Damage to plasmid DNA induced by low energy carbon ions

The damage induced in supercoiled plasmid DNA molecules by 1-6 keV carbon ions has been investigated as a function of ion exposure, energy and charge state. The production of short linear fragments through multiple double strand breaks has been demonstrated and exponential exposure responses for each of the topoisomers have been found. The cross section for the loss of supercoiling was calculated to be (2.2 +/- 0.5) x 10(-14) cm(2) for 2 keVC(+) ions. For singly charged carbon ions, increased damage was observed with increasing ion energy. In the case of 2 keV doubly charged ions, the damage was greater than for singly charged ions of the same energy. These observations demonstrate that ion induced damage is a function of both the kinetic and potential energies of the ion.

Creation of damage-free ferroelectric nanocapacitors via focused ion beam milling

We present a novel method for creating damage-free ferroelectric nanostructures with a focused ion beam milling machine. Using a standard e-beam photoresist followed by a dilute acid wash, nanostructures ranging in size from 1 mu m down to 250 nm were created in a 90 nm thick lead zirconate titanate ( PZT) wafer. Transmission electron microscopy and piezoresponse force microscopy ( PFM) confirmed that the surfaces of the nanostructures remained damage free during fabrication, and showed no gallium implantation, and that there was no degradation of ferroelectric properties. In fact DC strain loops, obtained using PFM, demonstrated that the nanostructures have a higher piezoresponse than unmilled films. As the samples did not have any top hard mask, the method presented is unique as it allows for imaging of the top surface to understand edge effects in well-defined nanostructures. In addition, as no post-mill annealing was necessary, it facilitates investigation of nanoscale domain mechanisms without process-induced artefacts.

Sandstone response to salt weathering following simulated fire damage: a comparison of furnace heating and fire.

Fire has long been recognized as an agent of rock weathering. Our understanding of the impact of fire on stone comes either from early anecdotal evidence, or from more recent laboratory simulation studies, using furnaces to simulate the effects of fire. This paper suggests that knowledge derived from simulated heating experiments is based on the preconceptions of the experiment designer – when using a furnace to simulate fire, the operator decides on the maximum temperature and the duration of the experiment. These are key factors in determining the response of the stone to fire, and if these are removed from realworld observations then knowledge based on these simulations must be questioned. To explore the differences between heating sandstone in a furnace and a real fire, sample blocks of Peakmoor Sandstone were subjected to different stress histories in combination (lime rendering and removal, furnace heating or fire, frost and salt weathering). Block response to furnace heating and fire is discussed, with emphasis placed on the non-uniformity of the fire and of block response to fire in contrast to the uniform response to surface heating in a furnace. Subsequent response to salt weathering (by a 10% solution of sodium chloride and magnesium sulphate) was then monitored by weight loss. Blocks that had experienced fire showed a more unpredictable response to salt weathering than those that had undergone furnace heating – spalling of corners and rapid catastrophic weight loss were evidenced in blocks that had been subjected to fire, after periods of relative quiescence. An important physical side-effect of the fire was soot accumulation, which created a waxy, relatively impermeable layer on some blocks. This layer repelled water and hindered salt ingress, but eventually detached when salt, able to enter the substrate through more permeable areas, concentrated and crystallized behind it, resulting in rapid weight loss and accelerated decay. Copyright ©2007 John Wiley & Sons, Ltd.

Chk1 Suppresses a Caspase-2 Apoptotic Response to DNA Damage that Bypasses p53, Bcl-2, and Caspase-3

Evasion of DNA damage-induced cell death, via mutation of the p53 tumor suppressor or overexpression of prosurvival Bcl-2 family proteins, is a key step toward malignant transformation and therapeutic resistance. We report that depletion or acute inhibition of checkpoint kinase 1 (Chk1) is sufficient to restore ?-radiation-induced apoptosis in p53 mutant zebrafish embryos. Surprisingly, caspase-3 is not activated prior to DNA fragmentation, in contrast to classical intrinsic or extrinsic apoptosis. Rather, an alternative apoptotic program is engaged that cell autonomously requires atm (ataxia telangiectasia mutated), atr (ATM and Rad3-related) and caspase-2, and is not affected by p53 loss or overexpression of bcl-2/xl. Similarly, Chk1 inhibitor-treated human tumor cells hyperactivate ATM, ATR, and caspase-2 after ?-radiation and trigger a caspase-2-dependent apoptotic program that bypasses p53 deficiency and excess Bcl-2. The evolutionarily conserved "Chk1-suppressed" pathway defines a novel apoptotic process, whose responsiveness to Chk1 inhibitors and insensitivity to p53 and BCL2 alterations have important implications for cancer therapy. © 2008 Elsevier Inc. All rights reserved.

Ultrafast Probing of Collective Electron Dynamics Driven by Dielectronic Repulsion

We use the time-dependent R-matrix approach to investigate an ultrashort pump-probe scheme to observe collective electron dynamics in C(+). The ionization probability of a coherent superposition of the 2s2p(2) (2)D and (2)S states shows rapid modulation due to collective dynamics of the two equivalent 2p electrons, with the modulation frequency linked to the dielectronic repulsion. The best insight into this collective dynamics is achieved by a transformation from LS symmetry to the uncoupled basis. Such dynamics may be important in high-harmonic generation using open-shell atoms and ions.

What role for DNA damage and repair in the bystander response?

The radiation-induced bystander effect challenges the accepted paradigm of direct DNA damage in response to energy deposition driving the biological consequences of radiation exposure. With the bystander response, cells which have not been directly exposed to radiation respond to their neighbours being targeted. In our own studies we have used novel targeted microbeam approaches to specifically irradiate parts of individual cells within a population to quantify the bystander response and obtain mechanistic information. Using this approach it has become clear that energy deposited by radiation in nuclear DNA is not required to trigger the effect, with cytoplasmic irradiation required. Irradiated cells also trigger a bystander response regardless of whether they themselves live or die, suggesting that the phenotype of the targeted cell is not a determining factor. Despite this however, a range of evidence has shown that repair status is important for dealing with the consequences of a bystander signal. Importantly, repair processes involved in the processing of dsb appear to be involved suggesting that the bystander response involves the delayed or indirect production of dsb-type lesions in bystander cells. Whether these are infact true dsb or complexes of oxidised bases in combination with strand breaks and the mechanisms for their formation, remains to be elucidated.

Radiation induced bystander signals are independent of DNA damage and DNA repair capacity of the irradiated cells.

Evidence is accumulating that irradiated cells produce signals, which interact with non-exposed cells in the same population. Here, we analysed the mechanism for bystander signal arising in wild-type CHO cells and repair deficient varients, focussing on the relationship between DNA repair capacity and bystander signal arising in irradiated cells. In order to investigate the bystander effect, we carried out medium transfer experiments after X-irradiation where micronuclei were scored in non-targeted DSB repair deficient xrs5 cells. When conditioned medium from irradiated cells was transferred to unirradiated xrs5 cells, the level of induction was independent of whether the medium came from irradiated wild-type, ssb or dsb repair deficient cells. This result suggests that the activation of a bystander signal is independent of the DNA repair capacity of the irradiated cells. Also, pre-treatment of the irradiated cells with 0.5% DMSO, which suppresses micronuclei induction in CHO but not in xrs5 cells, suppressed bystander effects completely in both conditioned media, suggesting that DMSO is effective for suppression of bystander signal arising independently of DNA damage in irradiated cells. Overall the work presented here adds to the understanding that it is the repair phenotype of the cells receiving bystander signals, which determines overall response rather than that of the cell producing the bystander signal.