, indicating that Aprataxin deficiency has far-reaching cellular consequences. Consistent with the literature, I show that Aprataxin is a nuclear protein with nucleoplasmic and nucleolar distribution. Previous studies have shown that Aprataxin interacts with the nucleolar rRNA processing factor nucleolin and that AOA1 cells appear to have a mild defect in rRNA synthesis. Given the nucleolar localization of Aprataxin I examined the protein-protein interactions of Aprataxin and found that Aprataxin interacts with a number of rRNA transcription and processing factors. Based on this and the nucleolar localization of Aprataxin I proposed that Aprataxin may have an alternative role in the nucleolus. I therefore examined the transcriptional activity of Aprataxin deficient cells using nucleotide analogue incorporation. I found that AOA1 cells do not display a defect in basal levels of RNA synthesis, however they display defective transcriptional responses to DNA damage. In summary, this thesis demonstrates that Aprataxin is a DNA repair enzyme responsible for the repair of adenylated DNA termini and that it is required for stabilization of at least two other DNA repair proteins. Thus not only do AOA1 cells have no Aprataxin protein or activity, they have additional deficiencies in PolyADP Ribose Polymerase-1 and Apurinic Endonuclease 1 dependant DNA repair mechanisms. I additionally demonstrate DNA-damage inducible transcriptional defects in AOA1 cells, indicating that Aprataxin deficiency confers a broad range of cellular defects and highlighting the complexity of the cellular response to DNA damage and the multiple defects which result from Aprataxin deficiency. My detailed characterization of the cellular consequences of Aprataxin deficiency provides an important contribution to our understanding of interlinking DNA repair processes.

Regional field measurement of soil moisture content with neutron probe

The neutron logging method has been widely used for field measurement of soil moisture content. This non-destructive method permitted the measurement of in-situ soil moisture content at various depths without the need for burying any sensor. Twenty-three sites located around regional Melbourne have been selected for long term monitoring of soil moisture content using neutron probe. Soil samples collected during the installation are used for site characterisation and neutron probe calibration purposes. A linear relationship is obtained between the corrected neutron probe reading and moisture content for both the individual and combined data from seven sites. It is observed that the liner relationship, developed using combined data, can be used for all sites with an average accuracy of about 80%. Monitoring of the variation of soil moisture content with depth in six months for two sites is presented in this paper.

PARP inhibition induces BAX/BAK-independent synthetic lethality of BRCA1-deficient non-small cell lung cancer

Evasion of apoptosis contributes to both tumourigenesis and drug resistance in non-small cell lung carcinoma (NSCLC). The pro-apoptotic BCL-2 family proteins BAX and BAK are critical regulators of mitochondrial apoptosis. New strategies for targeting NSCLC in a mitochondria-independent manner should bypass this common mechanism of apoptosis block. BRCA1 mutation frequency in lung cancer is low; however, decreased BRCA1 mRNA and protein expression levels have been reported in a significant proportion of lung adenocarcinomas. BRCA1 mutation/deficiency confers a defect in homologous recombination DNA repair that has been exploited by synthetic lethality through inhibition of PARP (PARPi) in breast and ovarian cells; however, it is not known whether this same synthetic lethal mechanism exists in NSCLC cells. Additionally, it is unknown whether the mitochondrial apoptotic pathway is required for BRCA1/PARPi-mediated synthetic lethality. Here we demonstrate that silencing of BRCA1 expression by RNA interference sensitizes NSCLC cells to PARP inhibition. Importantly, this sensitivity was not attenuated in cells harbouring mitochondrial apoptosis block induced by co-depletion of BAX and BAK. Furthermore, we demonstrate that BRCA1 inhibition cannot override platinum resistance, which is often mediated by loss of mitochondrial apoptosis signalling, but can still sensitize to PARP inhibition. Finally we demonstrate the existence of a BRCA1-deficient subgroup (11–19%) of NSCLC patients by analysing BRCA1 protein levels using immunohistochemistry in two independent primary NSCLC cohorts. Taken together, the existence of BRCA1-immunodeficient NSCLC suggests that this molecular subgroup could be effectively targeted by PARP inhibitors in the clinic and that PARP inhibitors could be used for the treatment of BRCA1-immunodeficient, platinum-resistant tumours.

Sensitivity of peak positions to flight-path parameters in a deep-inelastic scattering neutron TOF spectrometer

The effects of small changes in flight-path parameters (primary and secondary flight paths, detector angles), and of displacement of the sample along the beam axis away from its ideal position, are examined for an inelastic time-of-flight (TOF) neutron spectrometer, emphasising the deep-inelastic regime. The aim was to develop a rational basis for deciding what measured shifts in the positions of spectral peaks could be regarded as reliable in the light of the uncertainties in the calibrated flight-path parameters. Uncertainty in the length of the primary or secondary flight path has the least effect on the positions of the peaks of H, D and He, which are dominated by the accuracy of the calibration of the detector angles. This aspect of the calibration of a TOF spectrometer therefore demands close attention to achieve reliable outcomes where the position of the peaks is of significant scientific interest and is discussed in detail. The corresponding sensitivities of the position of peak of the Compton profile, J(y), to flight-path parameters and sample position are also examined, focusing on the comparability across experiments of results for H, D and He. We show that positioning the sample to within a few mm of the ideal position is required to ensure good comparability between experiments if data from detectors at high forward angles are to be reliably interpreted.

Measurement of anisotropies of the kinetic energy and anharmonicity in pyrolytic graphite by neutron Compton scattering

Neutron Compton scattering (NCS) measurements of the anisotropy of the momentum distribution and the mean Laplacian of the interatomic potential ∇2V have been performed using electron volt neutrons, with wave vector transfers between 24 Å−1 and 98 Å−1. The measured momentum distribution of the atoms displays significantly more anisotropy than a calculation using a model density of states. We have observed anisotropies in ∇2V for the first time. The results suggest that the atomic potential is harmonic within the graphite planes, but anharmonic for vibrations perpendicular to the planes.

Neutron Compton scattering from selectively deuterated acetanilide

With the aim of developing the application of neutron Compton scattering (NCS) to molecular systems of biophysical interest, we are using the Compton spectrometer EVS at ISIS to characterize the momentum distribution of protons in peptide groups. In this contribution we present NCS measurements of the recoil peak (Compton profile) due to the amide proton in otherwise fully deuterated acetanilide (ACN), a widely studied model system for H-bonding and energy transfer in biomolecules. We obtain values for the average width of the potential well of the amide proton and its mean kinetic energy. Deviations from the Gaussian form of the Compton profile, analyzed on the basis of an expansion due to Sears, provide data relating to the Laplacian of the proton potential. (C) 1998 Elsevier Science B.V. All rights reserved.

Multiple scattering in deep inelastic neutron scattering : Monte Carlo simulations and experiments at the ISIS eVS inverse geometry spectrometer

A procedure for the evaluation of multiple scattering contributions is described, for deep inelastic neutron scattering (DINS) studies using an inverse geometry time-of-flight spectrometer. The accuracy of a Monte Carlo code DINSMS, used to calculate the multiple scattering, is tested by comparison with analytic expressions and with experimental data collected from polythene, polycrystalline graphite and tin samples. It is shown that the Monte Carlo code gives an accurate representation of the measured data and can therefore be used to reliably correct DINS data.

Calibration of the electron volt spectrometer, a deep inelastic neutron scattering spectrometer at the ISIS pulsed neutron spallation source

The electron Volt Spectrometer (eVS) is an inverse geometry filter difference spectrometer that has been optimised to measure the single atom properties of condensed matter systems using a technique known as Neutron Compton Scattering (NCS) or Deep Inelastic Neutron Scattering (DINS). The spectrometer utilises the high flux of epithermal neutrons that are produced by the ISIS neutron spallation source enabling the direct measurement of atomic momentum distributions and ground state kinetic energies. In this paper the procedure that is used to calibrate the spectrometer is described. This includes details of the method used to determine detector positions and neutron flight path lengths as well as the determination of the instrument resolution. Examples of measurements on 3 different samples are shown, ZrH2, 4He and Sn which show the self-consistency of the calibration procedure.