Analysis of radiation induced DNA damage by LC-MS/MS in isolated and cellular DNA

Abstract: It is well established that ionizing radiation induces a variety of damage in DNA by direct effects that are mediated by one-electron oxidation and indirect effects that are mediated by the reaction of water radiolysis products, e.g., hydroxyl radicals (•OH). In cellular DNA, direct and indirect effects appear to have about an equal effect toward DNA damage. We have shown that ϒ-(gamma) ray irradiation of aqueous solutions of DNA, during which •OH is the major damaging ROS can lead to the formation several lesions. On the other hand, the methylation and oxidative demethylation of cytosine in CpG dinucleotides plays a critical role in the gene regulation. The C5 position of cytosine in CG dinucleotides is frequently methylated by DNA methyl transferees (DNMTs) and constitutes 4-5% of the total cytosine. Here, my PhD research work focuses on the analysis of oxidative base modifications of model compounds of methylated and non methylated oligonucleotides, isolated DNA (calf-thymus DNA) and F98 cultured cell by gamma radiation. In addition, we identified a series of modifications of the 2-deoxyribose moiety of DNA arising from the exposure of isolated and cellular DNA to ionizing radiation. We also studied one electron oxidation of cellular DNA in cultured human HeLa cells initiated by intense nanosecond 266 nm laser pulse irradiation, which produces cross-links between guanine and thymine bases (G*-T*). To achieve these goals, we developed several methods based on mass spectrometry to analyze base modifications in isolated DNA and cellular DNA.

Development of methods for the determination of cadmium and thallium in oil shale by-products with graphite furnace atomic absorption spectrometry using direct analysis.

2014

Reliability of graphite furnace atomic absorption spectrometry as alternative method for trace analysis of arsenic in natural medicinal products

Purpose: To evaluate the comparative efficiency of graphite furnace atomic absorption spectrometry (GFAAS) and hydride generation atomic absorption spectrometry (HGAAS) for trace analysis of arsenic (As) in natural herbal products (NHPs). Method: Arsenic analysis in natural herbal products and standard reference material was conducted using atomic absorption spectrometry (AAS), namely, hydride generation AAS (HGAAS) and graphite furnace (GFAAS). The samples were digested with HNO3–H2O2 in a ratio of 4:1 using microwaveassisted acid digestion. The methods were validated with the aid of the standard reference material 1515 Apple Leaves (SRM) from NIST Results: Mean recovery of three different samples of NHPs, using HGAAS and GFAAS, ranged from 89.3 - 91.4 %, and 91.7 - 93.0 %, respectively. The difference between the two methods was insignificant. A (P= 0.5), B (P=0.4) and C (P=0.88) Relative standard deviation (RSD) RSD, i.e., precision was 2.5 - 6.5 % and 2.3 - 6.7 % using HGAAS and GFAAS techniques, respectively. Recovery of arsenic in SRM was 98 and 102 % by GFAAS and HGAAS, respectively. Conclusion: GFAAS demonstrates acceptable levels of precision and accuracy. Both techniques possess comparable accuracy and repeatability. Thus, the two methods are recommended as an alternative approach for trace analysis of arsenic in natural herbal products.

Thermal Treatments of Fe—Mn Alkoxide of Glycerol: Infrared absorption and emission

Synthetic Fe—Mn alkoxide of glycerol samples are submitted to controlled heating conditions and examined by IR absorption spectroscopy. On the other hand, the same sample is studied by infrared emission spectroscopy (IRES), upon heating in situ from 100 to 600°C. The spectral techniques employed in this contribution, especially IRES, show that as a result of the thermal treatments ferromagnetic oxides (manganese ferrite) are formed between 350 and 400°C. Some further spectral changes are seen at higher temperatures.

Impact and energy absorption of empty and foam-filled conical tubes

Foam-filled conical tubes have recently emerged as efficient energy absorbing devices to mitigate the adverse effects of impacts. The primary aim of this thesis was to generate research and design information on the impact and energy absorption response of empty and foam-filled conical tubes, and to facilitate their application in energy absorbing systems under axial and oblique loading conditions representative of those typically encountered in crashworthiness and impact applications. Finite element techniques supported by experiments and existing results were used in the investigation. Major findings show that the energy absorption response can be effectively controlled by varying geometry and material parameters. A useful empirical formula was developed for providing engineering designers with an initial estimate of the load ratio and hence energy absorption performances of these devices. It was evident that foam-filled conical tubes enhance the energy absorption capacity and stabilise the crush response for both axial and oblique impact loading without a significant increase in the initial peak load. This is practically beneficial when higher kinetic energy needs to be absorbed, thus reducing the impact force transmitted to the protected structure and occupants. Such tubes also increase and maintain the energy absorption capacity under global bending as well as minimise the reduction of energy absorption capacity with increasing load angle. Furthermore, the results also highlight the feasibility of adding a foam-filled conical tube as a supplementary device in energy absorbing systems, since the overall energy absorption performance of such systems can be favourably enhanced by only including a relatively small energy absorbing device. Above all, the results demonstrate the superior performance of foam-filled conical tube for mitigating impact energy in impact and crashworthiness applications.

A critical analysis of sperm donation practices : the personal and social effects of disrupting the unity of biological and social relatedness for the offspring

This thesis critically analyses sperm donation practices from a child-centred perspective. It examines the effects, both personal and social, of disrupting the unity of biological and social relatedness in families affected by donor conception. It examines how disruption is facilitated by a process of mediation which is detailed using a model provided by Sunderland (2002). This model identifies mediating movements - alienation, translation, re-contextualisation and absorption - which help to explain the powerful and dominating material, and social and political processes which occur in biotechnology, or in reproductive technology in this case. The understanding of such movements and mediation of meanings is inspired by the complementary work of Silverstone (1999) and Sunderland. This model allows for a more critical appreciation of the movement of meaning from previously inalienable aspects of life to alienable products through biotechnology (Sunderland, 2002). Once this mediation in donor conception is subjected to critical examination here, it is then approached from different angles of investigation. The thesis posits that two conflicting notions of the self are being applied to fertility-frustrated adults and the offspring of reproductive interventions. Adults using reproductive interventions receive support to maximise their genetic continuity, but in so doing they create and dismiss the corresponding genetic discontinuity produced for the offspring. The offspring’s kinship and identity are then framed through an experimental postmodernist notion, presenting them as social rather than innate constructs. The adults using the reproductive intervention, on the other hand, have their identity and kinship continuity framed and supported as normative, innate, and based on genetic connection. This use of shifting frameworks is presented as unjust and harmful, creating double standards and a corrosion of kinship values, connection and intelligibility between generations; indeed, it is put forward as adult-centric. The analysis of other forms of human kinship dislocation provided by this thesis explores an under-utilised resource which is used to counter the commonly held opinion that any disruption of social and genetic relatedness for donor offspring is insignificant. The experiences of adoption and the stolen generations are used to inform understanding of the personal and social effects of such kinship disruption and potential reunion for donor offspring. These examples, along with laws governing international human rights, further strengthen the appeal here for normative principles and protections based on collective knowledge and standards to be applied to children of reproductive technology. The thesis presents the argument that the framing and regulation of reproductive technology is excessively influenced by industry providers and users. The interests of these parties collide with and corrode any accurate assessments and protections afforded to the children of reproductive technology. The thesis seeks to counter such encroachments and concludes by presenting these protections, frameworks, and human experiences as resources which can help to address the problems created for the offspring of such reproductive interventions, thereby illustrating why these reproductive interventions should be discontinued.

Elucidating the links between UV radiation and vitamin D synthesis : using an in vitro model

Ultraviolet radiation (UV) is the carcinogen that causes the most common malignancy in humans – skin cancer. However, moderate UV exposure is essential for producing vitaminDin our skin. VitaminDincreases the absorption of calcium from the diet, and adequate calcium is necessary for the building and maintenance of bones. Thus, low levels of vitamin D can cause osteomalacia and rickets and contribute to osteoporosis. Emerging evidence also suggests vitamin D may protect against falls, internal cancers, psychiatric conditions, autoimmune diseases and cardiovascular diseases. Since the dominant source of vitamin D is sunlight exposure, there is a need to understand what is a “balanced” level of sun exposure to maintain an adequate level of vitamin D but minimise the risks of eye damage, skin damage and skin cancer resulting from excessive UV exposure. There are many steps in the pathway from incoming solar UV to the eventual vitamin D status of humans (measured as 25-hydroxyvitamin D in the blood), and our knowledge about many of these steps is currently incomplete. This project begins by investigating the levels of UV available for synthesising vitamin D, and how these levels vary across seasons, latitudes and times of the day. The thesis then covers experiments conducted with an in vitro model, which was developed to study several aspects of vitamin D synthesis. Results from the model suggest the relationship between UV dose and vitamin D is not linear. This is an important input into public health messages regarding ‘safe’ UV exposure: larger doses of UV, beyond a certain limit, may not continue to produce vitamin D; however, they will increase the risk of skin cancers and eye damage. The model also showed that, when given identical doses of UV, the amount of vitamin D produced was impacted by temperature. In humans, a temperature-dependent reaction must occur in the top layers of human skin, prior to vitamin D entering the bloodstream. The hypothesis will be raised that cooler temperatures (occurring in winter and at high latitudes) may reduce vitamin D production in humans. Finally, the model has also been used to study the wavelengths of UV thought to be responsible for producing vitamin D. It appears that vitamin D production is limited to a small range of UV wavelengths, which may be narrower than previously thought. Together, these results suggest that further research is needed into the ability of humans to synthesise vitamin D from sunlight. In particular, more information is needed about the dose-response relationship in humans and to investigate the proposed impact of temperature. Having an accurate action spectrum will also be essential for measuring the available levels of vitamin D-effective UV. As this research continues, it will contribute to the scientific evidence-base needed for devising a public health message that will balance the risks of excessive UV exposure with maintaining adequate vitamin D.

Interventions for preventing and managing radiation-induced skin reactions in cancer patients (Protocol)

To assess the effects of any interventions which aim to prevent or manage radiation-induced skin reactions in people with cancer.

Photoinduced conjugation of Dithioester- and Trithiocarbonate-Functional RAFT polymers with alkenes

We report the photoinduced conjugation of polymers synthesized via reversible addition−fragmentation chain transfer (RAFT) polymerization with a number of low molecular weight (functional) olefins. Upon irradiation of a solution of an aliphatic alkene and the benzyl dithioacetic acid ester (CPDA) or dodecyl trithiocarbonate (DoPAT) functional poly(alkyl acrylate) at the absorption wavelength of the thiocarbonyl group (315 nm), incorporation of the alkene at the polymer chain-end occurred. The most efficient systems identified with regard to the rate of reaction and yield were poly(butyl acrylate)/CPDA/ethyl vinyl ether (78% monoinsertion product after 1 h) and poly(butyl acrylate)/CPDA/1-pentene (73% insertion product after 7 h) at ambient temperature. An in-depth analysis of the reaction mechanism by 1H NMR and online size-exclusion chromatography-electrospray ionization tandem mass spectrometry (SEC/ESI−MSn) revealed that a possible [2 + 2] photoaddition mechanism of conjugation does not take place. Instead, fast β-cleavage of the photoexcited RAFT-end group with subsequent radical addition of an alkene was observed for all employed systems. The presented reaction thus provides a means of spatial and temporal control for the conjugation of alkenes to thiocarbonyl thio-capped macromolecules via the use of UV radiation.

Impact and energy absorption of road safety barriers by coupled SPH/FEM

Road safety barriers are used to minimise the severity of road accidents and protect lives and property. There are several types of barrier in use today. This paper reports the initial phase of research carried out to study the impact response of portable water-filled barrier (PWFB) which has the potential to absorb impact energy and hence provide crash mitigation under low to moderate speeds. Current research on the impact and energy absorption capacity of water-filled road safety barriers is limited due to the complexity of fluid-structure interaction under dynamic impact. In this paper, a novel fluid-structure interaction method is developed based on the combination of Smooth Particle Hydrodynamics (SPH) and Finite Element Method (FEM). The sloshing phenomenon of water inside a PWFB is investigated to explore the energy absorption capacity of water under dynamic impact. It was found that water plays an important role in energy absorption. The coupling analysis developed in this paper will provide a platform to further the research in optimising the behaviour of the PWFB. The effect of the amount of water on its energy absorption capacity is investigated and the results have practical applications in the design of PWFBs.

Analysis of Cone-Beam CT using prior information

Treatment plans for conformal radiotherapy are based on an initial CT scan. The aim is to deliver the prescribed dose to the tumour, while minimising exposure to nearby organs. Recent advances make it possible to also obtain a Cone-Beam CT (CBCT) scan, once the patient has been positioned for treatment. A statistical model will be developed to compare these CBCT scans with the initial CT scan. Changes in the size, shape and position of the tumour and organs will be detected and quantified. Some progress has already been made in segmentation of prostate CBCT scans [1],[2],[3]. However, none of the existing approaches have taken full advantage of the prior information that is available. The planning CT scan is expertly annotated with contours of the tumour and nearby sensitive objects. This data is specific to the individual patient and can be viewed as a snapshot of spatial information at a point in time. There is an abundance of studies in the radiotherapy literature that describe the amount of variation in the relevant organs between treatments. The findings from these studies can form a basis for estimating the degree of uncertainty. All of this information can be incorporated as an informative prior into a Bayesian statistical model. This model will be developed using scans of CT phantoms, which are objects with known geometry. Thus, the accuracy of the model can be evaluated objectively. This will also enable comparison between alternative models.

Response to “Topical agent therapy for prevention and treatment of radiodermatitis : a meta-analysis”

To the Editor; It was with interest that I read the recent article by Zhang et al. published in Supportive Care in Cancer [1]. This paper highlighted the importance of radiodermatitis (RD) being an unresolved and distressing clinical issue in patients with cancer undergoing radiation therapy. However, I am concerned with a number of clinical and methodological issues within this paper: (i) the clinical and operational definition of prophylaxis and treatment of RD; (ii) the accuracy of the identification of trials; and (iii) the appropriateness of the conduct of the meta-analyses...

Natural convection flow in a strong cross magnetic field with radiation

The problem of MHD natural convection boundary layer flow of an electrically conducting and optically dense gray viscous fluid along a heated vertical plate is analyzed in the presence of strong cross magnetic field with radiative heat transfer. In the analysis radiative heat flux is considered by adopting optically thick radiation limit. Attempt is made to obtain the solutions valid for liquid metals by taking Pr≪1. Boundary layer equations are transformed in to a convenient dimensionless form by using stream function formulation (SFF) and primitive variable formulation (PVF). Non-similar equations obtained from SFF are then simulated by implicit finite difference (Keller-box) method whereas parabolic partial differential equations obtained from PVF are integrated numerically by hiring direct finite difference method over the entire range of local Hartmann parameter, $xi$ . Further, asymptotic solutions are also obtained for large and small values of local Hartmann parameter $xi$ . A favorable agreement is found between the results for small, large and all values of $xi$ . Numerical results are also demonstrated graphically by showing the effect of various physical parameters on shear stress, rate of heat transfer, velocity and temperature.

Near infrared (NIR) absorption spectra correlates with subchondral bone micro-CT parameters in osteoarthritic rat models

Determining the properties and integrity of subchondral bone in the developmental stages of osteoarthritis, especially in a form that can facilitate real-time characterization for diagnostic and decision-making purposes, is still a matter for research and development. This paper presents relationships between near infrared absorption spectra and properties of subchondral bone obtained from 3 models of osteoarthritic degeneration induced in laboratory rats via: (i) menisectomy (MSX); (ii) anterior cruciate ligament transaction (ACL); and (iii) intra-articular injection of mono-ido-acetate (1 mg) (MIA), in the right knee joint, with 12 rats per model group (N = 36). After 8 weeks, the animals were sacrificed and knee joints were collected. A custom-made diffuse reflectance NIR probe of diameter 5 mm was placed on the tibial surface and spectral data were acquired from each specimen in the wavenumber range 4000–12 500 cm− 1. After spectral acquisition, micro computed tomography (micro-CT) was performed on the samples and subchondral bone parameters namely: bone volume (BV) and bone mineral density (BMD) were extracted from the micro-CT data. Statistical correlation was then conducted between these parameters and regions of the near infrared spectra using multivariate techniques including principal component analysis (PCA), discriminant analysis (DA), and partial least squares (PLS) regression. Statistically significant linear correlations were found between the near infrared absorption spectra and subchondral bone BMD (R2 = 98.84%) and BV (R2 = 97.87%). In conclusion, near infrared spectroscopic probing can be used to detect, qualify and quantify changes in the composition of the subchondral bone, and could potentially assist in distinguishing healthy from OA bone as demonstrated with our laboratory rat models.