High-accuracy adaptive simulations of a Petri dish exposed to electromagnetic radiation

This paper analyses numerically the electric field distribution of a liquid contained in a Petri dish when exposed to electromagnetic waves excited in a rectangular waveguide. Solutions exhibit high-gradients due to the presence of the dielectric liquid contained in the dish. Furthermore, electromagnetic fields within the dielectric have a dramatically lower value than on the remaining part of the domain, which difficults its simulation. Additionally, various singularities of different intensity appear along the boundary of the Petri dish. To properly reproduce and numerically study those effects, we employ a highly-accurate hp-adaptive finite element method. Results of this study demonstrate that the electric field generated within the circular Petri dish is non-homogeneous, and thus, a better shape, size, or location of the dish is needed to achieve an equally distributed radiation enabling the uniform growth of cell cultives.

Validation of a phase space determination algorithm for intraoperative radiation therapy

Monte-Carlo (MC) methods are a valuable tool for dosimetry in radiotherapy, including Intra-Operative Electron Radiotherapy (IOERT), since effects such as inhomogeneities or beam hardening may be realistically reproduced.

Design and Simulation of Deep Nanometer SRAM Cells under Energy, Mismatch, and Radiation Constraints

La fiabilidad está pasando a ser el principal problema de los circuitos integrados según la tecnología desciende por debajo de los 22nm. Pequeñas imperfecciones en la fabricación de los dispositivos dan lugar ahora a importantes diferencias aleatorias en sus características eléctricas, que han de ser tenidas en cuenta durante la fase de diseño. Los nuevos procesos y materiales requeridos para la fabricación de dispositivos de dimensiones tan reducidas están dando lugar a diferentes efectos que resultan finalmente en un incremento del consumo estático, o una mayor vulnerabilidad frente a radiación. Las memorias SRAM son ya la parte más vulnerable de un sistema electrónico, no solo por representar más de la mitad del área de los SoCs y microprocesadores actuales, sino también porque las variaciones de proceso les afectan de forma crítica, donde el fallo de una única célula afecta a la memoria entera. Esta tesis aborda los diferentes retos que presenta el diseño de memorias SRAM en las tecnologías más pequeñas. En un escenario de aumento de la variabilidad, se consideran problemas como el consumo de energía, el diseño teniendo en cuenta efectos de la tecnología a bajo nivel o el endurecimiento frente a radiación. En primer lugar, dado el aumento de la variabilidad de los dispositivos pertenecientes a los nodos tecnológicos más pequeños, así como a la aparición de nuevas fuentes de variabilidad por la inclusión de nuevos dispositivos y la reducción de sus dimensiones, la precisión del modelado de dicha variabilidad es crucial. Se propone en la tesis extender el método de inyectores, que modela la variabilidad a nivel de circuito, abstrayendo sus causas físicas, añadiendo dos nuevas fuentes para modelar la pendiente sub-umbral y el DIBL, de creciente importancia en la tecnología FinFET. Los dos nuevos inyectores propuestos incrementan la exactitud de figuras de mérito a diferentes niveles de abstracción del diseño electrónico: a nivel de transistor, de puerta y de circuito. El error cuadrático medio al simular métricas de estabilidad y prestaciones de células SRAM se reduce un mínimo de 1,5 veces y hasta un máximo de 7,5 a la vez que la estimación de la probabilidad de fallo se mejora en varios ordenes de magnitud. El diseño para bajo consumo es una de las principales aplicaciones actuales dada la creciente importancia de los dispositivos móviles dependientes de baterías. Es igualmente necesario debido a las importantes densidades de potencia en los sistemas actuales, con el fin de reducir su disipación térmica y sus consecuencias en cuanto al envejecimiento. El método tradicional de reducir la tensión de alimentación para reducir el consumo es problemático en el caso de las memorias SRAM dado el creciente impacto de la variabilidad a bajas tensiones. Se propone el diseño de una célula que usa valores negativos en la bit-line para reducir los fallos de escritura según se reduce la tensión de alimentación principal. A pesar de usar una segunda fuente de alimentación para la tensión negativa en la bit-line, el diseño propuesto consigue reducir el consumo hasta en un 20 % comparado con una célula convencional. Una nueva métrica, el hold trip point se ha propuesto para prevenir nuevos tipos de fallo debidos al uso de tensiones negativas, así como un método alternativo para estimar la velocidad de lectura, reduciendo el número de simulaciones necesarias. Según continúa la reducción del tamaño de los dispositivos electrónicos, se incluyen nuevos mecanismos que permiten facilitar el proceso de fabricación, o alcanzar las prestaciones requeridas para cada nueva generación tecnológica. Se puede citar como ejemplo el estrés compresivo o extensivo aplicado a los fins en tecnologías FinFET, que altera la movilidad de los transistores fabricados a partir de dichos fins. Los efectos de estos mecanismos dependen mucho del layout, la posición de unos transistores afecta a los transistores colindantes y pudiendo ser el efecto diferente en diferentes tipos de transistores. Se propone el uso de una célula SRAM complementaria que utiliza dispositivos pMOS en los transistores de paso, así reduciendo la longitud de los fins de los transistores nMOS y alargando los de los pMOS, extendiéndolos a las células vecinas y hasta los límites de la matriz de células. Considerando los efectos del STI y estresores de SiGe, el diseño propuesto mejora los dos tipos de transistores, mejorando las prestaciones de la célula SRAM complementaria en más de un 10% para una misma probabilidad de fallo y un mismo consumo estático, sin que se requiera aumentar el área. Finalmente, la radiación ha sido un problema recurrente en la electrónica para aplicaciones espaciales, pero la reducción de las corrientes y tensiones de los dispositivos actuales los está volviendo vulnerables al ruido generado por radiación, incluso a nivel de suelo. Pese a que tecnologías como SOI o FinFET reducen la cantidad de energía colectada por el circuito durante el impacto de una partícula, las importantes variaciones de proceso en los nodos más pequeños va a afectar su inmunidad frente a la radiación. Se demuestra que los errores inducidos por radiación pueden aumentar hasta en un 40 % en el nodo de 7nm cuando se consideran las variaciones de proceso, comparado con el caso nominal. Este incremento es de una magnitud mayor que la mejora obtenida mediante el diseño de células de memoria específicamente endurecidas frente a radiación, sugiriendo que la reducción de la variabilidad representaría una mayor mejora. ABSTRACT Reliability is becoming the main concern on integrated circuit as the technology goes beyond 22nm. Small imperfections in the device manufacturing result now in important random differences of the devices at electrical level which must be dealt with during the design. New processes and materials, required to allow the fabrication of the extremely short devices, are making new effects appear resulting ultimately on increased static power consumption, or higher vulnerability to radiation SRAMs have become the most vulnerable part of electronic systems, not only they account for more than half of the chip area of nowadays SoCs and microprocessors, but they are critical as soon as different variation sources are regarded, with failures in a single cell making the whole memory fail. This thesis addresses the different challenges that SRAM design has in the smallest technologies. In a common scenario of increasing variability, issues like energy consumption, design aware of the technology and radiation hardening are considered. First, given the increasing magnitude of device variability in the smallest nodes, as well as new sources of variability appearing as a consequence of new devices and shortened lengths, an accurate modeling of the variability is crucial. We propose to extend the injectors method that models variability at circuit level, abstracting its physical sources, to better model sub-threshold slope and drain induced barrier lowering that are gaining importance in FinFET technology. The two new proposed injectors bring an increased accuracy of figures of merit at different abstraction levels of electronic design, at transistor, gate and circuit levels. The mean square error estimating performance and stability metrics of SRAM cells is reduced by at least 1.5 and up to 7.5 while the yield estimation is improved by orders of magnitude. Low power design is a major constraint given the high-growing market of mobile devices that run on battery. It is also relevant because of the increased power densities of nowadays systems, in order to reduce the thermal dissipation and its impact on aging. The traditional approach of reducing the voltage to lower the energy consumption if challenging in the case of SRAMs given the increased impact of process variations at low voltage supplies. We propose a cell design that makes use of negative bit-line write-assist to overcome write failures as the main supply voltage is lowered. Despite using a second power source for the negative bit-line, the design achieves an energy reduction up to 20% compared to a conventional cell. A new metric, the hold trip point has been introduced to deal with new sources of failures to cells using a negative bit-line voltage, as well as an alternative method to estimate cell speed, requiring less simulations. With the continuous reduction of device sizes, new mechanisms need to be included to ease the fabrication process and to meet the performance targets of the successive nodes. As example we can consider the compressive or tensile strains included in FinFET technology, that alter the mobility of the transistors made out of the concerned fins. The effects of these mechanisms are very dependent on the layout, with transistor being affected by their neighbors, and different types of transistors being affected in a different way. We propose to use complementary SRAM cells with pMOS pass-gates in order to reduce the fin length of nMOS devices and achieve long uncut fins for the pMOS devices when the cell is included in its corresponding array. Once Shallow Trench isolation and SiGe stressors are considered the proposed design improves both kinds of transistor, boosting the performance of complementary SRAM cells by more than 10% for a same failure probability and static power consumption, with no area overhead. While radiation has been a traditional concern in space electronics, the small currents and voltages used in the latest nodes are making them more vulnerable to radiation-induced transient noise, even at ground level. Even if SOI or FinFET technologies reduce the amount of energy transferred from the striking particle to the circuit, the important process variation that the smallest nodes will present will affect their radiation hardening capabilities. We demonstrate that process variations can increase the radiation-induced error rate by up to 40% in the 7nm node compared to the nominal case. This increase is higher than the improvement achieved by radiation-hardened cells suggesting that the reduction of process variations would bring a higher improvement.

Effects of a bifenthrin-treated net on the natural enemies Aphidius colemani (Haliday) and Adalia bipunctata L. in a cucumber crop in Central Spain. Semi-field experiments

Pest management practices that rely on pesticides are growing increasingly less effective and environmentally inappropriate in many cases and the search of alternatives is under focus nowadays. Exclusion of pests from the crop by means of pesticide-treated screens can be an eco-friendly method to protect crops, especially if pests are vectors of important diseases. The mesh size of nets is crucial to determine if insects can eventually cross the barrier or exclude them because there is a great variation in insect size depending on the species. Long-lasting insecticide-treated (LLITN) nets, factory pre-treated, have been used since years to fight against mosquitoes vector of malaria and are able to retain their biological efficacy under field for 3 years. In agriculture, treated nets with different insecticides have shown efficacy in controlling some insects and mites, so they seem to be a good tool in helping to solve some pest problems. However, treated nets must be carefully evaluated because can diminish air flow, increase temperature and humidity and decrease light transmission, which may affect plant growth, pests and natural enemies. As biological control is considered a key factor in IPM nowadays, the potential negative effects of treated nets on natural enemies need to be studied carefully. In this work, the effects of a bifentrhin-treated net (3 g/Kg) (supplied by the company Intelligent Insect Control, IIC) on natural enemies of aphids were tested on a cucumber crop in Central Spain in autumn 2011. The crop was sown in 8x6.5 m tunnels divided in 2 sealed compartments with control or treated nets, which were simple yellow netting with 25 mesh (10 x 10 threads/cm2; 1 x 1 mm hole size). Pieces of 2 m high of the treated-net were placed along the lateral sides of one of the two tunnel compartments in each of the 3 available tunnels (replicates); the rest was covered by a commercial untreated net of a similar mesh. The pest, Aphis gossypii Glover (Aphidae), the parasitoid Aphidius colemani (Haliday) (Braconidae) and the predator Adalia bipunctata L. (Coccinellidae) were artificially introduced in the crop. Weekly sampling was done determining the presence or absence of the pest and the natural enemies (NE) in the 42 plants/compartment as well as the number of insects in 11 marked plants. Environmental conditions (temperature, relative humidity, UV and PAR radiation) were recorded. Results show that when aphids were artificially released inside the tunnels, neither its number/plant nor their distribution was affected by the treated net. A lack of negative effect of the insecticide-treated net on natural enemies was also observed. Adalia bipunctata did not establish in the crop and only a short term control of aphids was observed one week after release. On the other hand, A. colemani did establish in the crop and a more long-term effect on the numbers of aphids/plant was detected irrespective of the type of net. KEY WORDS: bifenthrin-treated net, Adalia bipunctata, Aphidius colemani, Aphis gossypii, semi-field

Protein kinase mutants of human ATR increase sensitivity to UV and ionizing radiation and abrogate cell cycle checkpoint control

In fission yeast, the rad3 gene product plays a critical role in sensing DNA structure defects and activating damage response pathways. A structural homologue of rad3 in humans (ATR) has been identified based on sequence similarity in the protein kinase domain. General information regarding ATR expression, protein kinase activity, and cellular localization is known, but its function in human cells remains undetermined. In the current study, the ATR protein was examined by gel filtration of protein extracts and was found to exist predominantly as part of a large protein complex. A kinase-inactivated form of the ATR gene was prepared by site-directed mutagenesis and was used in transfection experiments to probe the function of this complex. Introduction of this kinase-dead ATR into a normal fibroblast cell line, an ATM-deficient fibroblast line derived from a patient with ataxia–telangiectasia, or a p53 mutant cell line all resulted in significant losses in cell viability. Clones expressing the kinase-dead ATR displayed increased sensitivity to x-rays and UV and a loss of checkpoint control. We conclude that ATR functions as a critical part of a protein complex that mediates responses to ionizing and UV radiation in human cells. These responses include effects on cell viability and cell cycle checkpoint control.

BAC-VAC, a novel generation of (DNA) vaccines: A bacterial artificial chromosome (BAC) containing a replication-competent, packaging-defective virus genome induces protective immunity against herpes simplex virus 1

This study aimed to exploit bacterial artificial chromosomes (BAC) as large antigen-capacity DNA vaccines (BAC-VAC) against complex pathogens, such as herpes simplex virus 1 (HSV-1). The 152-kbp HSV-1 genome recently has been cloned as an F-plasmid-based BAC in Escherichia coli (fHSV), which can efficiently produce infectious virus progeny upon transfection into mammalian cells. A safe modification of fHSV, fHSVΔpac, does not give rise to progeny virus because the signals necessary to package DNA into virions have been excluded. However, in mammalian cells fHSVΔpac DNA can still replicate, express the HSV-1 genes, cause cytotoxic effects, and produce virus-like particles. Because these functions mimic the lytic cycle of the HSV-1 infection, fHSVΔpac was expected to stimulate the immune system as efficiently as a modified live virus vaccine. To test this hypothesis, mice were immunized with fHSVΔpac DNA applied intradermally by gold-particle bombardment, and the immune responses were compared with those induced by infection with disabled infectious single cycle HSV-1. Immunization with either fHSVΔpac or disabled infectious single cycle HSV-1 induced the priming of HSV-1-specific cytotoxic T cells and the production of virus-specific antibodies and conferred protection against intracerebral injection of wild-type HSV-1 at a dose of 200 LD50. Protection probably was cell-mediated, as transfer of serum from immunized mice did not protect naive animals. We conclude that BAC-VACs per se, or in combination with genetic elements that support replicative amplification of the DNA in the cell nucleus, represent a useful new generation of DNA-based vaccination strategies for many viral and nonviral antigens.

Superoxide-mediated clastogenesis and anticlastogenic effects of exogenous superoxide dismutase

Superoxide-mediated clastogenesis is characteristic for various chronic inflammatory diseases with autoimmune reactions and probably plays a role in radiation-induced clastogenesis and in the congenital breakage syndromes. It is consistently prevented by exogenous superoxide dismutase (SOD), but not by heat-inactivated SOD, indicating that the anticlastogenic effect is related to the catalytic function of the enzyme. Increased superoxide production by activated monocytes/macrophages is followed by release of more long-lived metabolites, so-called clastogenic factors, which contain lipid peroxidation products, unusual nucleotides of inosine, and cytokines such as tumor necrosis factor α. Since these components are not only clastogenic, but can stimulate further superoxide production by monocytes and neutrophils, the genotoxic effects are self-sustaining. It is shown here that anticlastogenic effects of exogenous SOD are preserved despite extensive washing of the cells and removal of all extracellular SOD. Using flow cytometry and confocal laser microscopy, rapid adherence of the fluorescently labeled enzyme to the cell surface could be observed with slow uptake into the cell during the following hours. The degree of labeling was concentration and time dependent. It was most important for monocytes, compared with lymphocytes, neutrophils, and fibroblasts. The cytochrome c assay showed significantly diminished O2− production by monocytes, pretreated with SOD and washed thereafter. The preferential and rapid binding of SOD to monocytes may be of importance not only for the superoxide-mediated genotoxic effects, described above, but also from a therapeutic standpoint. It can explain the observation that beneficial effects of injected SOD lasted for weeks and months despite rapid clearance of the enzyme from the blood stream according to pharmacodynamic studies.

Case study of the effects of atmospheric aerosols and regional haze on agriculture: An opportunity to enhance crop yields in China through emission controls?

The effect of atmospheric aerosols and regional haze from air pollution on the yields of rice and winter wheat grown in China is assessed. The assessment is based on estimates of aerosol optical depths over China, the effect of these optical depths on the solar irradiance reaching the earth’s surface, and the response of rice and winter wheat grown in Nanjing to the change in solar irradiance. Two sets of aerosol optical depths are presented: one based on a coupled, regional climate/air quality model simulation and the other inferred from solar radiation measurements made over a 12-year period at meteorological stations in China. The model-estimated optical depths are significantly smaller than those derived from observations, perhaps because of errors in one or both sets of optical depths or because the data from the meteorological stations has been affected by local pollution. Radiative transfer calculations using the smaller, model-estimated aerosol optical depths indicate that the so-called “direct effect” of regional haze results in an ≈5–30% reduction in the solar irradiance reaching some of China’s most productive agricultural regions. Crop-response model simulations suggest an ≈1:1 relationship between a percentage increase (decrease) in total surface solar irradiance and a percentage increase (decrease) in the yields of rice and wheat. Collectively, these calculations suggest that regional haze in China is currently depressing optimal yields of ≈70% of the crops grown in China by at least 5–30%. Reducing the severity of regional haze in China through air pollution control could potentially result in a significant increase in crop yields and help the nation meet its growing food demands in the coming decades.

Susceptibility to the biological effects of polyaromatic hydrocarbons is influenced by genes of the major histocompatibility complex

Polyaromatic hydrocarbons are ubiquitous environmental chemicals that are important mutagens and carcinogens. The purpose of this study was to determine whether genes within the major histocompatibility complex (MHC) influence their biological activities. Cell-mediated immunity to dimethylbenz(a)anthracene (DMBA) was investigated in congenic strains of mice. On three different backgrounds, H-2k and H-2a haplotype mice developed significantly greater contact-hypersensitivity responses to DMBA than H-2b, H-2d, and H-2s mice. In B10.A(R1) mice, which are Kk and Id, a vigorous contact-hypersensitivity response was present, indicating that the response was governed by class I, rather than class II, MHC genes. C3H/HeN (H-2k) and C3H.SW (H-2s) strains were also compared for the development of skin tumors and the persistence of DMBA–DNA adducts. When subjected to a DMBA initiation, phorbol 12-tetradecanoate 13-acetate (TPA)-promotion skin-tumorigenesis protocol, C3H/HeN mice, (which develop cell-mediated immunity to DMBA) were found to have significantly fewer tumors than C3H.SW mice (a strain that failed to develop a cell-mediated immune response to DMBA). DMBA–DNA adducts were removed more rapidly in C3H/HeN than in C3H.SW mice. The results indicate that genes within the MHC play an important role in several of the biological activities of carcinogenic polyaromatic hydrocarbons. The observations are consistent with the hypothesis that cell-mediated immunity to chemical carcinogens serves to protect individuals by removing mutant cells before they can evolve into clinically apparent neoplasms.

Loss of p21 increases sensitivity to ionizing radiation and delays the onset of lymphoma in atm-deficient mice

Ataxia telangiectasia (AT) is an autosomal recessive disorder characterized by growth retardation, cerebellar ataxia, oculocutaneous telangiectasias, and a high incidence of lymphomas and leukemias. In addition, AT patients are sensitive to ionizing radiation. Atm-deficient mice recapitulate most of the AT phenotype. p21cip1/waf1 (p21 hereafter), an inhibitor of cyclin-dependent kinases, has been implicated in cellular senescence and response to γ-radiation-induced DNA damage. To study the role of p21 in ATM-mediated signal transduction pathways, we examined the combined effect of the genetic loss of atm and p21 on growth control, radiation sensitivity, and tumorigenesis. As might have been expected, our data provide evidence that p21 modifies the in vitro senescent response seen in AT fibroblasts. Further, it is a downstream effector of ATM-mediated growth control. In addition, however, we find that loss of p21 in the context of an atm-deficient mouse leads to a delay in thymic lymphomagenesis and an increase in acute radiation sensitivity in vivo (the latter principally because of effects on the gut epithelium). Modification of these two crucial aspects of the ATM phenotype can be related to an apparent increase in spontaneous apoptosis seen in tumor cells and in the irradiated intestinal epithelium of mice doubly null for atm and p21. Thus, loss of p21 seems to contribute to tumor suppression by a mechanism that operates via a sensitized apoptotic response. These results have implications for cancer therapy in general and AT patients in particular.

Protective anti-tumor immunity induced by vaccination with recombinant adenoviruses encoding multiple tumor-associated cytotoxic T lymphocyte epitopes in a string-of-beads fashion

Vaccines harboring genes that encode functional oncoproteins are intrinsically hazardous, as their application may lead to introduction of these genes into normal cells and thereby to tumorigenesis. On the other hand, oncoproteins are especially attractive targets for immunotherapy of cancer, as their expression is generally required for tumor growth, making the arisal of tumor variants lacking these antigens unlikely. Using murine tumor models, we investigated the efficacy of polyepitope recombinant adenovirus (rAd) vaccines, which encode only the immunogenic T cell epitopes derived from several oncogenes, for the induction of protective anti-tumor immunity. We chose to employ rAd, as these are safe vectors that do not induce the side effects associated with, for example, vaccinia virus vaccines. A single polyepitope rAd was shown to give rise to presentation of both H-2 and human leukocyte antigen-restricted cytotoxic T lymphocyte (CTL) epitopes. Moreover, vaccination with a rAd encoding H-2-restricted CTL epitopes, derived from human adenovirus type 5 early region 1 and human papilloma virus type 16-induced tumors, elicited strong tumor-reactive CTL and protected the vaccinated animals against an otherwise lethal challenge with either of these tumors. The protection induced was superior compared with that obtained by vaccination with irradiated tumor cells. Thus, vaccination with polyepitope rAd is a powerful approach for the induction of protective anti-tumor immunity that allows simultaneous immunization against multiple tumor-associated T cell epitopes, restricted by various major histocompatibility complex haplotypes.

Enzyme plus light therapy to repair DNA damage in ultraviolet-B-irradiated human skin

Ultraviolet-B (UVB) (290–320 nm) radiation-induced cyclobutane pyrimidine dimers within the DNA of epidermal cells are detrimental to human health by causing mutations and immunosuppressive effects that presumably contribute to photocarcinogenesis. Conventional photoprotection by sunscreens is exclusively prophylactic in nature and of no value once DNA damage has occurred. In this paper, we have therefore assessed whether it is possible to repair UVB radiation-induced DNA damage through topical application of the DNA-repair enzyme photolyase, derived from Anacystis nidulans, that specifically converts cyclobutane dimers into their original DNA structure after exposure to photoreactivating light. When a dose of UVB radiation sufficient to induce erythema was administered to the skin of healthy subjects, significant numbers of dimers were formed within epidermal cells. Topical application of photolyase-containing liposomes to UVB-irradiated skin and subsequent exposure to photoreactivating light decreased the number of UVB radiation-induced dimers by 40–45%. No reduction was observed if the liposomes were not filled with photolyase or if photoreactivating exposure preceded the application of filled liposomes. The UVB dose administered resulted in suppression of intercellular adhesion molecule-1 (ICAM-1), a molecule required for immunity and inflammatory events in the epidermis. In addition, in subjects hypersensitive to nickel sulfate, elicitation of the hypersensitivity reaction in irradiated skin areas was prevented. Photolyase-induced dimer repair completely prevented these UVB radiation-induced immunosuppressive effects as well as erythema and sunburn-cell formation. These studies demonstrate that topical application of photolyase is effective in dimer reversal and thereby leads to immunoprotection.

Clustered DNA damages induced in isolated DNA and in human cells by low doses of ionizing radiation

Clustered DNA damages—two or more closely spaced damages (strand breaks, abasic sites, or oxidized bases) on opposing strands—are suspects as critical lesions producing lethal and mutagenic effects of ionizing radiation. However, as a result of the lack of methods for measuring damage clusters induced by ionizing radiation in genomic DNA, neither the frequencies of their production by physiological doses of radiation, nor their repairability, nor their biological effects are known. On the basis of methods that we developed for quantitating damages in large DNAs, we have devised and validated a way of measuring ionizing radiation-induced clustered lesions in genomic DNA, including DNA from human cells. DNA is treated with an endonuclease that induces a single-strand cleavage at an oxidized base or abasic site. If there are two closely spaced damages on opposing strands, such cleavage will reduce the size of the DNA on a nondenaturing gel. We show that ionizing radiation does induce clustered DNA damages containing abasic sites, oxidized purines, or oxidized pyrimidines. Further, the frequency of each of these cluster classes is comparable to that of frank double-strand breaks; among all complex damages induced by ionizing radiation, double-strand breaks are only about 20%, with other clustered damage constituting some 80%. We also show that even low doses (0.1–1 Gy) of high linear energy transfer ionizing radiation induce clustered damages in human cells.

Predicted highly expressed and putative alien genes of Deinococcus radiodurans and implications for resistance to ionizing radiation damage

Predicted highly expressed (PHX) and putative alien genes determined by codon usages are characterized in the genome of Deinococcus radiodurans (strain R1). Deinococcus radiodurans (DEIRA) can survive very high doses of ionizing radiation that are lethal to virtually all other organisms. It has been argued that DEIRA is endowed with enhanced repair systems that provide protection and stability. However, predicted expression levels of DNA repair proteins with the exception of RecA tend to be low and do not distinguish DEIRA from other prokaryotes. In this paper, the capability of DEIRA to resist extreme doses of ionizing and UV radiation is attributed to an unusually high number of PHX chaperone/degradation, protease, and detoxification genes. Explicitly, compared with all current complete prokaryotic genomes, DEIRA contains the greatest number of PHX detoxification and protease proteins. Other sources of environmental protection against severe conditions of UV radiation, desiccation, and thermal effects for DEIRA are the several S-layer (surface structure) PHX proteins. The top PHX gene of DEIRA is the multifunctional tricarboxylic acid (TCA) gene aconitase, which, apart from its role in respiration, also alerts the cell to oxidative damage.

Airborne minerals and related aerosol particles: Effects on climate and the environment

Aerosol particles are ubiquitous in the troposphere and exert an important influence on global climate and the environment. They affect climate through scattering, transmission, and absorption of radiation as well as by acting as nuclei for cloud formation. A significant fraction of the aerosol particle burden consists of minerals, and most of the remainder— whether natural or anthropogenic—consists of materials that can be studied by the same methods as are used for fine-grained minerals. Our emphasis is on the study and character of the individual particles. Sulfate particles are the main cooling agents among aerosols; we found that in the remote oceanic atmosphere a significant fraction is aggregated with soot, a material that can diminish the cooling effect of sulfate. Our results suggest oxidization of SO2 may have occurred on soot surfaces, implying that even in the remote marine troposphere soot provided nuclei for heterogeneous sulfate formation. Sea salt is the dominant aerosol species (by mass) above the oceans. In addition to being important light scatterers and contributors to cloud condensation nuclei, sea-salt particles also provide large surface areas for heterogeneous atmospheric reactions. Minerals comprise the dominant mass fraction of the atmospheric aerosol burden. As all geologists know, they are a highly heterogeneous mixture. However, among atmospheric scientists they are commonly treated as a fairly uniform group, and one whose interaction with radiation is widely assumed to be unpredictable. Given their abundances, large total surface areas, and reactivities, their role in influencing climate will require increased attention as climate models are refined.