Chromosomal aberrations: formation, identification and distribution

Modelling DNA damage-repair and beyond

The paper presents a review of mechanistic modelling studies of DNA damage and DNA repair, and consequences to follow in mammalian cell nucleus. We hypothesize DNA deletions are consequences of repair of double strand breaks leading to the modifications of genome that play crucial role in long term development of genetic inheritance and diseases. The aim of the paper is to review formation mechanisms underlying naturally occurring DNA deletions in the human genome and their potential relevance for bridging the gap between induced DNA double strand breaks and deletions in damaged human genome from endogenous and exogenous events. The model of the cell nucleus presented enables simulation of DNA damage at molecular level identifying the spectrum of damage induced in all chromosomal territories and loops. Our mechanistic modelling of DNA repair for double stand breaks (DSB), single strand breaks (SSB) and base damage (BD), shows the complexity of DNA damage is responsible for the longer repair times and the reason for the biphasic feature of mammalian cells repair curves. In the absence of experimentally determined data, the mechanistic model of repair predicts the in vivo rate constants for the proteins involved in the repair of DSB, SSB, and of BD.

Biodegradation of commercial textile reactive dye mixtures by industrial effluent adapted bacterial consortium VITPBC6: a potential technique for treating textile effluents

Textile industries release major fraction of dyestuffs in effluents leading to a major environmental concern. These effluents often contain more than one dyestuff, which complicates dye degradation. In this study ten reactive dyes (Reactive Yellow 145, Reactive Yellow 160, Reactive Orange 16, Reactive Orange 107, Reactive Red 195, Reactive Blue 21, Reactive Blue 198, Reactive Blue 221, Reactive Blue 250, and Reactive Black 5) that are used in textile industries were subjected to biodegradation by a bacterial consortium VITPBC6, formulated in our previous study. Consortium VITPBC6 caused single dye degradation of all the mentioned dyes except for Reactive Yellow 160. Further, VITPBC6 efficiently degraded a five-dye mixture (Reactive Red 195, Reactive Orange 16, Reactive Black 5, Reactive Blue 221, and Reactive Blue 250). Kinetic studies revealed that the five-dye mixture was decolorized by VITPBC6 following zero order reaction kinetic; Vmax and Km values of the enzyme catalyzed five-dye decolorization were 128.88 mg L-1 day-1 and 1003.226 mg L-1 respectively. VITPBC6 degraded the dye mixture into delta-3,4,5,6-Tetrachlorocyclohexene, sulfuric acid, 1,2-dichloroethane, and hydroxyphenoxyethylaminohydroxypropanol. Phytotoxicity, cytogenotoxicity, microtoxicity, and biotoxicity assays conducted with the biodegraded metabolites revealed that VITPBC6 lowered the toxicity of five-dye mixture significantly after biodegradation.

Dynamics of Chromosome Aberrations and Cell Death in Zebrafish Embryos Exposed to 137Cs Total-Body Irradiation

Ionizing radiation exposure induces significant DNA damage and cell death in aquatic species. Accurate sensing and quantification play pivotal roles in environmental monitoring and surveillance. Zebrafish (Danio rerio) is a well-suited animal model for research into this aspect, especially with recent development of cytogenetic and transgenic tools. In this study, we present time-course studies of chromosome aberrations and cell death in zebrafish embryos exposed to 2 Gy 137Cs total-body irradiation. Using a cytogenetic approach, we quantified chromosome and chromatid aberrations in irradiated embryos at 6, 14, 20, and 24 h postirradiation. Metaphases with aberrations showed rapid declining kinetics, accompanied by incomplete karyotypes and irregular chromatin contents. Using an apoptosis-reporting transgenic zebrafish, we found increasing cell death along these time points, with the embryonic eyes and brain contributing the majority of the cell death volumes. We provide evidence that self-proliferating progenitor cells form the underlying linkage between the two kinetics and their positions define radiosensitive niches in zebrafish embryos. Our results provide detailed chromosome aberration and cell death dynamics in 137Cs-irradiated zebrafish embryos and unveil the appropriate timeline and tissue positions for accurate sensing and quantification of radiation-induced damages in zebrafish embryos.

Influence of Body Mass Index and Duration of Disease on Chromosome Damage in Lymphocytes of Patients with Diabetes

It is well-established that patients with diabetes mellitus (DM) have a higher incidence of several types of cancer. The precise mechanisms of this association are still unknown, but obesity and chronic inflammation-induced reactive oxygen species (ROS) are thought to be the main risk factors. ROS may produce different DNA damage, which could eventually lead to cancer. The main objective of this study was to evaluate the relation of chromosome aberrations (CA) with disease status, demographics, and clinical parameters in 33 subjects with type 1 DM (T1DM), 22 subjects with type 2 DM (T2DM), and 21 controls. CAs were analyzed in cultured peripheral blood lymphocytes and subdivided into chromatid (CTA)- and chromosome (CSA)-type aberrations. Compared with controls, higher levels of CTAs and CSAs were observed in T1DM (p = 0.0053 and p = 0.0203, respectively) and T2DM (p = 0.0133 and p = 0.00002, respectively). While there was no difference in CTAs between T1DM and T2DM, CSAs were higher in T2DM (p = 0.0173). A significant positive association between CTAs and disease duration (rs = 0.2938, p = 0.0099) and between CSAs and disease duration (rs = 0.4306, p = 0.0001), age (rs = 0.3932, p = 0.0004), and body mass index (BMI) (rs = 0.3502, p = 0.0019) was revealed. After multiple regression analysis, duration of disease remained significant for CTA, CSA, and CAs (p = 0.0042, p = 0.00003, and p = 0.00002, respectively). For CSA, BMI and the use of statins were the other important confounding variables (p = 0.0105 and p = 0.0763). Thus, this study demonstrated that both T1DM and T2DM patients had a higher number of all types of aberrations than controls, which increases with the prolonged disease duration. Higher BMI was associated with a higher frequency of CSA. The use of statins might be beneficial for reducing chromosome damage, but further investigations are needed to confirm this association.

Genotoxicity effects in freshwater fish species associated with gold mining activities in tropical aquatic ecosystems

The main aim of this study was to investigate total mercury (THg), methylmercury (MeHg) and arsenic (As) concentrations, and their genotoxic effects on fish species in freshwater habitats impacted by gold mining activities in the Mojana and Bajo Cauca regions (Northern Colombia). A total of 255 individuals of Prochilodus magdalenae (PM) and Hoplias malabaricus (HM) were collected in different areas of northern Colombia, 205 in the exposed groups: Mojana 1 (61), Mojana 2 (81) and Bajo Cauca (63); and 50 individuals in the control group. Dorsal muscle was analysed for pollutants and blood to perform micronucleus (MN) and erythrocytic nuclear alterations (ENA) tests. The results of the MN revealed statistically significant (p < 0.05) genetic damage in both PM (Mojana 1 = 29.7 ± 14.2; Mojana 2 = 25 ± 6.25; Bajo Cauca= 26.6 ± 10.6) and in HM (Mojana 1 = 17.7 ± 7.8; Mojana 2 = 20.4 ± 6.3; Bajo Cauca= 20.8 ± 9.8) compared to the control group (PM= 10.5 ± 3.6; HM= 9.1 ± 3.9). Likewise, the frequency of ENA was statistically higher in the exposed groups compared to the control group (p < 0.05). On the other hand, the concentrations of THg, MeHg and As found in tissue samples were significantly higher (p < 0.05) compared to the control group, being the Bajo Cauca region the area of highest risk due to high concentrations of THg (651.2 ± 344.5 μg/kg for HM and 678.5 ± 983.9 μg/kg for PM) and MeHg (504.6 ± 220.9 μg/kg for HM and 606.8 ± 886.4 μg/kg for PM). Results showed that mean THg values for both species in Bajo Cauca exceeded the WHO maximum limit (set in 500 μg Hg/kg) in fish for human consumption. Results suggest that DNA damage in erythrocytes is associated with the presence of Hg, MeHg and As, coming from mining activities.

Discovery and development of Factor Xa inhibitors (2015-2022)

As a pathological coagulation process, thrombus can lead to many serious diseases, including ischemic stroke, acute myocardial infarction (AMI), acute coronary syndrome (ACS), and deep venous thrombosis (DVT). And anticoagulant drugs are one of the most effective ways to prevent and treat these diseases. Although macromolecular anticoagulant drugs such as low molecular weight heparins (LMWHs) are widely used in the clinic, their characteristics of requiring injectable use hinder their further promotion in the clinic, and the disadvantages of oral anticoagulant drugs, such as warfarin and dabigatran etexilate, which can easily cause bleeding adverse effects, are also not addressed. Factor Xa (FXa) has gained attention because it lies at the intersection of the coagulation cascade pathways, whereas subsequently introduced Factor Xa inhibitors such as rivaroxaban and apixaban, among others, have gained market popularity because of their high potency for anticoagulation and high specificity for Factor Xa when administered orally. But some of the drawbacks that these Factor Xa inhibitors have simultaneously such as fewer indications and the lack of an effective reversal drug when bleeding occurs are urgently addressed. The development of new Factor Xa inhibitors therefore becomes one means of addressing these questions. This article summarizes the small molecule Factor Xainhibitors developed from 2015 to 2022, classifies them according to their scaffolds, focuses on the analysis of their structure-activity relationships, and provides a brief assessment of them.

Chromosomal Aberrations and Oxidative Stress in Psoriatic Patients with and without Metabolic Syndrome

Psoriasis and metabolic syndrome (MetS), a common comorbidity of psoriasis, are associated with mild chronic systemic inflammation that increases oxidative stress and causes cell and tissue damage. At the cellular level, chromosomal and DNA damage has been documented, thus confirming their genotoxic effect. The main objective of our study was to show the genotoxic potential of chronic inflammation and determine whether the presence of both pathologies increases chromosomal damage compared to psoriasis alone and to evaluate whether there are correlations between selected parameters and chromosomal aberrations in patients with psoriasis and MetS psoriasis. Clinical examination (PASI score and MetS diagnostics according to National Cholesterol Education Expert Panel on Detection, Evaluation, and Treatment of High Blood Cholesterol in Adults; NCE/ATPIII criteria), biochemical analysis of blood samples (fasting glucose, total cholesterol, low density and high density lipoproteins; LDL, HDL, non-HDL, and triglycerides;TAG), DNA/RNA oxidative damage, and chromosomal aberration test were performed in 41 participants (20 patients with psoriasis without MetS and 21 with MetS and psoriasis). Our results showed that patients with psoriasis without metabolic syndrome (nonMetS) and psoriasis and MetS had a higher rate of chromosomal aberrations than the healthy population for which the limit of spontaneous, natural aberration was <2%. No significant differences in the aberration rate were found between the groups. However, a higher aberration rate (higher than 10%) and four numerical aberrations were documented only in the MetS group. We found no correlations between the number of chromosomal aberrations and the parameters tested except for the correlation between aberrations and HDL levels in nonMetS patients (rho 0.44; p < 0.02). Interestingly, in the MetS group, a higher number of chromosomal aberrations was documented in non-smokers compared to smokers. Data from our current study revealed an increased number of chromosomal aberrations in patients with psoriasis and MetS compared to the healthy population, especially in psoriasis with MetS, which could increase the genotoxic effect of inflammation and the risk of genomic instability, thus increasing the risk of carcinogenesis.

AOP report: Development of an adverse outcome pathway for oxidative DNA damage leading to mutations and chromosomal aberrations

The Genetic Toxicology Technical Committee (GTTC) of the Health and Environmental Sciences Institute (HESI) is developing adverse outcome pathways (AOPs) that describe modes of action leading to potentially heritable genomic damage. The goal was to enhance the use of mechanistic information in genotoxicity assessment by building empirical support for the relationships between relevant molecular initiating events (MIEs) and regulatory endpoints in genetic toxicology. Herein, we present an AOP network that links oxidative DNA damage to two adverse outcomes (AOs): mutations and chromosomal aberrations. We collected empirical evidence from the literature to evaluate the key event relationships between the MIE and the AOs, and assessed the weight of evidence using the modified Bradford-Hill criteria for causality. Oxidative DNA damage is constantly induced and repaired in cells given the ubiquitous presence of reactive oxygen species and free radicals. However, xenobiotic exposures may increase damage above baseline levels through a variety of mechanisms and overwhelm DNA repair and endogenous antioxidant capacity. Unrepaired oxidative DNA base damage can lead to base substitutions during replication and, along with repair intermediates, can also cause DNA strand breaks that can lead to mutations and chromosomal aberrations if not repaired adequately. This AOP network identifies knowledge gaps that could be filled by targeted studies designed to better define the quantitative relationships between key events, which could be leveraged for quantitative chemical safety assessment. We anticipate that this AOP network will provide the building blocks for additional genotoxicity-associated AOPs and aid in designing novel integrated testing approaches for genotoxicity.

Metaphase-Based Cytogenetic Approach Identifies Radiation-Induced Chromosome and Chromatid Aberrations in Zebrafish Embryos

Metaphase-based cytogenetic methods based on scoring of chromosome aberrations for the estimation of the radiation dose received provide a powerful approach for evaluating the associated risk upon radiation exposure and form the bulk of our current knowledge of radiation-induced chromosome damages. They mainly rely on inducing quiescent peripheral lymphocytes into proliferation and blocking them at metaphases to quantify the damages at the chromosome level. However, human organs and tissues demonstrate various sensitivity towards radiation and within them, self-proliferating progenitor/stem cells are believed to be the most sensitive populations. The radiation-induced chromosome aberrations in these cells remain largely unknown, especially in the context of an intact living organism. Zebrafish is an ideal animal model for research into this aspect due to their small size and the large quantities of progenitor cells present during the embryonic stages. In this study, we employ a novel metaphase-based cytogenetic approach on zebrafish embryos and demonstrate that chromosome-type and chromatid-type aberrations could be identified in progenitor cells at different cell-cycle stages at the point of radiation exposure. Our work positions zebrafish at the forefront as a useful animal model for studying radiation-induced chromosome structural changes in vivo.

Chromosomal Instability at Fragile Sites in Blue Foxes, Silver Foxes, and Their Interspecific Hybrids

Simple Summary

The paper describes the karyotypes of blue and silver foxes and their hybrids, in terms of the numbers of A and B chromosomes and the frequency of fragile sites on chromosomes. Genome stability in these species is affected by Robertson translocations in the karyotype of the blue fox and by B chromosomes in the silver fox. The fragile sites assay was used as a biomarker to assess genome stability in foxes. This test enables the identification of breaks, chromatid gaps, and deletions. In healthy individuals, the number of these instabilities remains low. The test can be used to select individuals with the most stable genome for breeding of blue and silver foxes. The fewer an individual’s susceptible sites, the more likely it is to have good reproductive performance. This factor is extremely important in the case of blue foxes, which are an endangered species.

Abstract

A cytogenetic assay based on fragile sites (FS) enables the identification of breaks, chromatid gaps, and deletions. In healthy individuals, the number of these instabilities remains low. Genome stability in these species is affected by Robertsonian translocations in the karyotype of the blue fox and by B chromosomes in the silver fox. The aims of the study were to characterise the karyotype of blue foxes, silver foxes, and their hybrids and to identify chromosomal fragile sites used to evaluate genome stability. The diploid number of A chromosomes in blue foxes ranged from 48 to 50, while the number of B chromosomes in silver foxes varied from one to four, with a constant number of A chromosomes (2n = 34). In interspecific hybrids, both types of karyotypic variation were identified, with the diploid number of A chromosomes ranging from 40 to 44 and the number of B chromosomes varying from 0 to 3. The mean frequency of FS in foxes was 4.06 ± 0.19: 4.61 ± 0.37 in blue foxes, 3.46 ± 0.28 in silver foxes, and 4.12 ± 0.22 in hybrids. A relationship was identified between an increased number of A chromosomes in the karyotype of the hybrids and the frequency of chromosomal breaks. The FS assay was used as a biomarker for the evaluation of genomic stability in the animals in the study.

H. pylori infection alters repair of DNA double-strand breaks via SNHG17

Chronic infections can lead to carcinogenesis through inflammation-related mechanisms. Chronic infection of the human gastric mucosa with Helicobacter pylori is a well-known risk factor for gastric cancer. However, the mechanisms underlying H. pylori-induced gastric carcinogenesis are incompletely defined. We aimed to screen and clarify the functions of long noncoding RNAs (lncRNAs) that are differentially expressed in H. pylori-related gastric cancer. We found that lncRNA SNHG17 was upregulated by H. pylori infection and markedly increased the levels of double-strand breaks (DSBs). SNHG17 overexpression correlated with poor overall survival in patients with gastric cancer. The recruitment of NONO by overabundant nuclear SNHG17, along with the role of cytoplasmic SNHG17 as a decoy for miR-3909, which regulates Rad51 expression, shifted the DSB repair balance from homologous recombination toward nonhomologous end joining. Notably, during chronic H. pylori infection, SNHG17 knockdown inhibited chromosomal aberrations. Our findings suggest that spatially independent deregulation of the SNHG17/NONO and SNHG17/miR-3909/RING1/Rad51 pathways upon H. pylori infection promotes tumorigenesis in gastric cancer by altering the DNA repair system, which is critical for the maintenance of genomic stability. Upregulation of SNHG17 by H. pylori infection might be an undefined link between cancer and inflammation.

Toxicogenetic effects on fish species in two sub-basins of the upper Paraguay river, Southern Pantanal - Brazil

This study aimed to evaluate water quality using limnological parameters in two sub-basins of the Negro and Apa Rivers, along with the composition and structure of the landscape around the locations sampled in the two sub-basins and their possible contribution to the loss of water quality. We also set out to identify the genotoxic effects on the erythrocytes of Prochilodus lineatus and Leporinus friderici. In particular, we quantified total Cr, Ni and Pb in the muscle of these fish species to determine which genotoxic changes are related to the concentration of metals detected in the fish from these two sub-basins of the Paraguay River Basin. The sub-basin of the Apa River presented a greater proportion of surrounding pastureland in relation to the basin of the Negro River. The erythrocytes of P. lineatus showed a significant difference between the sub-basins for nuclear pyknosis, binucleated cells and lobed nuclei (p < 0.05). In L. friderici, vacuolated nuclei, nuclear pyknosis and lobed nuclei alterations also showed a significant difference between the sub-basins (p < 0.05). The genotoxicity index of the Apa River sub-basin presented higher frequencies of nuclear alterations in P. lineatus and L. friderici (p < 0.05), compared to the Negro River sub-basin. The concentration of total Cr, Ni and Pb in the muscles of P. lineatus and L. friderici in the Negro River sub-basin leads to genotoxic damage, mainly from the induction of lobed nuclei. Based on our results, it can be concluded that toxicogenetic effects in native fish species are an important source of environmental diagnosis in the Upper Paraguay River Basin.

Effect of Smartphone Light Fluxes on Cornea: A Biophysical Study

Objective

Biophysical study to investigate (a) the effects of smartphone light fluxes (SPLF) on isolated mammalian cornea and model protein (insulin), (b) to predict the possible visual interference of SPLF.

Materials and Methods

Fresh goat cornea and insulin protein were used as an experimental model system. The energy of absorbed SPLF was measured using chemical dosimeter. The effect of SPLF on the aggregation of model protein was studied using fluorescence spectroscopy and dynamic light scattering (DLS). Fluorescence microscopy, scanning electron microscopy (SEM), DLS, were used for cornea imaging.

Results

The spectral emission peak of SPLF was observed at 380 nm and 420 nm. Absorbed radiation of SPLF was found to be 2.82 mWm^-2 and 1.92 mWm^-2 for collimated (focussed) and noncollimated (nonfocussed) condition, respectively. Secondary structural changes of insulin were observed by fluorescence and zeta potential after SPLF exposure. SEM study revealed the disorganization of the epithelial cell surface, increase in intercellular space, disorganization of primary epithelium layer, and exposure of the second layer is seen in depth. Differential Interference Microscopy showed an optical gradient in images that appears to be changed in specimen structure. Fluorescence microscopy showed disorganization in epithelial cell pattern. A significant difference in bio-molecular permeation was observed in the exposed cornea. Ultraviolet UV-visible spectroscopy study indicated a reduction in light transmission through the cornea.

Conclusions

The obtained results indicate changes in physicochemical and morphological modifications in the cornea and insulin modifications after exposed to SPLF.

Radioprotection and Radiomitigation: From the Bench to Clinical Practice

The development of protective agents against harmful radiations has been a subject of investigation for decades. However, effective (ideal) radioprotectors and radiomitigators remain an unsolved problem. Because ionizing radiation-induced cellular damage is primarily attributed to free radicals, radical scavengers are promising as potential radioprotectors. Early development of such agents focused on thiol synthetic compounds, e.g., amifostine (2-(3-aminopropylamino) ethylsulfanylphosphonic acid), approved as a radioprotector by the Food and Drug Administration (FDA, USA) but for limited clinical indications and not for nonclinical uses. To date, no new chemical entity has been approved by the FDA as a radiation countermeasure for acute radiation syndrome (ARS). All FDA-approved radiation countermeasures (filgrastim, a recombinant DNA form of the naturally occurring granulocyte colony-stimulating factor, G-CSF; pegfilgrastim, a PEGylated form of the recombinant human G-CSF; sargramostim, a recombinant granulocyte macrophage colony-stimulating factor, GM-CSF) are classified as radiomitigators. No radioprotector that can be administered prior to exposure has been approved for ARS. This differentiates radioprotectors (reduce direct damage caused by radiation) and radiomitigators (minimize toxicity even after radiation has been delivered). Molecules under development with the aim of reaching clinical practice and other nonclinical applications are discussed. Assays to evaluate the biological effects of ionizing radiations are also analyzed.

Sperm DNA fragmentation testing: Summary evidence and clinical practice recommendations

We herein summarise the evidence concerning the impact of sperm DNA fragmentation in various clinical infertility scenarios and the advances on sperm DNA fragmentation tests. The collected evidence was used to formulate 41 recommendations. Of these, 13 recommendations concern technical aspects of sperm DNA fragmentation testing, including pre‐analytical information, clinical thresholds and interpretation of results. The remaining 28 recommendations relate to indications for sperm DNA fragmentation testing and clinical management. Clinical scenarios like varicocele, unexplained infertility, idiopathic infertility, recurrent pregnancy loss, intrauterine insemination, in vitro fertilisation/intracytoplasmic sperm injection, fertility counselling for men with infertility risk factors and sperm cryopreservation have been contemplated. The bulk evidence supporting the recommendations has increased in recent years, but it is still of moderate to low quality. This guideline provides clinicians with advice on best practices in sperm DNA fragmentation testing. Also, recommendations are provided on possible management strategies to overcome infertility related to sperm DNA fragmentation, based on the best available evidence. Lastly, we identified gaps in knowledge and opportunities for research and elaborated a list of recommendations to stimulate further investigation.

Mutagenicity monitoring in humans: Global versus specific origin of mutations

An underappreciated aspect of human mutagenicity biomonitoring is tissue specificity reflected in different assays, especially those that measure events that can only occur in developing bone marrow (BM) cells. Reviewed here are 9 currently-employed human mutagenicity biomonitoring assays. Several assays measure chromosome-level events in circulating T-lymphocytes (T-cells), i.e., traditional analyses of aberrations, translocation studies involving chromosome painting and fluorescence in situ hybridization (FISH) and determinations of micronuclei (MN). Other T-cell assays measure gene mutations. i.e., hypoxanthine-guanine phosphoriboslytransferase (HPRT) and phosphoribosylinositol glycan class A (PIGA). In addition to the T-cell assays, also reviewed are those assays that measure events in peripheral blood cells that necessarily arose in BM cells, i.e., MN in reticulocytes; glycophorin A (GPA) gene mutations in red blood cells (RBCs), and PIGA gene mutations in RBC or granulocytes. This review considers only cell culture- or cytometry-based assays to describe endpoints measured, methods, optimal sampling times, and sample summaries of typical quantitative and qualitative results. However, to achieve its intended focus on the target cells where events occur, kinetics of the cells of peripheral blood that derive at some point from precursor cells are reviewed to identify body sites and tissues where the genotoxic events originate. Kinetics indicate that in normal adults, measured events in T-cells afford global assessments of in vivo mutagenicity but are not specific for BM effects. Therefore, an agent's capacity for inducing mutations in BM cells cannot be reliably inferred from T-cell assays as the magnitude of effect in BM, if any, is unknown. By contrast, chromosome or gene level mutations measured in RBCs/reticulocytes or granulocytes must originate in BM cells, i.e. in RBC or granulocyte precursors, thereby making them specific indicators for effects in BM. Assays of mutations arising directly in BM cells may quantitatively reflect the mutagenicity of potential leukemogenic agents.

Discovery of tandem and interspersed segmental duplications using high-throughput sequencing

MOTIVATION

Several algorithms have been developed that use high-throughput sequencing technology to characterize structural variations (SVs). Most of the existing approaches focus on detecting relatively simple types of SVs such as insertions, deletions and short inversions. In fact, complex SVs are of crucial importance and several have been associated with genomic disorders. To better understand the contribution of complex SVs to human disease, we need new algorithms to accurately discover and genotype such variants. Additionally, due to similar sequencing signatures, inverted duplications or gene conversion events that include inverted segmental duplications are often characterized as simple inversions, likewise, duplications and gene conversions in direct orientation may be called as simple deletions. Therefore, there is still a need for accurate algorithms to fully characterize complex SVs and thus improve calling accuracy of more simple variants.

RESULTS

We developed novel algorithms to accurately characterize tandem, direct and inverted interspersed segmental duplications using short read whole genome sequencing datasets. We integrated these methods to our TARDIS tool, which is now capable of detecting various types of SVs using multiple sequence signatures such as read pair, read depth and split read. We evaluated the prediction performance of our algorithms through several experiments using both simulated and real datasets. In the simulation experiments, using a 30× coverage TARDIS achieved 96% sensitivity with only 4% false discovery rate. For experiments that involve real data, we used two haploid genomes (CHM1 and CHM13) and one human genome (NA12878) from the Illumina Platinum Genomes set. Comparison of our results with orthogonal PacBio call sets from the same genomes revealed higher accuracy for TARDIS than state-of-the-art methods. Furthermore, we showed a surprisingly low false discovery rate of our approach for discovery of tandem, direct and inverted interspersed segmental duplications prediction on CHM1 (<5% for the top 50 predictions).

AVAILABILITY AND IMPLEMENTATION

TARDIS source code is available at https://github.com/BilkentCompGen/tardis, and a corresponding Docker image is available at https://hub.docker.com/r/alkanlab/tardis/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Ionizing Radiation and Complex DNA Damage: Quantifying the Radiobiological Damage Using Monte Carlo Simulations

Ionizing radiation is a common tool in medical procedures. Monte Carlo (MC) techniques are widely used when dosimetry is the matter of investigation. The scientific community has invested, over the last 20 years, a lot of effort into improving the knowledge of radiation biology. The present article aims to summarize the understanding of the field of DNA damage response (DDR) to ionizing radiation by providing an overview on MC simulation studies that try to explain several aspects of radiation biology. The need for accurate techniques for the quantification of DNA damage is crucial, as it becomes a clinical need to evaluate the outcome of various applications including both low- and high-energy radiation medical procedures. Understanding DNA repair processes would improve radiation therapy procedures. Monte Carlo simulations are a promising tool in radiobiology studies, as there are clear prospects for more advanced tools that could be used in multidisciplinary studies, in the fields of physics, medicine, biology and chemistry. Still, lot of effort is needed to evolve MC simulation tools and apply them in multiscale studies starting from small DNA segments and reaching a population of cells.

The effects of DNA repair polymorphisms on chromosome aberrations in the population of Kazakhstan

Purpose: To analyze the effects of DNA repair polymorphism and other factors on the frequency chromosome aberrations in an irradiated cohort of subjects living around the Semipalatinsk nuclear test site and non-exposed group of subjects from ecologically favorable zones of Kazakhstan.Materials and methods: Blood samples were collected in the rural areas of the East Kazakhstan district around the Semipalatinsk nuclear test site and ecologically favorable zones of Almaty region of Kazakhstan. Chromosome aberrations in the fresh and cryopreserved peripheral blood lymphocyte cultures were analyzed by Giemsa staining. Single nucleotide polymorphisms at eight DNA repair genes (XRCC1 rs1799782, XRCC1 rs25487, XRCC3 rs861539, ATM rs1801516, XPD rs1799793, XPD rs13181, APEX1 rs1130409, and hOGG1 rs1052133) were determined by PCR-RFLP method.Results: The age of donors and smoking significantly affected the frequency of chromosome aberrations among the irradiated and control subjects. In the irradiated and control cohorts, the frequency of chromosome aberrations was significantly increased in the heterozygous ATM rs1801516 (1853 Asp/Asn) individuals; for the rest of the loci no significant associations between polymorphism and the frequency of chromosome aberrations were detected.Conclusions: The age of donors, smoking, and the ATM rs1801516 polymorphism significantly affect the frequency of chromosome aberrations among individuals inhabiting contaminated area around the Semipalatinsk nuclear weapon test site, as well as among those inhabiting ecologically favorable zones of Kazakhstan.

Processive DNA synthesis is associated with localized decompaction of constitutive heterochromatin at the sites of DNA replication and repair

Constitutive heterochromatin is considered as a functionally inert genome compartment, important for its architecture and stability. How such stable structure is maintained is not well understood. Here, we apply four different visualization schemes to label it and investigate its dynamics during DNA replication and repair. We show that replisomes assemble over the heterochromatin in a temporally ordered manner. Furthermore, heterochromatin undergoes transient decompaction locally at the active sites of DNA synthesis. Using selective laser microirradiation conditions that lead to damage repaired via processive DNA synthesis, we measured similarly local decompaction of heterochromatin. In both cases, we could not observe large-scale movement of heterochromatin to the domain surface. Instead, the processive DNA synthesis machinery assembled at the replication/repair sites. Altogether, our data are compatible with a progression of DNA replication/repair along the chromatin in a dynamic mode with localized and transient decompaction that does not globally remodels the whole heterochromatin compartment.

Infrared nanospectroscopic mapping of a single metaphase chromosome

The integrity of the chromatin structure is essential to every process occurring within eukaryotic nuclei. However, there are no reliable tools to decipher the molecular composition of metaphase chromosomes. Here, we have applied infrared nanospectroscopy (AFM-IR) to demonstrate molecular difference between eu- and heterochromatin and generate infrared maps of single metaphase chromosomes revealing detailed information on their molecular composition, with nanometric lateral spatial resolution. AFM-IR coupled with principal component analysis has confirmed that chromosome areas containing euchromatin and heterochromatin are distinguishable based on differences in the degree of methylation. AFM-IR distribution of eu- and heterochromatin was compared to standard fluorescent staining. We demonstrate the ability of our methodology to locate spatially the presence of anticancer drug sites in metaphase chromosomes and cellular nuclei. We show that the anticancer 'rule breaker' platinum compound [Pt[N(p-HC6F4)CH2]2py2] preferentially binds to heterochromatin, forming localized discrete foci due to condensation of DNA interacting with the drug. Given the importance of DNA methylation in the development of nearly all types of cancer, there is potential for infrared nanospectroscopy to be used to detect gene expression/suppression sites in the whole genome and to become an early screening tool for malignancy.

Chromosomal Aberration Test in Human Lymphocytes

Human peripheral lymphocytes (HPL) are non-cycling primary cells (G0 cells). They are easily collectable by venipuncture. In the presence of suitable culture media and stimulants in vitro HPL enter the cell cycle and divide mitotically. Metaphase-like stages can be arrested using the spindle fiber poison colcemid and prepared on microscopic slides. Following appropriate staining, chromosomal aberrations can be analyzed in the microscope. These aberrations may either be induced in vivo by environmental or occupational influences or in vitro after experimentally controlled manipulations in order to detect or to test the mutagenic potency of various agents.

Identification of novel breakpoints for locus- and region-specific translocations in 293 cells by molecular cytogenetics before and after irradiation

The human kidney embryonic 293 cell line (293 cells) is extensively used in biomedical and pharmaceutical research. These cells exhibit a number of numerical and structural chromosomal anomalies. However, the breakpoints responsible for these structural chromosomal rearrangements have not been comprehensively characterized. In addition, it is not known whether chromosomes with structural rearrangement are more sensitive to external toxic agents, such as ionizing radiation. We used G-banding, spectral karyotyping (SKY), and locus- and region-specific fluorescence in situ hybridization (FISH) probes designed in our lab or obtained from commercial vendor to address this gap. Our G-banding analysis revealed that the chromosome number varies from 66 to 71, with multiple rearrangements and partial additions and deletions. SKY analysis confirmed 3 consistent rearrangements, two simple and one complex in nature. Multicolor FISH analysis identified an array of breakpoints responsible for locus- and region-specific translocations. Finally, SKY analysis revealed that radio-sensitivity of structurally rearranged chromosomes is dependent on radiation dose. These findings will advance our knowledge in 293 cell biology and will enrich the understanding of radiation biology studies.

Comparison of the toxicogenetic potential of sewage sludges from different treatment processes focusing agricultural use

A problem that has been dragging in recent decades is the final disposal of the waste produced in the wastewater treatment process. In addition to its high amount of organic matter and nutrients, this waste, known as sewage sludge (SS), may also contain toxic compounds that, when in the environment, can cause deleterious effects to organisms and lead to severe and irreversible consequences to human health. In order to understand the potential of inducing cellular and chromosomal instabilities, the species Allium cepa was employed to assess the presence of toxic agents in SS samples. Seeds of A. cepa were exposed to several dilutions of aqueous extract of SSs from 5 wastewater treatment plants (WWTPs), whose characteristics of treated sewage and the technologies employed differ among them. The results obtained showed that all the studied SSs induced significant genotoxic and mutagenic alterations, even in smaller dilutions tested. With these results, it was also possible to observe that SSs from WWTPs that present system of activated sludge and receive sewage of industrial origin induced a greater number of toxicogenetic alterations in the test organism. The high frequencies of chromosomal and nuclear aberrations observed, induced by contaminants present in the SS, represent worrying results because it proves a direct action of this agent on the genetic material of the exposed organism. Therefore, the agronomic application of SS in agriculture requires additional and more effective technologies in order to promote its complete decontamination and its safe disposal in the environment.

Temperature affects the toxicity of lead-contaminated food in Geophagus brasiliensis (QUOY & GAIMARD, 1824)

Lead is toxic to fish, and its toxicity can be aggravated by the water temperature. Geophagus brasiliensis populations are geographically widespread and thus live in areas with different temperatures. The objective of this work was to evaluate the effects of lead-contaminated feed in fish (Geophagus brasiliensis) exposed to different temperatures. A factorial experiment was performed with two temperatures (25 and 28°C), and two feeds (control and lead contaminated - 60 mg/kg) for a sum of four treatments (25°C, Control = 25/C; 25°C, 60 mg/kg = 25/60; 28°C, Control = 28/C and 28°C, 60 mg/kg = 28/60). Analyses of the lead accumulation, oxidative stress and genotoxic damage were performed. The gills and liver showed increased lead concentrations in fish receiving lead-contaminated food at both temperatures. The lead concentrations in the intestines and muscles of fish exposed to the 25/60 treatment was greater than it was in fish exposed to the 25/C treatment. The enzyme response in the gills and the micronuclei count increased in fish exposed to the 25/60 treatment. Higher temperatures can be a beneficial factor for Geophagus brasiliensis because they can hinder the absorption of lead, thereby reducing the damage caused to the organism.

A historical reflection on our understanding of radiation-induced DNA double strand break repair in somatic mammalian cells; interfacing the past with the present

Purpose: The International Journal of Radiation Biology (IJRB) is celebrating 60 years of publishing in 2019. IJRB has made an enormous contribution to publishing papers that have enhanced our understanding of the DNA damage response (DDR) activated following exposure to ionizing radiation (IR). The IR-induced DDR field has a rich history but many outstanding papers pass unread by young scientists overwhelmed by the current literature. We provide a historical reflection on key advances in the DDR field and interface them with current knowledge. Conclusions: DNA double strand breaks (DSBs) were identified as the major biological lesion induced by IR. But early studies on cells from IR-sensitive ataxia telangiectasia patients showed that DSB repair was not sufficient to prevent IR hypersensitivity. Subsequently, the ATM-dependent signal transduction process was revealed, with the breadth of the response being slowly unearthed. Early studies demonstrated at least two processes of DSB repair and revealed that mis-repair causes translocation formation. Recent studies, however, are unraveling more complexity in the repair process, including the specific processing of DSBs within transcriptionally active regions, and the significance of the chromatin environment. Despite the quality of these early and current studies, many questions remain to be addressed.

A new role for Drosophila Aurora-A in maintaining chromosome integrity

Aurora-A is a conserved mitotic kinase overexpressed in many types of cancer. Growing evidence shows that Aurora-A plays a crucial role in DNA damage response (DDR) although this aspect has been less characterized. We isolated a new aur-A mutation, named aur-A⁹⁴⁹, in Drosophila, and we showed that it causes chromosome aberrations (CABs). In addition, aur-A⁹⁴⁹ mutants were sensitive to X-ray treatment and showed impaired γ-H2Av foci dissolution kinetics. To identify the pathway in which Aur-A works, we conducted an epistasis analysis by evaluating CAB frequencies in double mutants carrying aur-A⁹⁴⁹ mutation combined to mutations in genes related to DNA damage response (DDR). We found that mutations in tefu (ATM) and in the histone variant H2Av were epistatic over aur-A⁹⁴⁹ indicating that Aur-A works in DDR and that it is required for γ-H2Av foci dissolution. More interestingly, we found that a mutation in lig4, a gene belonging to the non-homologous end joining (NHEJ) repair pathway, was epistatic over aur-A⁹⁴⁹. Based on studies in other systems, which show that phosphorylation is important to target Lig4 for degradation, we hypothesized that in aur-A⁹⁴⁹ mutant cells, there is a persistence of Lig4 that could be, in the end, responsible for CABs. Finally, we observed a synergistic interaction between Aur-A and the homologous recombination (HR) repair system component Rad 51 in the process that converts chromatid deletions into isochromatid deletions. Altogether, these data indicate that Aur-A depletion can elicit chromosome damage. This conclusion should be taken into consideration, since some anticancer therapies are aimed at reducing Aurora-A expression.

In Vitro Cytogenetic Assays: Chromosomal Aberrations and Micronucleus Tests

Chromosome damage is a very important indicator of genetic damage relevant to environmental and clinical studies. Detailed descriptions of the protocols used for detection of chromosomal aberrations induced by genotoxic agents in vitro both in the presence or absence of rat liver-derived metabolizing systems are given in this chapter. Structural chromosomal aberrations that can be observed and quantified at metaphases are described here. For the detection of chromosomal damage (fragments or whole chromosome) in interphase, the micronucleus test can be used, and a description of this test is also presented. Criteria for determining a positive result using appropriate statistical methods are described.

Induction of DNA Damage by Light Ions Relative to 60Co γ-rays

The specific types and numbers of clusters of DNA lesions, including both DNA double-strand breaks (DSBs) and non-DSB clusters, are widely considered 1 of the most important initiating events underlying the relative biological effectiveness (RBE) of the light ions of interest in the treatment of cancer related to megavoltage x-rays and ⁶⁰Co γ-rays. This review summarizes the categorization of DNA damage, reviews the underlying mechanisms of action by ionizing radiation, and quantifies the general trends in DSB and non-DSB cluster formation by light ions under normoxic and anoxic conditions, as predicted by Monte Carlo simulations that reflect the accumulated evidence from decades of research on radiation damage to DNA. The significance of the absolute and relative numbers of clusters and the local complexity of DSB and non-DSB clusters are discussed in relation to the formation of chromosome aberrations and the loss of cell reproductive capacity. Clinical implications of the dependence of DSB induction on ionization density is reviewed with an eye towards increasing the therapeutic ratio of proton and carbon ion therapy through the explicit optimization of RBE-weighted dose.

Metal loads and biomarker suite responses in a tropical carnivorous fish indicative of anthropogenic impacts in a Southeastern Brazilian lagoon

Tropical coastal lagoons are highly productive environments exhibiting high biodiversity. However, the use of these ecosystems by local communities is of concern, since this generally leads to environmental degradation. The Imboassica coastal lagoon, located in Macaé city, in Northern Rio de Janeiro, is an important ecosystem in the state, however, already displaying signs of anthropogenic impacts. Carnivorous fish Hoplias malabaricus specimens were sampled from this impacted site, as well as from a reference area. Fish from Imboassica Lagoon presented lower condition factor, lower cholinesterase activity, and higher percentage of erythrocyte micronuclei when compared to fish from the reference site. Metals in fish from Imboassica Lagoon were always higher than Encantada Lagoon, with some seasonal differences, where some metals were higher in the rainy season compared to the dry season in muscle tissue, with the exception of Cu, Fe, Sr, and Zn; and in the liver, except for Ba, Cd, Cr, Ni, and Sr. Cr and Mn in the edible muscle portion of the fish were higher than the limits established by Brazilian and International legislations as permissible for human consumption, thus leading to concerns regarding public health risks for the local population that use fish as their main protein source.

Association of DNA repair gene polymorphisms with genotoxic stress in underground coal miners

In underground coal mining, numerous harmful substances and ionising radiation pose a major threat to the occupational safety and health of workers. Because cell DNA repair machinery eliminates genotoxic stress conferred by these agents, we examined whether single nucleotide polymorphisms in hOGG1 (rs1052133), XRCC1 (rs25487), ADPRT (rs1136410), XRCC4 (rs6869366) and LIG4 (rs1805388) genes modulate the genotoxic damage assessed by the cytokinesis-block micronucleus assay in lymphocytes from 143 underground coal miners and 127 healthy non-exposed males. We also analyzed models of gene-gene interactions associated with increased cytogenetic damage in coal miners and determined 'protective' and 'risk' combinations of alleles. We showed that miners with the G/G genotype of the hOGG1 (rs1052133) gene had a significantly increased frequency of binucleated lymphocytes with micronuclei (13.17‰, 95% CI = 10.78-15.56) compared to the C/C genotype carriers (10.35‰, 95% CI = 9.59-11.18). In addition, in the exposed group this indicator was significantly increased in carriers of the T/T genotype of the LIG4 (rs1805388) gene compared to miners harbouring the C/T genotype (13.00‰, 95% CI = 10.96-15.04 and 9.69‰, 95% CI = 8.32-11.06, respectively). Using the multifactor dimensionality reduction method, we found the three-locus model of gene-gene interactions hOGG1 (rs1052133) × ADPRT (rs1136410) × XRCC4 (rs6869366) associated with high genotoxic risk in coal miners. These results indicate that the studied polymorphisms and their combinations are associated with cytogenetic status in miners and may be used as molecular predictors of occupational risks in underground coal mines.

A combination of resveratrol and 3,3'-diindolylmethane, a potent radioprotector

PURPOSE

Exposure to ionizing radiation causes damage to the genomic integrity and stability of the cell. Though a large number of molecules have been studied for their radioprotective capability, no single agent is available today that meets all the requirements of a good radiprotector. In this study, we have investigated a combination of Resveratrol (RSV) and 3,3'-Diindolyl methane (DIM) for its efficacy for radioprotection. It is our hypothesis that this combination that possesses less toxicity than synthetic compounds, free radical scavenging potential, and the capacity to interfere with the several of the signaling cascades that trigger damage to cell by ionizing radiation may possess good radioprotective capability.

MATERIALS AND METHODS

Mice were pre-treated with a combination of RSV and DIM and the 30-day mortality assay, endogenous antioxidant levels in intestinal mucosa, metaphase chromosomal aberrations, and micronuclei formation were assessed after exposed to ionizing radiation.

RESULTS

The dose modifying factor (DRF) obtained for RSV, DIM, and the combination is 1.15, 1.17, and 1.3, respectively. Pre-treatment of mice with the combination results in significant (***p = .001) protection of the endogenous antioxidant levels, chromosomal aberrations, micronuclei formation, after exposure to ionizing radiation.

CONCLUSIONS

Our findings suggest that pre-treatment with the combination of RSV and DIM protects effectively from the ionizing radiation-induced damage at the molecular, cellular, and tissue levels by counteracting both the direct and indirect effects.

The protective function of noncoding DNA in genome defense of eukaryotic male germ cells

Peripheral and abundant noncoding DNA has been hypothesized to protect the genome and the central protein-coding sequences against DNA damage in somatic genome. In the cytosol, invading exogenous nucleic acids may first be deactivated by small RNAs encoded by noncoding DNA via mechanisms similar to the prokaryotic CRISPR-Cas system. In the nucleus, the radicals generated by radiation in the cytosol, radiation energy and invading exogenous nucleic acids are absorbed, blocked and/or reduced by peripheral heterochromatin, and damaged DNA in heterochromatin is removed and excluded from the nucleus to the cytoplasm through nuclear pore complexes. To further strengthen the hypothesis, this review summarizes the experimental evidence supporting the protective function of noncoding DNA in the genome of male germ cells. Based on these data, this review provides evidence supporting the protective role of noncoding DNA in the genome defense of sperm genome through similar mechanisms to those of the somatic genome.

Differential effects of silver nanoparticles on DNA damage and DNA repair gene expression in Ogg1-deficient and wild type mice

Due to extensive use in consumer goods, it is important to understand the genotoxicity of silver nanoparticles (AgNPs) and identify susceptible populations. 8-Oxoguanine DNA glycosylase 1 (OGG1) excises 8-oxo-7,8-dihydro-2-deoxyguanine (8-oxoG), a pro-mutagenic lesion induced by oxidative stress. To understand whether defects in OGG1 is a possible genetic factor increasing an individual's susceptibly to AgNPs, we determined DNA damage, genome rearrangements, and expression of DNA repair genes in Ogg1-deficient and wild type mice exposed orally to 4 mg/kg of citrate-coated AgNPs over a period of 7 d. DNA damage was examined at 3 and 7 d of exposure and 7 and 14 d post-exposure. AgNPs induced 8-oxoG, double strand breaks (DSBs), chromosomal damage, and DNA deletions in both genotypes. However, 8-oxoG was induced earlier in Ogg1-deficient mice and 8-oxoG levels were higher after 7-d treatment and persisted longer after exposure termination. AgNPs downregulated DNA glycosylases Ogg1, Neil1, and Neil2 in wild type mice, but upregulated Myh, Neil1, and Neil2 glycosylases in Ogg1-deficient mice. Neil1 and Neil2 can repair 8-oxoG. Thus, AgNP-mediated downregulation of DNA glycosylases in wild type mice may contribute to genotoxicity, while upregulation thereof in Ogg1-deficient mice could serve as an adaptive response to AgNP-induced DNA damage. However, our data show that Ogg1 is indispensable for the efficient repair of AgNP-induced damage. In summary, citrate-coated AgNPs are genotoxic in both genotypes and Ogg1 deficiency exacerbates the effect. These data suggest that humans with genetic polymorphisms and mutations in OGG1 may have increased susceptibility to AgNP-mediated DNA damage.

The Hybrid Incompatibility Genes Lhr and Hmr Are Required for Sister Chromatid Detachment During Anaphase but Not for Centromere Function

Crosses between Drosophila melanogaster females and Drosophila simulans males produce hybrid sons that die at the larval stage. This hybrid lethality is suppressed by loss-of-function mutations in the D. melanogaster Hybrid male rescue (Hmr) or in the D. simulans Lethal hybrid rescue (Lhr) genes. Previous studies have shown that Hmr and Lhr interact with heterochromatin proteins and suppress expression of transposable elements within D. melanogaster It also has been proposed that Hmr and Lhr function at the centromere. We examined mitotic divisions in larval brains from Hmr and Lhr single mutants and Hmr; Lhr double mutants in D. melanogaster In none of the mutants did we observe defects in metaphase chromosome alignment or hyperploid cells, which are hallmarks of centromere or kinetochore dysfunction. In addition, we found that Hmr-HA and Lhr-HA do not colocalize with centromeres either during interphase or mitotic division. However, all mutants displayed anaphase bridges and chromosome aberrations resulting from the breakage of these bridges, predominantly at the euchromatin-heterochromatin junction. The few dividing cells present in hybrid males showed fuzzy and irregularly condensed chromosomes with unresolved sister chromatids. Despite this defect in condensation, chromosomes in hybrids managed to align on the metaphase plate and undergo anaphase. We conclude that there is no evidence for a centromeric function of Hmr and Lhr within D. melanogaster nor for a centromere defect causing hybrid lethality. Instead, we find that Hmr and Lhr are required in D. melanogaster for detachment of sister chromatids during anaphase.

Feline vaccine-associated sarcomagenesis: Is there an inflammation-independent role for aluminium?

Aluminium has been found in feline vaccine-associated sarcomas. In this study, we investigated the potential for aluminium to contribute directly to tumourigenesis. Our results indicated that an aluminium hydroxide adjuvant preparation was cytotoxic and mutagenic in human-Chinese hamster ovary (CHO) hybrid cells in vitro. Moreover, CHO cells deficient in DNA double strand break (DSB), but not single-strand break (SSB), repair, were particularly sensitive to aluminium exposure compared with repair proficient cells, suggesting that aluminium is associated with DSBs. In contrast to CHO cells, primary feline skin fibroblasts were resistant to the cytotoxic effects of aluminium compounds and exposure to an aluminium chloride salt promoted cell growth and cell cycle progression at concentrations much less than those measured in particular feline rabies vaccines. These findings suggest that aluminium exposure may contribute, theoretically, to both initiation and promotion of tumours in the absence of an inflammatory response.

In silico genotoxicity of coumarins: application of the Phenol-Explorer food database to functional food science

Coumarins are a group of phytochemicals that may be beneficial or harmful to health depending on their type and dosage and the matrix that contains them. Some of these compounds have been proven to display pro-oxidant and clastogenic activities. Therefore, in the current work, we have studied the coumarins that are present in food sources extracted from the Phenol-Explorer database in order to predict their clastogenic activity and identify the structure-activity relationships and genotoxic structural alerts using alternative methods in the field of computational toxicology. It was necessary to compile information on the type and amount of coumarins in different food sources through the analysis of databases of food composition available online. A virtual screening using a clastogenic model and different software, such as MODESLAB, ChemDraw and STATISTIC, was performed. As a result, a table of food composition was prepared and qualitative information from this data was extracted. The virtual screening showed that the esterified substituents inactivate molecules, while the methoxyl and hydroxyl substituents contribute to their activity and constitute, together with the basic structures of the studied subclasses, clastogenic structural alerts. Chemical subclasses of simple coumarins and furocoumarins were classified as active (xanthotoxin, isopimpinellin, esculin, scopoletin, scopolin and bergapten). In silico genotoxicity was mainly predicted for coumarins found in beer, sherry, dried parsley, fresh parsley and raw celery stalks. The results obtained can be interesting for the future design of functional foods and dietary supplements. These studies constitute a reference for the genotoxic chemoinformatic analysis of bioactive compounds present in databases of food composition.

DNA double strand break (DSB) induction and cell survival in iodine-enhanced computed tomography (CT)

A multi-scale Monte Carlo model is proposed to assess the dosimetric and biological impact of iodine-based contrast agents commonly used in computed tomography. As presented, the model integrates the general purpose MCNP6 code system for larger-scale radiation transport and dose assessment with the Monte Carlo damage simulation to determine the sub-cellular characteristics and spatial distribution of initial DNA damage. The repair-misrepair-fixation model is then used to relate DNA double strand break (DSB) induction to reproductive cell death. Comparisons of measured and modeled changes in reproductive cell survival for ultrasoft characteristic k-shell x-rays (0.25-4.55 keV) up to orthovoltage (200-500 kVp) x-rays indicate that the relative biological effectiveness (RBE) for DSB induction is within a few percent of the RBE for cell survival. Because of the very short range of secondary electrons produced by low energy x-ray interactions with contrast agents, the concentration and subcellular distribution of iodine within and near cellular targets have a significant impact on the estimated absorbed dose and number of DSB produced in the cell nucleus. For some plausible models of the cell-level distribution of contrast agent, the model predicts an increase in RBE-weighted dose (RWD) for the endpoint of DSB induction of 1.22-1.40 for a 5-10 mg ml^-1 iodine concentration in blood compared to an RWD increase of 1.07  ±  0.19 from a recent clinical trial. The modeled RWD of 2.58  ±  0.03 is also in good agreement with the measured RWD of 2.3  ±  0.5 for an iodine concentration of 50 mg ml^-1 relative to no iodine. The good agreement between modeled and measured DSB and cell survival estimates provides some confidence that the presented model can be used to accurately assess biological dose for other concentrations of the same or different contrast agents.

A Role for the Twins Protein Phosphatase (PP2A-B55) in the Maintenance of Drosophila Genome Integrity

The protein phosphatase 2A (PP2A) is a conserved heterotrimeric enzyme that regulates several cellular processes including the DNA damage response and mitosis. Consistent with these functions, PP2A is mutated in many types of cancer and acts as a tumor suppressor. In mammalian cells, PP2A inhibition results in DNA double strand breaks (DSBs) and chromosome aberrations (CABs). However, the mechanisms through which PP2A prevents DNA damage are still unclear. Here, we focus on the role of the Drosophila twins (tws) gene in the maintenance of chromosome integrity; tws encodes the B regulatory subunit (B/B55) of PP2A. Mutations in tws cause high frequencies of CABs (0.5 CABs/cell) in Drosophila larval brain cells and lead to an abnormal persistence of γ-H2Av repair foci. However, mutations that disrupt the PP4 phosphatase activity impair foci dissolution but do not cause CABs, suggesting that a delayed foci regression is not clastogenic. We also show that Tws is required for activation of the G2/M DNA damage checkpoint while PP4 is required for checkpoint recovery, a result that points to a conserved function of these phosphatases from flies to humans. Mutations in the ATM-coding gene tefu are strictly epistatic to tws mutations for the CAB phenotype, suggesting that failure to dephosphorylate an ATM substrate(s) impairs DNA DSBs repair. In addition, mutations in the Ku70 gene, which do not cause CABs, completely suppress CAB formation in tws Ku70 double mutants. These results suggest the hypothesis that an improperly phosphorylated Ku70 protein can lead to DNA damage and CABs.

Evaluation of genetic toxicity caused by acid mine drainage of coal mines on fish fauna of Simsang River, Garohills, Meghalaya, India

Fishery ecology of the Simsang River, Meghalaya is being threatened by large scale environmental degradation due to acid mine drainage (AMD) of coal mines. In the present paper, effort has been made to evaluate the genotoxicity caused due to AMD of coal mines on Channa punctata under laboratory condition through comet assay, micronucleus and chromosome aberration tests. Water samples were collected seasonally from affected and unaffected sites of the River and physico-chemical quality of water indicated low pH (4.6), high concentration of sulphates (270mgL(-1)) and iron (7.2mgL(-1)) beyond permissible limits. Polycyclic aromatic hydrocarbon (PAH) showed highest concentration of 4-ring PAH and Benzo[a]anthracene was the most important pollutant in the water collected from affected sites. The highest and the lowest mean concentrations of PAHs were estimated in monsoon and winter season, respectively. The index of DNA damage assessed by comet assay, micronucleus and chromosome aberration tests demonstrated significant differences season wise in different sampling sites. Frequency of DNA-damaged cells was found highest in the water samples collected from affected site in monsoon season.