DNA complex lesions induced by protons and ⋅-particles: track structure characteristics determining linear energy transfer and particle type dependence

The yield of DNA double-strand breaks (dsb) and DNA complex lesions induced by protons and α-particles of various energies was simulated using a Monte Carlo track structure code (MOCA15) and a simple model of the DNA molecule. DNA breaks of different complexity were analysed. The linear energy transfer (LET) and particle-type dependence of lesions of higher complexity seems to confirm the importance of clustered damage in DNA as a relevant step leading to biological endpoints such as cell inactivation. The detailed structure of proton and α-particle tracks was analysed to identify the main characteristics possibly responsible for such a dependence. The role of the primary ion and of its secondary electrons in inducing dsb and complex lesions is described, showing that the relative contribution of secondary electron tracks alone in inducing clustered lesions is almost negligible at high LET, but tends to dominate below ≈10 keV/μm. This is consistent with the observed similar effectiveness of low-LET fast particle radiation and sparsely ionizing radiation such as x-rays. The dependence on LET and particle type is mainly due to energy deposition events of the primary ion together with short range electrons surrounding the ion track; the yield of complex lesions due to secondary electron tracks alone is substantially LET independent. The radial distributions of the energy contributing to the induction of complex lesions were analyzed and compared with the radial distributions of energy deposition of the full tracks. The results suggest that the stochastic behaviour (i.e. cluster properties) of the energy deposition pattern within a radius of a few nanometers around the ion track plays a relevant role in determining the biological radiation effectiveness. Received: 20 December 1996 / Accepted in revised form: 5 March 1997     

Locations of radiation-produced DNA double strand breaks along chromosomes: a stochastic cluster process formalism.

Ionizing radiation produces DNA double strand breaks (DSBs) in chromosomes. For densely ionizing radiation, the DSBs are not spaced randomly along a chromosome: recent data for size distributions of DNA fragments indicate break clustering on kbp-Mbp scales. Different DSB clusters on a chromosome are typically made by different, statistically independent, stochastically structured radiation tracks, and the average number of tracks involved can be small. We therefore model DSB positions along a chromosome as a stationary Poisson cluster process, i.e. a stochastic process consisting of secondary point processes whose locations are determined by a primary point process that is Poisson. Each secondary process represents a break cluster, typically consisting of 1-10 DSBs in a comparatively localized stochastic pattern determined by chromatin geometry and radiation track structure. Using this Poisson cluster process model, which we call the randomly located clusters (RLC) formalism, theorems are derived for how the DNA fragment-size distribution depends on radiation dose. The RLC dose-response relations become non-linear when the dose becomes so high that DSB clusters from different tracks overlap or adjoin closely. The RLC formalism generalizes previous models, fits current data adequately and facilitates mechanistically based extrapolations from high-dose experiments to the much lower doses of interest for most applications.     

The BIANCA model/code of radiation-induced cell death: application to human cells exposed to different radiation types

This paper presents a biophysical model of radiation-induced cell death, implemented as a Monte Carlo code called BIophysical ANalysis of Cell death and chromosome Aberrations (BIANCA), based on the assumption that some chromosome aberrations (dicentrics, rings, and large deletions, called “lethal aberrations”) lead to clonogenic inactivation. In turn, chromosome aberrations are assumed to derive from clustered, and thus severe, DNA lesions (called “cluster lesions,” or CL) interacting at the micrometer scale; the CL yield and the threshold distance governing CL interaction are the only model parameters. After a pilot study on V79 hamster cells exposed to protons and carbon ions, in the present work the model was extended and applied to AG1522 human cells exposed to photons, He ions, and heavier ions including carbon and neon. The agreement with experimental survival data taken from the literature supported the assumptions. In particular, the inactivation of AG1522 cells was explained by lethal aberrations not only for X-rays, as already reported by others, but also for the aforementioned radiation types. Furthermore, the results are consistent with the hypothesis that the critical initial lesions leading to cell death are DNA cluster lesions having yields in the order of ~2 CL Gy^?1 cell^?1 at low LET and ~20 CL Gy^?1 cell^?1 at high LET, and that the processing of these lesions is modulated by proximity effects at the micrometer scale related to interphase chromatin organization. The model was then applied to calculate the fraction of inactivated cells, as well as the yields of lethal aberrations and cluster lesions, as a function of LET; the results showed a maximum around 130 keV/μm, and such maximum was much higher for cluster lesions and lethal aberrations than for cell inactivation.     

The probabilities of one- and multi-track events for modeling radiation-induced cell kill

In view of the clinical importance of hypofractionated radiotherapy, track models which are based on multi-hit events are currently reinvestigated. These models are often criticized, because it is believed that the probability of multi-track hits is negligible. In this work, the probabilities for one- and multi-track events are determined for different biological targets. The obtained probabilities can be used with nano-dosimetric cluster size distributions to obtain the parameters of track models. We quantitatively determined the probabilities for one- and multi-track events for 100, 500 and 1000 keV electrons, respectively. It is assumed that the single tracks are statistically independent and follow a Poisson distribution. Three different biological targets were investigated: (1) a DNA strand (2 nm scale); (2) two adjacent chromatin fibers (60 nm); and (3) fiber loops (300 nm). It was shown that the probabilities for one- and multi-track events are increasing with energy, size of the sensitive target structure, and dose. For a 2 × 2 × 2 nm³ target, one-track events are around 10,000 times more frequent than multi-track events. If the size of the sensitive structure is increased to 100–300 nm, the probabilities for one- and multi-track events are of the same order of magnitude. It was shown that target theories can play a role for describing radiation-induced cell death if the targets are of the size of two adjacent chromatin fibers or fiber loops. The obtained probabilities can be used together with the nano-dosimetric cluster size distributions to determine model parameters for target theories.     

A random-walk model of human mortality and aging

Consideration is made of the roles of certain types of state space and time scales for a random-walk model of individual physiological status change and death. Because the actual measurement of physiological variables omits many variables relevant to survival, we are forced to view this model as operating in a stochastic state space for a population of individuals where only the frequency distributions are deterministic. In this stochastic state space, under the assumption that the “history” of prior movement contains no additional information, the forward partial differential equation is obtained for the distribution of a population whose movement in the selected space is determined by the randomwalk equations. If the initial distribution of the population in the state space is normal, then certain assumptions about movement and mortality will operate to preserve normality thereafter. Under the assumption of normality, simultaneous ordinary differential equations can be derived from the forward partial differential equation defining the distribution function. Examination of the ordinary simultaneous differential equations shows how parameters for certain models of aging and mortality can be obtained.     

A New Pterosaur Tracksite from the Jurassic Summerville Formation,Near Ferron,Utah

Pterosaur tracks (cf. Pteraichnus) from the Summerville Formation of the Ferron area of central Utah add to the growing record of Pteraichnus tracksites in the Late Jurassic Summerville Formation and time-equivalent, or near time-equivalent, deposits. The site is typical in revealing high pterosaur track densities, but low ichnodiversity suggesting congregations or “flocks” of many individuals. Footprint length varies from 2.0 to 7.0 cms. The ratio of well-preserved pes:manus tracks is about 1:3.4. This reflects a bias in favor of preservation of manus tracks due to the greater weight-bearing role of the front limbs, as noted in other pterosaur track assemblages. The sample also reveals a number of well-preserved trackways including one suggestive of pes-only progression that might be associated with take off or landing, and another that shows pronounced lengthening of stride indicating acceleration.

One well-preserved medium-sized theropod trackway (Therangospodus) and other larger theropod track casts (cf. Megalosauripus) are associated with what otherwise appears to be a nearly monospecific pterosaur track assemblage. However, traces of a fifth pes digit suggest some tracks are of rhamphorynchoid rather than pterodactyloid origin, as usually inferred for Pteraichnus. The tracks occur at several horizons in a thin stratigraphic interval of ripple marked sandstones and siltstones. Overall the assemblage is similar to others found in the same time interval in the Western Interior from central and eastern Utah through central and southern Wyoming, Colorado, northeastern Arizona, and western Oklahoma. This vast “Pteraichnus ichnofacies,” with associated saurischian tracks, remains the only ichnological evidence of pre-Cretaceous pterosaurs in North America and sheds important light on the vertebrate ecology of the Summerville Formation and contiguous deposits.     

Nanoscale analysis of clustered DNA damage after high-LET irradiation by quantitative electron microscopy – The heavy burden to repair

Low- and high-linear energy transfer (LET) ionising radiation are effective cancer therapies, but produce structurally different forms of DNA damage. Isolated DNA damage is repaired efficiently; however, clustered lesions may be more difficult to repair, and are considered as significant biological endpoints. We investigated the formation and repair of DNA double-strand breaks (DSBs) and clustered lesions in human fibroblasts after exposure to sparsely (low-LET; delivered by photons) and densely (high-LET; delivered by carbon ions) ionising radiation. DNA repair factors (pKu70, 53BP1, γH2AX, and pXRCC1) were detected using immunogold-labelling and electron microscopy, and spatiotemporal DNA damage patterns were analysed within the nuclear ultrastructure at the nanoscale level. By labelling activated Ku-heterodimers (pKu70) the number of DSBs was determined in electron-lucent euchromatin and electron-dense heterochromatin. Directly after low-LET exposure (5 min post-irradiation), single pKu70 dimers, which reflect isolated DSBs, were randomly distributed throughout the entire nucleus with a linear dose correlation up to 30 Gy. Most euchromatic DSBs were sensed and repaired within 40 min, whereas heterochromatic DSBs were processed with slower kinetics. Essentially all DNA lesions induced by low-LET irradiation were efficiently rejoined within 24 h post-irradiation. High-LET irradiation caused localised energy deposition within the particle tracks, and generated highly clustered DNA lesions with multiple DSBs in close proximity. The dimensions of these clustered lesions along the particle trajectories depended on the chromatin packing density, with huge DSB clusters predominantly localised in condensed heterochromatin. High-LET irradiation-induced clearly higher DSB yields than low-LET irradiation, with up to ∼500 DSBs per μm³ track volume, and large fractions of these heterochromatic DSBs remained unrepaired. Hence, the spacing and quantity of DSBs in clustered lesions influence DNA repair efficiency, and may determine the radiobiological outcome.     

Comparison and assessment of electron cross sections for Monte Carlo track structure codes.

The purpose of this study was to make an intercomparison and assessment of cross sections for electrons in water used in electron track structure codes. This study is intended to shed light on the extent to which the differences between the input data and physical and chemical assumptions influence the outcome in biophysical modeling of radiation effects. Ionization cross sections and spectra of secondary electrons were calculated by various theories. The analyses were carried out for water vapor cross sections, as these are more abundant and readily available. All suitable published experimental total ionization cross sections were fitted by an appropriate function and used for generation of electron tracks. Three sets of compiled data were used for comparison of total excitation cross sections and mean excitation energy. The tracks generated by a Monte Carlo track code, using various combinations of cross sections, were compared in terms of radial distributions of interactions and point kernels. The spectrum of secondary electrons emitted by the ionization process was found to be the factor that has the most influence on these quantities. A different set of cross sections for excitation and elastic scattering did not affect the electron track structure as much as did ionization cross sections. It is concluded that all codes, using different cross sections and in different phase, currently used for biophysical modeling exhibit close similarities for energy deposition in larger size targets while appreciable differences are observed in B-DNA-size targets. We recommend fitted functions to all available suitable experimental data for the total ionization and elastic cross sections. We conclude that most codes produce tracks in reasonable agreement with the macroscopic quantities such as total stopping power and total yield of strand breaks. However, we predict differences in frequencies of clustering in tracks from the different models.     

The role of short-lived DNA lesions in the production of chromosome-exchange aberrations

Human lymphocytes were treated with combined UVC radiation and X-rays or they were X-irradiated and incubated for 60–90 min in the presence of DNA-repair inhibitor ara-C. The X-ray induced chromosome exchange aberration yield was enhanced both by UVC and ara-C by approximately a factor of two in the linear (low dose) portion of the dose-response curve. The enhancement was small in the dose squared (high dose) portion where previous dose-fractionation experiments have shown that X-ray-induced lesions leading to aberrations exist for several hours. The yield of aberrations in lymphocytes incubated after irradiation in the presence of ara-C reaches a saturation level almost immediately after irradiation (5–15 min). These cytogenetic observations together with a previous finding (Holmberg and Strausmanis, 1983) give direct and indirect evidence that the enhanced aberration yield is due to short-lived DNA breaks formed immediately after X-irradiation.

Measurements on the repair kinetics of the DNA breaks induced by X-irradiation show that ara-C strongly impairs the repair of short-lived X-ray-induced DNA breaks. It was also observed that the DNA breaks generated after UVC irradiation occur almost immediately after irradiation and the level of these transient DNA breaks reaches saturation even for short incubation times. Thus, the repair of these breaks can compete with the repair of short-lived X-ray-induced DNA-breaks in combined irradiation with UVC and X-rays.

The experimental results can be explained on the assumption that X-ray-induced aberrations originate from exchange complexes formed in interactions between both short-lived DNA breaks. The short-lived DNA breaks give rise to exchange complexes mainly within single ionization tracks where the DNA breaks are close together. The time between irradiation and exchange complex formation is of the order of 5–15 min within such a track, and short-lived breaks might be repaired before complexes have been formed. If the DNA repair of these breaks is delayed by UVC or ara-C treatment this results in a higher probability of exchange-complex formation. In contrast, interactions between breaks in different tracks originate from long-lived DNA breaks and the probability for complex formation from these breaks is not markedly affected by UVC or ara-C.     

Foraging efficiency and the fitness consequences of spatial marking by ladybeetle larvae

Marking and avoiding poor‐quality resources can be an important mechanism by which animals lacking a spatial memory can maximize their foraging efficiency. Here, we investigate the behaviour of larval Harmonia axyridis ladybeetles that leave chemical tracks as they forage. We built a model of an individual larva foraging for aphids, parameterized it using experimental data, and used the model to predict the effect of larval track production and detection on foraging efficiency, an important component of fitness. The model predicted that there is an optimal sensitivity of larvae to tracks which maximizes foraging efficiency; if the larva is too sensitive to tracks, it will avoid areas that might still contain resources, whereas if it is too insensitive, it will forage in areas that have depleted resources. Furthermore, the increased efficiency conferred by detecting tracks depends on the spatial arrangement of resources, with more aggregated resource distributions allowing greater benefits of detecting tracks. We tested the predictions of the model experimentally by measuring predation on aggregated versus dispersed soybean aphids by H. axyridis larvae whose ability to produce tracks was experimentally manipulated. The experiments corroborated the results of the model: larvae that could produce tracks consumed more aphids than those that could not, and this difference was greatest when aphids were aggregated among plants. Our results suggest that larval tracks play an important role in foraging efficiency, and we discuss implications for the evolution of larval track production and detection in ladybeetles.     

Model for radial dependence of frequency distributions for energy imparted in nanometer volumes from HZE particles

This paper develops a deterministic model of frequency distributions for energy imparted (total energy deposition) in small volumes similar to DNA molecules from high-energy ions of interest for space radiation protection and cancer therapy. Frequency distributions for energy imparted are useful for considering radiation quality and for modeling biological damage produced by ionizing radiation. For high-energy ions, secondary electron (delta-ray) tracks originating from a primary ion track make dominant contributions to energy deposition events in small volumes. Our method uses the distribution of electrons produced about an ion's path and incorporates results from Monte Carlo simulation of electron tracks to predict frequency distributions for ions, including their dependence on radial distance. The contribution from primary ion events is treated using an impact parameter formalism of spatially restricted linear energy transfer (LET) and energy-transfer straggling. We validate our model by comparing it directly to results from Monte Carlo simulations for proton and alpha-particle tracks. We show for the first time frequency distributions of energy imparted in DNA structures by several high-energy ions such as cosmic-ray iron ions. Our comparison with results from Monte Carlo simulations at low energies indicates the accuracy of the method.     

Genome-wide 5-Hydroxymethylcytosine Profiling Analysis Identifies MAP7D1 as A Novel Regulator of Lymph Node Metastasis in Breast Cancer

Although DNA 5-hydroxymethylcytosine(5 hmC) is recognized as an important epigenetic mark in cancer, its precise role in lymph node metastasis remains elusive. In this study, we investigated how 5 hmC associates with lymph node metastasis in breast cancer. Accompanying with high expression of TET1 and TET2 proteins, large numbers of genes in the metastasis-positive primary tumors exhibit higher 5 hmC levels than those in the metastasis-negative primary tumors. In contrast, the TET protein expression and DNA 5 hmC decrease significantly within the metastatic lesions in the lymph nodes compared to those in their matched primary tumors. Through genomewide analysis of 8 sets of primary tumors, we identified 100 high-confidence metastasis-associated5 hmC signatures, and it is found that increased levels of DNA 5 hmC and gene expression of MAP7 D1 associate with high risk of lymph node metastasis. Furthermore, we demonstrate that MAP7 D1, regulated by TET1, promotes tumor growth and metastasis. In conclusion, the dynamic5 hmC profiles during lymph node metastasis suggest a link between DNA 5 hmC and lymph node metastasis. Meanwhile, the role of MAP7 D1 in breast cancer progression suggests that the metastasis-associated 5 hmC signatures are potential biomarkers to predict the risk for lymph node metastasis, which may serve as diagnostic and therapeutic targets for metastatic breast cancer.     

A track structure model for simulation of strand breaks in plasmid DNA after heavy ion irradiation

We present a track structure model based on the local dose deposited around heavy ion tracks to explain the cross sections for single-strand and double-strand break induction in plasmid DNA in different aqueous buffers. The model is based only on measurable quantities, namely the effect distribution for inducing strand breaks after x-ray irradiation as a function of dose, and the radial dose distribution of the heavy ion track. The effect of indirect DNA damage mediated by free radicals produced in the water surrounding the DNA is accounted for by allowing the radial dose distribution to be smeared in space by an effective target size corresponding to the squared sum of the geometrical extension of the plasmid molecule and the mean free drift path of the radicals in the buffer solution. Our calculations reproduce well the measured cross sections for single-strand and double-strand break induction in SV40 plasmid DNA in various buffer solutions both as a function of the LET and of the specific energy of the heavy ion.     

Detection of complex DNA damage in gamma-irradiated acute lymphoblastic leukemia Pre-b NALM-6 cells

Bistranded complex DNA damage, i.e., double-strand breaks (DSBs) and non-DSB oxidative clustered DNA lesions, is hypothesized to challenge the repair mechanisms of the cell and consequently the genomic integrity. The oxidative clustered DNA lesions may be persistent and may accumulate in human cancer cells for long times after irradiation. To evaluate the detection and possible accumulation of oxidative clustered DNA lesions in leukemia cells exposed to doses equivalent to those used in radiotherapy, we measured the induction of DSBs and three different types of oxidative clustered DNA lesions in NALM-6 cells, a human acute lymphoblastic leukemia (ALL) pre-B cell line, after exposure to (137)Cs gamma rays. For the detection and measurement of DSBs and oxidative clustered DNA lesions, we used an adaptation of the neutral comet assay (single-cell gel electrophoresis) using E. coli repair enzymes (Endo IV, Fpg and Endo III) as enzymatic probes. We found a linear dose response for the induction of DSBs and oxidative clustered DNA lesions. Clustered DNA lesions were more prevalent than prompt DSBs. For each DSB induced by radiation, approximately 2.5 oxidative clustered DNA lesions were detected. To our knowledge, this is the first study to demonstrate the detection and linear induction of oxidative clustered DNA lesions with radiation dose in an ALL cell line. These results point to the biological significance of clustered DNA lesions.     

A polymer, random walk model for the size-distribution of large DNA fragments after high linear energy transfer radiation

DNA double-strand breaks (DSBs) produced by densely ionizing radiation are not located randomly in the genome: recent data indicate DSB clustering along chromosomes. Stochastic DSB clustering at large scales, from >100 Mbp down to <0.01 Mbp, is modeled using computer simulations and analytic equations. A random-walk, coarse-grained polymer model for chromatin is combined with a simple track structure model in Monte Carlo software called DNAbreak and is applied to data on alpha-particle irradiation of V-79 cells. The chromatin model neglects molecular details but systematically incorporates an increase in average spatial separation between two DNA loci as the number of base-pairs between the loci increases. Fragment-size distributions obtained using DNAbreak match data on large fragments about as well as distributions previously obtained with a less mechanistic approach. Dose-response relations, linear at small doses of high linear energy transfer (LET) radiation, are obtained. They are found to be non-linear when the dose becomes so large that there is a significant probability of overlapping or close juxtaposition, along one chromosome, for different DSB clusters from different tracks. The non-linearity is more evident for large fragments than for small. The DNAbreak results furnish an example of the RLC (randomly located clusters) analytic formalism, which generalizes the broken-stick fragment-size distribution of the random-breakage model that is often applied to low-LET data. Received: 19 July 1999 / Accepted in revised form: 10 December 1999     

On the Additive and Multiplicative Models of Relative Risk

Two popular models of absence of synergism in epidemiologic cohort studies are analyzed and compared. It is shown that the statistical concept of the union of independent events that traditionally has given rise to the “additive” model of relative risk can also generate the “multiplicative” model of relative risk. In fact, the same set of approximating conditions can be used to generate both models, which suggests a lack of identifiability under the traditional approach. An alternate approach is proposed in this paper. The new approach does not require the assumption that background risk factors are independent from causal agents of interest. The concept of “dose additivity” is discussed.     

Cooperativity can reduce stochasticity in intracellular calcium dynamics

The opening of inositol (1,4,5)-triphosphate (IP(3)) receptors, clustered at discrete sites on the endoplasmic reticulum, can lead to large-scale intracellular calcium waves. Recent experiments in Xenopus oocytes have shown that the inter-wave intervals for these waves have a standard deviation that is much smaller than their mean and that the background calcium concentration exhibits a slow rise during the interwave interval. Using a simple mathematical model, we examine the possibility that this slow rise increases the cooperativity between the openings of the clusters. We find that our model, coupled to the usual assumption that the pumps on the endoplasmic reticulum are activated instantaneously, is unable to explain the observed data: the clusters are found to fire independently and the inter-wave interval distribution is a Poisson distribution with a standard deviation that is approximately equal to its mean. On the other hand, we find that incorporating pumps that slowly activate leads to a slow increase in the background calcium concentration which makes global events progressively more likely to occur. We show that this cooperativity results in much smaller standard deviations and inter-wave interval distributions that are clearly not Poisson distributions.     

Mechanistic modeling of salmonellosis: Update and future directions

Microbial risk assessors often make simplifying assumptions that lead to the selection of simple concave functions with low-dose linearity, consistent with no-threshold and single-hit hypotheses, as default dose–response model forms. However, evidence is accumulating as the “microbiome revolution” progresses that challenge these assumptions that influence the estimates of the nature and magnitude of uncertainties associated with microbial risks. Scientific advances in the knowledge of the human “superorganism” (hybrid consortium of human plus microbial communities that cooperatively regulates health and disease) enable the design of definitive studies to estimate the pathogen doses overcome by the innate defenses, including the protective microbiota. The systematic investigation of the events of non-typhoid salmonellosis in humans undertaken nearly 2 decades ago was updated to incorporate recent scientific advances in the understanding of impact of the healthy superorganism that strengthens and extends the biological motivations for sublinear or convex dose–response curves in microbial risk assessment. The knowledge of colonization resistance (innate protection of the human superorganism from low doses of ingested pathogens) and microbiota-mediated clearance is advancing mechanistically for many pathosystems. However, until more detailed mechanistic data become available for salmonellosis, the consideration of a variety of empirical model forms is essential for depicting the uncertainty of the “true” dose–response model.