The role of higher-order chromatin structure in the yield and distribution of DNA double-strand breaks in cells irradiated with X-rays or alpha-particles

Purpose: To determine whether the non-random distributions of DNA double-strand breaks in cells observed after alpha-particle irradiation are related to the higher-order structure of the chromatin within the nucleus.

A review of studies of ionizing radiation-induced double-strand break clustering

Underpinning current models of the mechanisms of the action of radiation is a central role for DNA damage and in particular double-strand breaks (DSBs). For radiations of different LET, there is a need to know the exact yields and distributions of DSBs in human cells. Most measurements of DSB yields within cells now rely on pulsed-field gel electrophoresis as the technique of choice. Previous measurements of DSB yields have suggested that the yields are remarkably similar for different types of radiation with RBE values less than or equal to1.0. More recent studies in mammalian cells, however, have suggested that both the yield and the spatial distribution of DSBs are influenced by radiation quality. RBE values for DSBs induced by high-LET radiations are greater than 1.0, and the distributions are nonrandom. Underlying this is the interaction of particle tracks with the higher-order chromosomal structures within cell nuclei. Further studies are needed to relate nonrandom distributions of DSBs to their rejoining kinetics. At the molecular level, we need to determine the involvement of clustering of damaged bases with strand breakage, and the relationship between higher-order clustering over sizes of kilobase pairs and above to localized clustering at the DNA level. Overall, these studies will allow us to elucidate whether the nonrandom distributions of breaks produced by high-LET particle tracks have any consequences for their repair and biological effectiveness. (C) 2001 by Radiation Research Society.

A Monte Carlo model of DNA double-strand break clustering and rejoining kinetics for the analysis of pulsed-field gel electrophoresis data

In studies of radiation-induced DNA fragmentation and repair, analytical models may provide rapid and easy-to-use methods to test simple hypotheses regarding the breakage and rejoining mechanisms involved. The random breakage model, according to which lesions are distributed uniformly and independently of each other along the DNA, has been the model most used to describe spatial distribution of radiation-induced DNA damage. Recently several mechanistic approaches have been proposed that model clustered damage to DNA. In general, such approaches focus on the study of initial radiation-induced DNA damage and repair, without considering the effects of additional (unwanted and unavoidable) fragmentation that may take place during the experimental procedures. While most approaches, including measurement of total DNA mass below a specified value, allow for the occurrence of background experimental damage by means of simple subtractive procedures, a more detailed analysis of DNA fragmentation necessitates a more accurate treatment. We have developed a new, relatively simple model of DNA breakage and the resulting rejoining kinetics of broken fragments. Initial radiation-induced DNA damage is simulated using a clustered breakage approach, with three free parameters: the number of independently located clusters, each containing several DNA double-strand breaks (DSBs), the average number of DSBs within a cluster (multiplicity of the cluster), and the maximum allowed radius within which DSBs belonging to the same cluster are distributed. Random breakage is simulated as a special case of the DSB clustering procedure. When the model is applied to the analysis of DNA fragmentation as measured with pulsed-field gel electrophoresis (PFGE), the hypothesis that DSBs in proximity rejoin at a different rate from that of sparse isolated breaks can be tested, since the kinetics of rejoining of fragments of varying size may be followed by means of computer simulations. The problem of how to account for background damage from experimental handling is also carefully considered. We have shown that the conventional procedure of subtracting the background damage from the experimental data may lead to erroneous conclusions during the analysis of both initial fragmentation and DSB rejoining. Despite its relative simplicity, the method presented allows both the quantitative and qualitative description of radiation-induced DNA fragmentation and subsequent rejoining of double-stranded DNA fragments. (C) 2004 by Radiation Research Society.

Millimeter-wave printed circuit board characterization using substrate integrated waveguide resonators

This paper proposes a substrate integrated waveguide
(SIW) cavity-based method that is compliant with
ground-signal–ground (GSG) probing technology for dielectric
characterization of printed circuit board materials at millimeter
wavelengths. This paper presents the theory necessary to retrieve
dielectric parameters from the resonant characteristics of SIW
cavities with particular attention placed on the coupling scheme
and means for obtaining the unloaded resonant frequency. Different
sets of samples are designed and measured to address the
influence of the manufacturing process on the method. Material
parameters are extracted at - and -band from measured data
with the effect of surface roughness of the circuit metallization
taken into account.

Excess electron interactions with solvated DNA nucleotides:Strand breaks possible at room temperature

When biological matter is subjected to ionizing radiation, a wealth of secondary low-energy (<20 eV) electrons are produced. These electrons propagate inelastically, losing energy to the medium until they reach energies low enough to localize in regions of high electron affinity. We have recently shown that in fully solvated DNA fragments, nucleobases are particularly attractive for such excess electrons. The next question is what is their longer-term effect on DNA. It has been advocated that they can lead to strand breaks by cleavage of the phosphodiester C-3'-O-3' bond. Here we present a first-principles study of free energy barriers for the cleavage of this bond in fully solvated nucleotides. We have found that except for dAMP, the barriers are on the order of 6 kcal/mol, suggesting that bond cleavage is a regular feature at 300 K. Such low barriers are possible only as a result of solvent and thermal fluctuations. These findings support the notion that low-energy electrons can indeed lead to strand breaks in DNA.

Fasciola hepatica:Histological demonstration of apoptosis in the reproductive organs of flukes of triclabendazole-sensitive and triclabendazole-resistant isolates, and in field-derived flukes from triclabendazole-treated hosts, using in situ hybridisation to visualise endonuclease-generated DNA strand breaks

Investigation of the triclabendazole (TCBZ) resistance status of populations of Fasciola hepatica in field cases of fasciolosis, where treatment failure has been reported, can be supported by histological examination of flukes collected from recently treated hosts. In TCBZ-sensitive flukes (TCBZ-S) exposed to TCBZ metabolites for 1-4. days in vivo, but not in TCBZ-resistant flukes (TCBZ-R), morphological changes suggestive of apoptosis occur in cells undergoing meiosis or mitosis in the testis, ovary and vitelline follicles. In order to verify or refute the contention that efficacy of TCBZ treatment is associated with apoptosis in the reproductive organs of flukes, histological sections of TCBZ-S (Cullompton isolate) flukes and TCBZ-R (Sligo isolate) flukes were subjected to the TdT-mediated dUDP nick end labelling (TUNEL) in situ hybridisation method, a commercially available test specifically designed to label endonuclease-induced DNA strand breaks associated with apoptosis. Additionally, sections of in vivo-treated and untreated flukes originating from field outbreaks of suspected TCBZ-S and TCBZ-R fasciolosis were labelled by the TUNEL method. It was found that in treated TCBZ-S flukes, strong positive labelling indicating apoptosis was associated with morphologically abnormal cells undergoing mitosis or meiosis in the testis, ovary and vitelline follicles. Background labelling in the positive testis sections was attributed to heterophagy of cell debris by the sustentacular tissue. The triggering of apoptosis was probably related to failure of spindle formation at cell division, supporting the contention that TCBZ inhibits microtubule formation. In treated TCBZ-R (Sligo Type 1) flukes, and in treated flukes from field outbreaks of suspected TCBZ-R fasciolosis, no significant labelling was observed, while sections of fluke derived from a field case of fasciolosis where TCBZ resistance was not suspected were heavily labelled. Light labelling was associated with the testis of untreated Cullompton (TCBZ-S) and Sligo Type 2 (TCBZ-R) flukes, which exhibit abnormal spermatogenesis and spermiogenesis, respectively. This was attributed to apoptosis and to heterophagy of effete germ line cells by the sustentacular tissue. It is concluded that demonstration of apoptosis by in situ hybridisation using the TUNEL method on sections of 1-4. days in vivo TCBZ-treated F. hepatica can contribute to the diagnosis of TCBZ resistance in field outbreaks of fasciolosis. © 2012 Elsevier B.V.

Genomic Analysis of Pseudomonas putida Phage tf with Localized Single-Strand DNA Interruptions

The complete sequence of the 46,267 bp genome of the lytic bacteriophage tf specific to Pseudomonas putida PpG1 has been determined. The phage genome has two sets of convergently transcribed genes and 186 bp long direct terminal repeats. The overall genomic architecture of the tf phage is similar to that of the previously described Pseudomonas aeruginosa phages PaP3, LUZ24 and phiMR299-2, and 39 out of the 72 products of predicted tf open reading frames have orthologs in these phages. Accordingly, tf was classified as belonging to the LUZ24-like bacteriophage group. However, taking into account very low homology levels between tf DNA and that of the other phages, tf should be considered as an evolutionary divergent member of the group. Two distinguishing features not reported for other members of the group were found in the tf genome. Firstly, a unique end structure - a blunt right end and a 4-nucleotide 3'-protruding left end - was observed. Secondly, 14 single-chain interruptions (nicks) were found in the top strand of the tf DNA. All nicks were mapped within a consensus sequence 5'-TACT/RTGMC-3'. Two nicks were analyzed in detail and were shown to be present in more than 90% of the phage population. Although localized nicks were previously found only in the DNA of T5-like and phiKMV-like phages, it seems increasingly likely that this enigmatic structural feature is common to various other bacteriophages.

Single crystal CVD diamond growth strategy by the use of a 3D geometrical model: Growth on (113) oriented substrates

The quality of single crystal diamond obtained by microwave CVD processes has been drastically improved in the last 5 years thanks to surface pretreatment of the substrates [A. Tallaire, J. Achard, F. Silva, R.S. Sussmann, A. Gicquel, E. Rzepka, Physica Status Solidi (A) 201, 2419-2424 (2004); G. Bogdan, M. Nesladek, J. D'Haen, J. Maes, V.V. Moshchalkov, K. Haenen, M. D'Olieslaeger, Physica Status Solidi (A) 202, 2066-2072 (2005); M. Yamamoto, T. Teraji, T. Ito, Journal of Crystal Growth 285, 130-136 (2005)]. Additionally, recent results have unambiguously shown the occurrence of (110) faces on crystal edges and (113) faces on crystal corners [F. Silva, J. Achard, X. Bonnin, A. Michau, A. Tallaire, O. Brinza, A. Gicquel, Physica Status Solidi (A) 203, 3049-3055 (2006)]. We have developed a 3D geometrical growth model to account for the final crystal morphology. The basic parameters of this growth model are the relative displacement speeds of (111), (110) and (113) faces normalized to that of the (100) faces, respectively alpha, beta, and gamma. This model predicts both the final equilibrium shape of the crystal (i.e. after infinite growth time) and the crystal morphology as a function of alpha, beta, gamma, and deposition time.

An optimized operating point, deduced from the model, has been validated experimentally by measuring the growth rate in (100), (111), (110), and (113) orientations. Furthermore, the evolution of alpha, beta, gamma as a function of methane concentration in the gas discharge has been established. From these results, crystal growth strategies can be proposed in order, for example, to enlarge the deposition area. In particular, we will show, using the growth model, that the only possibility to significantly increase the deposition area is, for our growth conditions, to use a (113) oriented substrate. A comparison between the grown crystal and the model results will be discussed and characterizations of the grown film (Photoluminescence spectroscopy, EPR, SEM) will be presented. (C) 2008 Elsevier B.V. All rights reserved.

Assessing pain in preterm infants in the neonatal intensive care unit:moving to a 'brain-oriented' approach

Preterm infants in the neonatal intensive care unit undergo repeated exposure to procedural and ongoing pain. Early and long-term changes in pain processing, stress-response systems and development may result from cumulative early pain exposure. So that appropriate treatment can be given, accurate assessment of pain is vital, but is also complex because these infants' responses may differ from those of full-term infants. A variety of uni- and multidimensional assessment tools are available; however, many have incomplete psychometric testing and may not incorporate developmentally important cues. Near-infrared spectroscopy and/or EEG techniques that measure neonatal pain responses at a cortical level offer new opportunities to validate neonatal pain assessment tools.

MTERF1 Binds mtDNA to Prevent Transcriptional Interference at the Light-Strand Promoter but Is Dispensable for rRNA Gene Transcription Regulation

Mitochondrial transcription termination factor 1, MTERF1, has been reported to couple rRNA gene transcription initiation with termination and is therefore thought to be a key regulator of mammalian mitochondrial ribosome biogenesis. The prevailing model is based on a series of observations published over the last two decades, but no in vivo evidence exists to show that MTERF1 regulates transcription of the heavy-strand region of mtDNA containing the rRNA genes. Here, we demonstrate that knockout of Mterf1 in mice has no effect on mitochondrial rRNA levels or mitochondrial translation. Instead, loss of Mterf1 influences transcription initiation at the light-strand promoter, resulting in a decrease of de novo transcription manifested as reduced 7S RNA levels. Based on these observations, we suggest that MTERF1 does not regulate heavy-strand transcription, but rather acts to block transcription on the opposite strand of mtDNA to prevent transcription interference at the light-strand promoter.