Plasmid DNA damage following exposure to atmospheric pressure non-thermal plasma: kinetics and influence of oxygen admixture

The nature and kinetics of plasmid DNA damage after DNA exposure to a kHz-driven atmospheric pressure nonthermal plasma jet has been investigated. Both single-strand break (SSB) and double-strand break (DSB) processes are reported here. While SSB had a higher rate constant, DSB is recognized to be more significant in living systems, often resulting in loss of viability. In a helium-operated plasma jet, adding oxygen to the feed gas resulted in higher rates of DNA DSB, which increased linearly with increasing oxygen content, up to an optimum level of 0.75% oxygen, after which the DSB rate decreased slightly, indicating an essential role for reactive oxygen species in the rapid degradation of DNA.

Concrete damage plasticity model for modeling FRP-to-concrete bond behavior

The technique of externally bonding fiber-reinforced polymer (FRP) composites has become very popular worldwide for retrofitting existing reinforced concrete (RC) structures. Debonding of FRP from the concrete substrate is a typical failure mode in such strengthened structures. The bond behavior between FRP and concrete thus plays a crucial role in these structures. The FRP-to-concrete bond behavior has been extensively investigated experimentally, commonly using a single or double shear test of the FRP-to-concrete bonded joint. Comparatively, much less research has been concerned with numerical simulation, chiefly due to difficulties in the accurate modeling of the complex behavior of concrete. This paper presents a simple but robust finite-element (FE) model for simulating the bond behavior in the entire debonding process for the single shear test. A concrete damage plasticity model is proposed to capture the concrete-to-FRP bond behavior. Numerical results are in close agreement with test data, validating the model. In addition to accuracy, the model has two further advantages: it only requires the basic material parameters (i.e., no arbitrary user-defined parameter such as the shear retention factor is required) and it can be directly implemented in the FE software ABAQUS.

Finite element modelling of FRP-to-concrete bond behaviour using the concrete damage plasticity theory combined with a plastic degradation model

The technique of externally bonding fibre reinforced polymer (FRP) composites has been becoming popular worldwide for retrofitting existing reinforced concrete (RC) structures. A major failure mode in such strengthened structures is the debonding of FRP from the concrete substrate. The bond behaviour between FRP and concrete thus plays a crucial role in these structures. The FRP-to-concrete bond behaviour has been extensively investigated experimentally, commonly using the pull-off test of FRP-to-concrete bonded joint. Comparatively, much less research has been concerned with the numerical simulation of this bond behaviour, chiefly due to difficulties in accurately modelling the complex behaviour of concrete. This paper proposes a robust finite element (FE) model for simulating the bond behaviour in the entire loading process in the pull-off test. A concrete damage plasticity model based on the plastic degradation theory is proposed to overcome the weakness of the elastic degradation theory which has been commonly adopted in previous studies. The model produces results in very close agreement with test data. © Tsinghua University Press, Beijing and Springer-Verlag Berlin Heidelberg 2011.

Closure to “Concrete Damage Plasticity Model for Modeling FRP-to-Concrete Bond Behavior” by Y. Tao and J. F. Chen

The authors appreciate the discusser’s interest in the original paper and for the valuable discussion, which provides the opportunity to clarify and reiterate a few points made in the original paper. The comments and questions raised by the discusser are addressed in the following sections.

DNA mismatch repair and the DNA damage response to ionizing radiation:making sense of apparently conflicting data

The DNA mismatch repair (MMR) pathway detects and repairs DNA replication errors. While DNA MMR-proficiency is known to play a key role in the sensitivity to a number of DNA damaging agents, its role in the cytotoxicity of ionizing radiation (IR) is less well characterized. Available literature to date is conflicting regarding the influence of MMR status on radiosensitivity, and this has arisen as a subject of controversy in the field. The aim of this paper is to provide the first comprehensive overview of the experimental data linking MMR proteins and the DNA damage response to IR. A PubMed search was conducted using the key words "DNA mismatch repair" and "ionizing radiation". Relevant articles and their references were reviewed for their association between DNA MMR and IR. Recent data suggest that radiation dose and the type of DNA damage induced may dictate the involvement of the MMR system in the cellular response to IR. In particular, the literature supports a role for the MMR system in DNA damage recognition, cell cycle arrest, DNA repair and apoptosis. In this review we discuss our current understanding of the impact of MMR status on the cellular response to radiation in mammalian cells gained from past and present studies and attempt to provide an explanation for how MMR may determine the response to radiation.

Targeting of photooxidative damage on single-stranded DNA representing the bcr-abl chimeric gene using oligonucleotide-conjugates containing [Ru(phen)3](2+)-like photosensitiser groups

Photooxidative damage was induced predominantly at a single guanine base in a target DNA by irradiation (lambda > 330 nm) in the presence of complementary oligodeoxynucleotide conjugates (ODN-5'-linker-[Ru(phen)3]2+) (phen = 1,10-phenanthroline). The target DNA represents the b2a2 variant of the chimeric bcr-abl gene implicated in the pathogenesis of chronic myeloid leukaemia, and the sequence of the 17mer ODN component of the conjugate (3' G G T A G T T A T T C C T T C T T 5') was complementary to the junction region of the sense strand sequence of this oncogene. Two different conjugates were prepared, both of them by reaction of the appropriate succinimide ester with 5'-hexylamino-derivatised 17mer ODN. In Ru-ODN-1 (7) the linker was -(CH2)6-NHCO-bpyMe (-bpyMe = 4'-[4-methyl-2,2'-bipyridyl]), whereas in Ru-ODN-2 (13) it was -(CH2)6-NHCO-(CH2)3-CONH-phen. Photoexcitation of either of the conjugates when hybridised with the 32P-5'-end-labelled target 34mer 5'T G A C C A T C A A T A A G G A A G A A G21 C C C T T C A G C G G C C 3' (ODN binding site underlined) led to an alkali-labile site predominantly (> 90%) at the G21 base, which is at the junction of double-stranded and single-stranded regions of the hybrid. Greater yields were found with Ru-ODN-1 (7) than with Ru ODN-2 (13). In contrast to this specific cleavage with Ru-ODN-1 (7) or Ru-ODN-2 (13), alkali-labile sites were generated at all guanines when the 34mer was photolysed in the presence of the free sensitiser [Ru(phen)3]2+. Since [Ru(phen)3]2+ was shown to react with 2'-deoxyguanosine to form the diastereomers of a spiroiminodihydantoin derivative (the product from 1O2 reaction), 1O2 might also be an oxidizing species in the case of Ru-ODN-1 (7) and Ru-ODN-2 (13). Therefore to determine the range of reaction, a series of 'variant' targets was prepared, in which G21 was replaced with a cytosine and a guanine substituted for a base further towards the 3'-end (e.g. Variant 3; 5'T G A C C A T C A A T A A G G A A G A A C C G23 C T T C A G C G G32 C C3'). While it was noted that efficient reaction took place at distances apparently remote from the photosensitiser (e.g at G32, but not G23 for Variant 3), this effect could be attributed to hairpinning of the single-stranded region of the target. These results are therefore consistent with the photooxidative damage being induced by a reaction close to the photosensitiser rather than by a diffusible species such as 1O2.

AURKA overexpression accompanies dysregulation of DNA-damage response genes in invasive urothelial cell carcinoma

Invasive urothelial cell carcinoma (UCC) is characterized by increased chromosomal instability and follows an aggressive clinical course in contrast to non-invasive disease. To identify molecular processes that confer and maintain an aggressive malignant phenotype, we used a high-throughput genome-wide approach to interrogate a cohort of high and low clinical risk UCC tumors. Differential expression analyses highlighted cohesive dysregulation of critical genes involved in the G(2)/M checkpoint in aggressive UCC. Hierarchical clustering based on DNA Damage Response (DDR) genes separated tumors according to a pre-defined clinical risk phenotype. Using array-comparative genomic hybridization, we confirmed that the DDR was disrupted in tumors displaying high genomic instability. We identified DNA copy number gains at 20q13.2-q13.3 (AURKA locus) and determined that overexpression of AURKA accompanied dysregulation of DDR genes in high risk tumors. We postulated that DDR-deficient UCC tumors are advantaged by a selective pressure for AURKA associated override of M phase barriers and confirmed this in an independent tissue microarray series. This mechanism that enables cancer cells to maintain an aggressive phenotype forms a rationale for targeting AURKA as a therapeutic strategy in advanced stage UCC.

Regulation of human dUTPase gene expression and p53-mediated transcriptional repression in response to oxaliplatin-induced DNA damage

Deoxyuridine triphosphate nucleotidohydrolase (dUTPase) catalyzes the hydrolysis of dUTP to dUMP and PPi. Although dUTP is a normal intermediate in DNA synthesis, its accumulation and misincorporation into DNA is lethal. Importantly, uracil misincorporation is a mechanism of cytotoxicity induced by fluoropyrimidine chemotherapeutic agents including 5-fluorouracil (5-FU) and elevated expression of dUTPase is negatively correlated with clinical response to 5-FU-therapy. In this study we performed the first functional characterization of the dUTPase promoter and demonstrate a role for E2F-1 and Sp1 in driving dUTPase expression. We establish a direct role for both mutant and wild-type forms of p53 in modulating dUTPase promoter activity. Treatment of HCT116 p53(+/+) cells with the DNA-damaging agent oxaliplatin induced a p53-dependent transcriptional downregulation of dUTPase not observed in the isogenic null cell line. Oxaliplatin treatment induced enrichment of p53 at the dUTPase promoter with a concomitant reduction in Sp1. The suppression of dUTPase by oxaliplatin promoted increased levels of dUTP that was enhanced by subsequent addition of fluoropyrimidines. The novel observation that oxaliplatin downregulates dUTPase expression may provide a mechanistic basis contributing to the synergy observed between 5-FU and oxaliplatin in the clinic. Furthermore, these studies provide the first evidence of a direct transcriptional link between the essential enzyme dUTPase and the tumor suppressor p53.

Using Instrumented Vehicles To Detect Damage in Bridges

Bridge structures are subject to continuous degradation due to the environment, ageing and excess loading. Monitoring of bridges is a key part of any maintenance strategy as it can give early warning if a bridge is becoming unsafe. This paper will theoretically assess the ability of a vehicle fitted with accelerometers on its axles to detect changes in damping of bridges, which may be the result of damage. Two vehicle models are used in this investigation. The first is a two degree-of-freedom quarter-car and the second is a four degree-of-freedom halfcar. The bridge is modelled as a simply supported beam and the interaction between the vehicle and the bridge is a coupled dynamic interaction algorithm. Both smooth and rough road profiles are used in the simulation and results indicate that changes in bridge damping can be detected by the vehicle models for a range of vehicle velocities and bridge spans.

Using Instrumented Vehicles to Detect Damage in Bridges

This paper describes a ‘drive-by’ method of bridge inspection using an instrumented vehicle. Accelerometers on the vehicle are proposed as a means of detecting damage on the bridge in the time it takes for the vehicle to cross the bridge at full highway speed. For a perfectly smooth road profile, the method is shown to be feasible. Changes in bridge damping, which is an indicator of damage, are clearly visible in the acceleration signal of a quarter-car vehicle on a smooth road surface modelled using MatLab. When road profile is considered, the influence of changes in bridge damping on the vehicle acceleration signal is much less clear. However, when a half-car model is used on a road with a rough profile, it is again possible to detect changes in bridge damping, provided the vehicle has two identical axles.

Improving composite damage modelling through automatic placement of cohesive elements

Numerous experimental studies of damage in composite laminates have shown that intralaminar (in-plane) matrix cracks lead to interlaminar delamination (out-of-plane) at ply interfaces. The smearing of in-plane cracks over a volume, as a consequence of the use of continuum damage mechanics, does not always effectively capture the full extent of the interaction between the two failure mechanisms. A more accurate representation is obtained by adopting a discrete crack approach via the use of cohesive elements, for both in-plane and out-of-plane damage. The difficulty with cohesive elements is that their location must be determined a priori in order to generate the model; while ideally the position of the crack migration, and more generally the propagation path, should be obtained as part of the problem’s solution. With the aim of enhancing current modelling capabilities with truly predictive capabilities, a concept of automatic insertion of interface elements is utilized. The consideration of a simple traction criterion in relation to material strength, evaluated at each node of the model (or of the regions of the model where it is estimated cracks might form), allows for the determination of initial crack location and subsequent propagation by the insertion of cohesive elements during the course of the analysis. Several experimental results are modelled using the commercial package ABAQUS/Standard with an automatic insertion subroutine developed in this work, and the results are presented to demonstrate the capabilities of this technique.

Optimising postbuckling composite panels for damage resistance

The design of current composite primary aerostructures, such as fuselage or wing stiffened panels, tends to be conservative due to the susceptibility of the relatively weak skin-stiffener interface. This weakness is due to through-thickness stresses which are exacerbated by deformations due to buckling. This paper presents a finite-elementbased optimization strategy, utilizing a global-local modelling approach, for postbuckling stiffened panels which takes into account damage mechanisms which may lead to delamination and subsequent failure of the panel due to stiffener debonding. A genetic algorithm was linked to a finite element package to automate the iterative procedure and maximize the damage resistance of the panel in postbuckling. For a given loading condition, the procedure optimized the panel’s skin layup leading to a design displaying superior damage resistance compared to non-optimized designs

Impact of fractionation on out-of-field survival and DNA damage responses following exposure to intensity modulated radiation fields

To limit toxicity to normal tissues adjacent to the target tumour volume, radiotherapy is delivered using fractionated regimes whereby the total prescribed dose is given as a series of sequential smaller doses separated by specific time intervals. The impact of fractionation on out-of-field survival and DNA damage responses was determined in AGO-1522 primary human fibroblasts and MCF-7 breast tumour cells using uniform and modulated exposures delivered using a 225 kVp x-ray source. Responses to fractionated schedules (two equal fractions delivered with time intervals from 4 h to 48 h) were compared to those following acute exposures. Cell survival and DNA damage repair measurements indicate that cellular responses to fractionated non-uniform exposures differ from those seen in uniform exposures for the investigated cell lines. Specifically, there is a consistent lack of repair observed in the out-of-field populations during intervals between fractions, confirming the importance of cell signalling to out-of-field responses in a fractionated radiation schedule, and this needs to be confirmed for a wider range of cell lines and conditions.