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1.  Studies on Brahma rasayana in male swiss albino mice: Chromosomal aberrations and sperm abnormalities 
Ayurveda, the Indian holistic healthcare system encompasses traditional medicines with a principle of creating harmony and maintaining balance within the natural rhythms of the body. Rasayana is one of the branches of Ayurveda frequently used as rejuvenant therapy to overcome many discomforts and prevent diseases. It has been reported that rasayanas have immunomodulatory, antioxidant and antitumor functions. However, the genotoxic potential of many rasayanas remains to be evaluated. The present study was undertaken to assess the role of Brahma rasayana(BR) on genotoxicity in vivo in a mouse test system. The older mice (9 months) were orally fed with rasayana for 8 weeks. The treated groups showed no signs of dose-dependent toxicity at the dosage levels tested. The body weight loss/gain and feed consumption were unaffected at tested doses. Furthermore, sperm abnormalities and chromosomal aberrations were insignificant in the treatment group when compared to controls. However, there was a marginal increase in sperm count in the BR treated animals. These findings clearly indicate that there are no observed adverse genotoxic effects elicited by BR in experimental animals such as mice.
doi:10.4103/0975-9476.59826
PMCID: PMC3149391  PMID: 21829300
Aging; Brahma rasayana; chromosomal aberrations; genotoxicity; sperm abnormalities
2.  In Vivo Assessment of Genotoxic, Antigenotoxic and Anticarcinogenic Activities of Solanum lycocarpum Fruits Glycoalkaloidic Extract 
PLoS ONE  2014;9(11):e111999.
The fruits of Solanum lycocarpum, known as wolf-fruit, are used in folk medicine, and because of that we have evaluated both the genotoxic potential of its glycoalkaloidic extract (SL) and its influence on the genotoxicity induced by methyl methanesulfonate. Furthermore, the potential blocking effect of SL intake in the initial stage of colon carcinogenesis in Wistar rats was investigated in a short-term (4-week) bioassay using aberrant crypt foci (ACF) as biomarker. The genotoxic potential was evaluated using the Swiss mice peripheral blood micronucleus test. The animals were treated with different doses of SL (15, 30 and 60 mg/kg b.w.) for 14 days, and the peripheral blood samples were collected at 48 h, 7 days and 14 days after starting the treatment. For antigenotoxicity assessment, MMS was administered on the 14th day, and after 24 h the harvesting of bone marrow and liver cells was performed, for the micronucleus and comet assays, respectively. In the ACF assay, male Wistar rats were given four subcutaneous injections of the carcinogen 1,2-dimethylhydrazine (DMH, 40 mg/kg b.w.), twice a week, during two weeks to induce ACF. The treatment with SL (15, 30 and 60 mg/kg b.w.) was given for four weeks during and after carcinogen treatment to investigate the potential beneficial effects of SL on DMH-induced ACF. The results demonstrated that SL was not genotoxic in the mouse micronucleus test. In animals treated with SL and MMS, the frequencies of micronucleus and extensions of DNA damage were significantly reduced in comparison with the animals receiving only MMS. Regarding the ACF assay, SL significantly reduced the frequency of ACF induced by DMH.
doi:10.1371/journal.pone.0111999
PMCID: PMC4236050  PMID: 25405606
3.  Induction of Homologous Recombination Following in utero Exposure to DNA-Damaging Agents 
DNA repair  2013;12(11):912-921.
Much of our understanding of homologous recombination, as well as the development of the working models for these processes, has been derived from extensive work in model organisms, such as yeast and fruit flies, and mammalian systems by studying the repair of induced double strand breaks or repair following exposure to genotoxic agents in vitro. We therefore set out to expand this in vitro work to ask whether DNA-damaging agents with varying modes of action could induce somatic change in an in vivo mouse model of homologous recombination. We exposed pregnant dams to DNA-damaging agents, conferring a variety of lesions at a specific time in embryo development. To monitor homologous recombination frequency, we used the well-established retinal pigment epithelium pink-eyed unstable assay. Homologous recombination resulting in the deletion of a duplicated 70 kb fragment in the coding region of the Oca2 gene renders this gene functional and can be visualized as a pigmented eyespot in the retinal pigment epithelium. We observed an increased frequency of pigmented eyespots in resultant litters following exposure to cisplatin, methyl methanesulfonate, ethyl methanesulfonate, 3-aminobenzamide, bleomycin, and etoposide with a contrasting decrease in the frequency of detectable reversion events following camptothecin and hydroxyurea exposure. The somatic genomic rearrangements that result from such a wide variety of differently acting damaging agents implies long-term potential effects from even short-term in utero exposures.
doi:10.1016/j.dnarep.2013.08.005
PMCID: PMC4059048  PMID: 24029142
Homologous recombination; DNA damaging agents; mouse; pink-eyed unstable; in utero exposure; in vivo
4.  Hyperactivation of PARP Triggers Nonhomologous End-Joining in Repair-Deficient Mouse Fibroblasts 
PLoS ONE  2012;7(11):e49301.
Regulation of poly(ADP-ribose) (PAR) synthesis and turnover is critical to determining cell fate after genotoxic stress. Hyperactivation of PAR synthesis by poly(ADP-ribose) polymerase-1 (PARP-1) occurs when cells deficient in DNA repair are exposed to genotoxic agents; however, the function of this hyperactivation has not been adequately explained. Here, we examine PAR synthesis in mouse fibroblasts deficient in the base excision repair enzyme DNA polymerase β (pol β). The extent and duration of PARP-1 activation was measured after exposure to either the DNA alkylating agent, methyl methanesulfonate (MMS), or to low energy laser-induced DNA damage. There was strong DNA damage-induced hyperactivation of PARP-1 in pol β nullcells, but not in wild-type cells. In the case of MMS treatment, PAR synthesis did not lead to cell death in the pol β null cells, but instead resulted in increased PARylation of the nonhomologous end-joining (NHEJ) protein Ku70 and increased association of Ku70 with PARP-1. Inhibition of the NHEJ factor DNA-PK, under conditions of MMS-induced PARP-1 hyperactivation, enhanced necrotic cell death. These data suggest that PARP-1 hyperactivation is a protective mechanism triggering the classical-NHEJ DNA repair pathway when the primary alkylated base damage repair pathway is compromised.
doi:10.1371/journal.pone.0049301
PMCID: PMC3492265  PMID: 23145148
5.  Comparative Study of the Clastogenicity of Functionalized and Non-functionalized Multi-walled Carbon Nanotubes in Bone Marrow Cells of Swiss-Webster Mice 
Environmental toxicology  2010;25(6):608-621.
The development of nanotechnologies may lead to environmental release of nanomaterials that are potentially harmful to human health. Among the nanomaterials, multi walled carbon nanotubes (MWCNTs) are already commercialized in various products which can be in direct contact with populations. However, few studies address their potential toxicity. Although a few reports on the cytotoxicity of carbon nanotubes (CNTs) have been published, very little is known about their toxicity or genotoxicity in mammalian cells. We have for the first time compared the clastogenic/genotoxic potential of functionalized and non-functionalized MWCNTs in bone marrow cells of Swiss-Webster mice; using mitotic index (MI), chromosome aberrations (CA), micronuclei (MN) formation, and DNA damage in leukocytes as toxicologic endpoints. Six groups of five male mice, each weighing approximately 30 ± 2 g, were administered intraperitoneally, once a day for five days with doses of 0.25, 0.5, 0.75, mg/kg body weight (BW) of functionalized and non-functionalized MWCNTs. Four vehicle control groups (negative) and a positive control group (carbon black) were also made of 5 mice each. Chromosome and micronuclei from bone marrow cells and comet slides from leukocytes were examined following standard protocols. The results demonstrated that MWCNTs exposure significantly increased (p<0.05) the number of structural chromosomal aberrations, the frequency of micro-nucleated cells and the level of DNA damage, and decreased the mitotic index in treated groups compared to control groups. MWCNTs were shown to be toxic at sufficiently high concentrations, however purified functionalized MWCNTs had a higher clastogenic/genotoxic potential compared to non-functionalized form of MWCNT. The results of our study suggest that exposure to MWCNT has the potential to cause genetic damage. Hence, careful monitoring should be done with respect to designing/synthesing biocompatible carbon nanomaterials. Further characterization of their systemic toxicity, genotoxicity and carcinogenicity is also essential.
doi:10.1002/tox.20621
PMCID: PMC2944913  PMID: 20549644
multiwalled carbon nanotubes; bone marrow cells; leukocytes; Swiss-Webster mice; chromosomal aberrations; micronucleus formation; mitotic index; Comet assay; DNA damage
6.  Protective effect of Triphala Rasayana against paracetamol-induced hepato–renal toxicity in mice 
Background:
Paracetamol, a widely used analgesic and antipyretic, is known to cause liver and renal injury in humans when administered in higher and repeated doses that cause acute liver injury. Triphala is a well-known Ayurvedic Rasayana formulation that is prescribed for balancing of Vata, Pitta and Kapha. Traditionally, it is used for the treatment of liver and kidney diseases.
Objective:
The present study was undertaken to examine the protective effect of Triphala extract against paracetamol-induced hepato–renal injury in Swiss albino mice.
Materials and Methods:
Swiss albino mice (weight 20–25 g) were used in this study. The mice were divided into five groups of six animals each. The aqueous extract of Triphala was given orally at two different doses (100 and 300 mg/kg body weight) for seven consecutive days, followed by a single intraperitoneal injection of paracetamol (500 mg/kg body weight) to induce hepato–renal toxicity. Serum levels of liver enzymes, aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP), bilirubin, creatinine, urea and uric acid were measured as indices of liver and renal injury. All the statistical analyses were performed with the help of one-way analysis of variance (ANOVA) followed by Student–Newman–Keuls test as post hoc test. Results were considered statistically significant when P < 0.05.
Results:
Pre-treatment with Triphala extract at 100 mg/kg and 300 mg/kg body weight exhibited a significant (P < 0.01) hepatoprotective activity. The protective effect of Triphala extract at 300 mg/kg body weight appears more effective than 100 mg/kg body weight.
Conclusion:
The present study gives an evidence of the protective role of Triphala extract against paracetamol-induced hepato–renal toxicity and validates its traditional claim in the Ayurveda system.
doi:10.4103/0975-9476.146553
PMCID: PMC4630692  PMID: 26604553
Ayurveda; kidney; liver; paracetamol; Triphala
7.  XRCC1 Deficiency Sensitizes Human Lung Epithelial Cells to Genotoxicity by Crocidolite Asbestos and Libby Amphibole 
Environmental Health Perspectives  2010;118(12):1707-1713.
Background: Asbestos induces DNA and chromosomal damage, but the DNA repair pathways protecting human cells against its genotoxicity are largely unknown. Polymorphisms in XRCC1 have been associated with altered susceptibility to asbestos-related diseases. However, it is unclear whether oxidative DNA damage repaired by XRCC1 contributes to asbestos-induced chromosomal damage.
Objectives: We sought to examine the importance of XRCC1 in protection against genotoxic effects of crocidolite and Libby amphibole asbestos.
Methods: We developed a genetic model of XRCC1 deficiency in human lung epithelial H460 cells and evaluated genotoxic responses to carcinogenic fibers (crocidolite asbestos, Libby amphibole) and nongenotoxic materials (wollastonite, titanium dioxide).
Results: XRCC1 knockdown sensitized cells to the clastogenic and cytotoxic effects of oxidants [hydrogen peroxide (H2O2), bleomycin] but not to the nonoxidant paclitaxel. XRCC1 knockdown strongly enhanced genotoxicity of amphibole fibers as evidenced by elevated formation of clastogenic micronuclei. Crocidolite induced primarily clastogenic micronuclei, whereas Libby amphibole induced both clastogenic and aneugenic micronuclei. Crocidolite and bleomycin were potent inducers of nuclear buds, which were enhanced by XRCC1 deficiency. Libby amphibole and H2O2 did not induce nuclear buds, irrespective of XRCC1 status. Crocidolite and Libby amphibole similarly activated the p53 pathway.
Conclusions: Oxidative DNA damage repaired by XRCC1 (oxidized bases, single-strand breaks) is a major cause of chromosomal breaks induced by crocidolite and Libby amphibole. Nuclear buds are a novel biomarker of genetic damage induced by exposure to crocidolite asbestos, which we suggest are associated with clustered DNA damage. These results provide mechanistic evidence for the epidemiological association between XRCC1 polymorphisms and susceptibility to asbestos-related disease.
Editor's Summary
Pathways involved in the repair of asbestos-induced DNA damage are largely unknown, but XRCC1 polymorphisms that may influence the efficacy of DNA repair have been associated with susceptibility to asbestos-related diseases. Pietruska et al. (p. 1707) examined the role of XRCC1 in genotoxic effects of crocidolite and Libby amphibole asbestos in normal and XRCC1-deficient human lung epithelial H460 cells. The authors report that oxidative DNA damage, including oxidized bases and single-strand breaks, was increased following asbestos exposure in XRCC1-deficient cells compared with control cells, and was a major cause of chromosomal breaks induced by crocidolite and Libby amphibole. Nuclear buds, a possible marker of clustered DNA damage, were induced by crocidolite asbestos but not Libby amphibole. The authors conclude that their findings provide mechanistic support for epidemiologic evidence linking XRCC1 polymorphisms and susceptibility to asbestos-related disease.
doi:10.1289/ehp.1002312
PMCID: PMC3205592  PMID: 20705543
asbestos; crocidolite; DNA breaks; DNA repair; Libby amphibole; micronuclei; nuclear buds; XRCC1
8.  Is the Comet Assay a Sensitive Procedure for Detecting Genotoxicity? 
Journal of Nucleic Acids  2010;2010:541050.
Although the Comet assay, a procedure for quantitating DNA damage in mammalian cells, is considered sensitive, it has never been ascertained that its sensitivity is higher than the sensitivity of other genotoxicity assays in mammalian cells. To determine whether the power of the Comet assay to detect a low level of genotoxic potential is superior to those of other genotoxicity assays in mammalian cells, we compared the results of Comet assay with those of micronucleus test (MN test). WTK1 human lymphoblastoid cells were exposed to methyl nitrosourea (MNU), ethyl nitrosourea (ENU), methyl methanesulfonate (MMS), ethyl methanesulfonate (EMS), bleomycin (BLM), or UVC. In Comet assay, cells were exposed to each mutagen with (Comet assay/araC) and without (Comet assay) DNA repair inhibitors (araC and hydroxyurea). Furthermore, acellular Comet assay (acellular assay) was performed to determine how single-strand breaks (SSBs) as the initial damage contributes to DNA migration and/or to micronucleus formation. The lowest genotoxic dose (LGD), which is defined as the lowest dose at which each mutagen causes a positive response on each genotoxicity assay, was used to compare the power of the Comet assay to detect a low level of genotoxic potential and that of MN test; that is, a low LGD indicates a high power. Results are summarized as follows: (1) for all mutagens studied, LGDs were MN test ≦ Comet assay; (2) except for BLM, LGDs were Comet assay/araC ≦ MN test; (3) except for UVC and MNU, LGDs were acellular assay ≦ Comet assay/araC ≦ MN test ≦ Comet assay. The following is suggested by the present findings: (1) LGD in the Comet assay is higher than that in MN test, which suggests that the power of the MN test to detect a low level of genotoxic potential is superior to that of the Comet assay; (2) for the studied mutagens, all assays were able to detect all mutagens correctly, which suggests that the sensitivity of the Comet assay and that of the MN test were exactly identical; (3) the power of the Comet assay to detect a low level of genotoxic potential can be elevated to a level higher than that of MN test by using DNA resynthesis inhibitors, such as araC and HU.
doi:10.4061/2010/541050
PMCID: PMC2967831  PMID: 21052491
9.  Repression of mutagenesis by Rad51D-mediated homologous recombination 
Nucleic Acids Research  2006;34(5):1358-1368.
Homologous recombinational repair (HRR) restores chromatid breaks arising during DNA replication and prevents chromosomal rearrangements that can occur from the misrepair of such breaks. In vertebrates, five Rad51 paralogs are identified that contribute in a nonessential but critical manner to HRR proficiency. We constructed and characterized a knockout of the paralog Rad51D in widely studied CHO cells. The rad51d mutant (clone 51D1) displays sensitivity to a diverse spectrum of induced DNA damage including γ-rays, ultraviolet (UV)-C radiation, and methyl methanesulfonate (MMS), indicating the broad relevance of HRR to genotoxicity. Spontaneous chromatid breaks/gaps and isochromatid breaks are elevated 3- to 12-fold, but the chromosome number distribution remains unchanged. Most importantly, 51D1 cells exhibit a 12-fold-increased rate of hprt mutation, as well as 4- to 10-fold increased rates of gene amplification at the dhfr and CAD loci, respectively. Xrcc3 irs1SF cells from the same parental CHO line show similarly elevated mutagenesis at these three loci. Collectively, these results confirm the a priori expectation that HRR acts in an error-free manner to repress three classes of genetic alterations (chromosomal aberrations, loss of gene function and increased gene expression), all of which are associated with carcinogenesis.
doi:10.1093/nar/gkl020
PMCID: PMC1390685  PMID: 16522646
10.  Up-regulation of base excision repair correlates with enhanced protection against a DNA damaging agent in mouse cell lines. 
Nucleic Acids Research  1998;26(8):2001-2007.
DNA polymerase beta is required in mammalian cells for the predominant pathway of base excision repair involving single nucleotide gap filling DNA synthesis. Here we examine the relationship between oxidative stress, cellular levels of DNA polymerase beta and base excision repair capacity in vitro , using mouse monocytes and either wild-type mouse fibroblasts or those deleted of the DNA polymerase beta gene. Treatment with an oxidative stress-inducing agent such as hydrogen peroxide, 3-morpholinosydnonimine, xanthine/xanthine oxidase or lipopolysaccharide was found to increase the level of DNA polymerase beta in both monocytes and fibroblasts. Base excision repair capacity in vitro , as measured in crude cell extracts, was also increased by lipopolysaccharide treatment in both cell types. In monocytes lipopolysaccharide-mediated up-regulation of the base excision repair system correlated with increased resistance to the monofunctional DNA alkylating agent methyl methanesulfonate. By making use of a quantitative PCR assay to detect lesions in genomic DNA we show that lipopolysaccharide treatment of fibroblast cells reduces the incidence of spontaneous DNA lesions. This effect may be due to the enhanced DNA polymerase beta-dependent base excision repair capacity of the cells, because a similar decrease in DNA lesions was not observed in cells deficient in base excision repair by virtue of DNA polymerase beta gene deletion. Similarly, fibroblasts treated with lipopolysaccharide were more resistant to methyl methanesulfonate than untreated cells. This effect was not observed in cells deleted of the DNA polymerase beta gene. These results suggest that the DNA polymerase beta-dependent base excision repair pathway can be up-regulated by oxidative stress-inducing agents in mouse cell lines.
PMCID: PMC147493  PMID: 9518496
11.  Alkylation Base Damage Is Converted into Repairable Double-Strand Breaks and Complex Intermediates in G2 Cells Lacking AP Endonuclease 
PLoS Genetics  2011;7(4):e1002059.
DNA double-strand breaks (DSBs) are potent sources of genome instability. While there is considerable genetic and molecular information about the disposition of direct DSBs and breaks that arise during replication, relatively little is known about DSBs derived during processing of single-strand lesions, especially for the case of single-strand breaks (SSBs) with 3′-blocked termini generated in vivo. Using our recently developed assay for detecting end-processing at random DSBs in budding yeast, we show that single-strand lesions produced by the alkylating agent methyl methanesulfonate (MMS) can generate DSBs in G2-arrested cells, i.e., S-phase independent. These derived DSBs were observed in apn1/2 endonuclease mutants and resulted from aborted base excision repair leading to 3′ blocked single-strand breaks following the creation of abasic (AP) sites. DSB formation was reduced by additional mutations that affect processing of AP sites including ntg1, ntg2, and, unexpectedly, ogg1, or by a lack of AP sites due to deletion of the MAG1 glycosylase gene. Similar to direct DSBs, the derived DSBs were subject to MRX (Mre11, Rad50, Xrs2)-determined resection and relied upon the recombinational repair genes RAD51, RAD52, as well as on the MCD1 cohesin gene, for repair. In addition, we identified a novel DNA intermediate, detected as slow-moving chromosomal DNA (SMD) in pulsed field electrophoresis gels shortly after MMS exposure in apn1/2 cells. The SMD requires nicked AP sites, but is independent of resection/recombination processes, suggesting that it is a novel structure generated during processing of 3′-blocked SSBs. Collectively, this study provides new insights into the potential consequences of alkylation base damage in vivo, including creation of novel structures as well as generation and repair of DSBs in nonreplicating cells.
Author Summary
DNA double-strand breaks (DSBs) are an important source of genome instability that can lead to severe biological consequences including tumorigenesis and cell death. Although much is known about DSBs induced directly by ionizing radiation and radiomimetic cancer drugs, there is a relative dearth of information about the formation of derived DSBs that arise from processing of single-strand lesions. Since as many as 10,000–200,000 single-strand lesions have been estimated to occur each day in mammalian cells, conversion of even a small percentage of such lesions to DSBs could dramatically affect genome stability. Here we addressed the mechanism of formation and repair of derived DSBs in vivo during the processing of DNA methylation damage in yeast that are defective in base excision repair (BER) due to a lack of AP endonucleases. Armed with a technique developed in our lab that detects resection at DSBs, a first step in DSB repair, we demonstrated formation of DSBs in G2 cells and the role of recombinational repair in subsequent chromosome restitution. Furthermore, we have identified a novel repair intermediate that can be generated if abasic sites are nicked by AP lyases, providing additional insights into the processing of 3′-blocked groups at single-strand breaks.
doi:10.1371/journal.pgen.1002059
PMCID: PMC3084215  PMID: 21552545
12.  Deletion of MAG1 and MRE11 enhances the sensitivity of the Saccharomyces cerevisiae HUG1P-GFP promoter-reporter construct to genotoxicity 
Biosensors & bioelectronics  2008;24(4):736-741.
Eukaryotic yeast-based DNA damage cellular sensors offer many advantages to traditional prokaryotic-based mutagenicity assays. The HUG1P-GFP promoter-reporter construct has proven to be an effective method to selectively screen for multiple types of DNA damage. To enhance the sensitivity and selectivity of the system to different types of DNA damage, two genes involved in distinct DNA damage responses were deleted. Deletion of MAG1, a gene encoding a DNA glycosylase and member of the base excision repair (BER) pathway, increased the biosensor's sensitivity to the alkylating agents methyl methanesulfonate (MMS) (lowering the sensitivity threshold to 0.0001% (v/v)) and ethyl methanesulfonate (EMS). Deletion of MRE11, part of the highly conserved RMX complex that aids in sensing and repairing double strand breaks in budding yeasts, enhanced sensitivity to gamma radiation (γ-ray) (detection threshold of 50 Gy) and camptothecin. The mre11Δ phenotype dominated in mag1Δ mre11Δ strains. Through the deletions, we were able to engineer increased selectivity to alkylating agents, γ-ray, and camptothecin, since increased sensitivity to one type of damage did not alter the quantitative response to other genotoxins. The enhancements to the HUG1P-GFP system did not affect its ability to detect several other DNA damaging agents, including 1,2-dimethyl hydrazine (SDMH), phleomycin, and hydroxyurea (HU), or affect its lack of response to the potentially non-genotoxic carcinogen formaldehyde.
doi:10.1016/j.bios.2008.06.033
PMCID: PMC4526160  PMID: 18693109
Saccharomyces cerevisiae; HUG1; DNA damage; Genotoxicity; DNA repair; Mutagenesis
13.  Automation and validation of micronucleus detection in the 3D EpiDerm™ human reconstructed skin assay and correlation with 2D dose responses 
Mutagenesis  2014;29(3):165-175.
Recent restrictions on the testing of cosmetic ingredients in animals have resulted in the need to test the genotoxic potential of chemicals exclusively in vitro prior to licensing. However, as current in vitro tests produce some misleading positive results, sole reliance on such tests could prevent some chemicals with safe or beneficial exposure levels from being marketed. The 3D human reconstructed skin micronucleus (RSMN) assay is a promising new in vitro approach designed to assess genotoxicity of dermally applied compounds. The assay utilises a highly differentiated in vitro model of the human epidermis. For the first time, we have applied automated micronucleus detection to this assay using MetaSystems Metafer Slide Scanning Platform (Metafer), demonstrating concordance with manual scoring. The RSMN assay’s fixation protocol was found to be compatible with the Metafer, providing a considerably shorter alternative to the recommended Metafer protocol. Lowest observed genotoxic effect levels (LOGELs) were observed for mitomycin-C at 4.8 µg/ml and methyl methanesulfonate (MMS) at 1750 µg/ml when applied topically to the skin surface. In-medium dosing with MMS produced a LOGEL of 20 µg/ml, which was very similar to the topical LOGEL when considering the total mass of MMS added. Comparisons between 3D medium and 2D LOGELs resulted in a 7-fold difference in total mass of MMS applied to each system, suggesting a protective function of the 3D microarchitecture. Interestingly, hydrogen peroxide (H2O2), a positive clastogen in 2D systems, tested negative in this assay. A non-genotoxic carcinogen, methyl carbamate, produced negative results, as expected. We also demonstrated expression of the DNA repair protein N-methylpurine-DNA glycosylase in EpiDerm™. Our preliminary validation here demonstrates that the RSMN assay may be a valuable follow-up to the current in vitro test battery, and together with its automation, could contribute to minimising unnecessary in vivo tests by reducing in vitro misleading positives.
doi:10.1093/mutage/geu011
PMCID: PMC3983754  PMID: 24675152
14.  Inducible Protective Processes in Animal Systems XIII: Comparative Analysis of Induction of Adaptive Response by EMS and MMS in Ehrlich Ascites Carcinoma Cells 
Scientifica  2014;2014:703136.
In order to investigate the presence of adaptive response in cancerous cells, two monofunctional alkylating agents, namely, ethyl methanesulfonate (EMS) and methyl methanesulfonate (MMS), were employed to treat Ehrlich ascites carcinoma (EAC) cells in vivo. Conditioning dose of 80 mg/kg body weight of EMS or 50 mg/kg body weight of MMS and challenging dose of 240 mg/kg body weight of EMS or 150 mg/kg body weight of MMS were selected by pilot toxicity studies. Conditioned EAC cells when challenged after 8 h time lag resulted in significant reduction in chromosomal aberrations compared to challenging dose of respective agents. As has been proved in earlier studies with normal organisms, even in cancerous cells (EAC), there is presence of adaptive response to methylating and ethylating agents. Furthermore, it is also interesting to note in the present studies that the methylating agent, MMS, is a stronger inducer of the adaptive response than the ethylating agent, EMS.
doi:10.1155/2014/703136
PMCID: PMC4066937  PMID: 24999435
15.  Apn1 and Apn2 endonucleases prevent accumulation of repair-associated DNA breaks in budding yeast as revealed by direct chromosomal analysis 
Nucleic Acids Research  2008;36(6):1836-1846.
Base excision repair (BER) provides relief from many DNA lesions. While BER enzymes have been characterized biochemically, BER functions within cells are much less understood, in part because replication bypass and double-strand break (DSB) repair can also impact resistance to base damage. To investigate BER in vivo, we examined the repair of methyl methanesulfonate (MMS) induced DNA damage in haploid G1 yeast cells, so that replication bypass and recombinational DSB repair cannot occur. Based on the heat-lability of MMS-induced base damage, an assay was developed that monitors secondary breaks in full-length yeast chromosomes where closely spaced breaks yield DSBs that are observed by pulsed-field gel electrophoresis. The assay detects damaged bases and abasic (AP) sites as heat-dependent breaks as well as intermediate heat-independent breaks that arise during BER. Using a circular chromosome, lesion frequency and repair kinetics could be easily determined. Monitoring BER in single and multiple glycosylase and AP-endonuclease mutants confirmed that Mag1 is the major enzyme that removes MMS-damaged bases. This approach provided direct physical evidence that Apn1 and Apn2 not only repair cellular base damage but also prevent break accumulation that can result from AP sites being channeled into other BER pathway(s).
doi:10.1093/nar/gkm1148
PMCID: PMC2346603  PMID: 18267974
16.  Functional Interplay of the Mre11 Nuclease and Ku in the Response to Replication-Associated DNA Damage ▿  
Molecular and Cellular Biology  2011;31(21):4379-4389.
The Mre11 complex is a central component of the DNA damage response, with roles in damage sensing, molecular bridging, and end resection. We have previously shown that in Saccharomyces cerevisiae, Ku70 (yKu70) deficiency reduces the ionizing radiation sensitivity of mre11Δ mutants. In this study, we show that yKu70 deficiency suppressed the camptothecin (CPT) and methyl methanesulfonate (MMS) sensitivity of nuclease-deficient mre11-3 and sae2Δ mutants in an Exo1-dependent manner. CPT-induced G2/M arrest, γ-H2AX persistence, and chromosome breaks were elevated in mre11-3 mutants. These outcomes were reduced by yKu70 deficiency. Given that the genotoxic effects of CPT are manifest during DNA replication, these data suggest that Ku limits Exo1-dependent double-strand break (DSB) resection during DNA replication, inhibiting the initial processing steps required for homology-directed repair. We propose that Mre11 nuclease- and Sae2-dependent DNA end processing, which initiates DSB resection prevents Ku from engaging DSBs, thus promoting Exo1-dependent resection. In agreement with this idea, we show that Ku affinity for binding to short single-stranded overhangs is much lower than for blunt DNA ends. Collectively, the data define a nonhomologous end joining (NHEJ)-independent, S-phase-specific function of the Ku heterodimer.
doi:10.1128/MCB.05854-11
PMCID: PMC3209331  PMID: 21876003
17.  Molecular analysis of ethyl methanesulfonate-induced reversion of a chromosomally integrated mutant shuttle vector gene in mammalian cells. 
Molecular and Cellular Biology  1988;8(10):4185-4189.
The molecular mechanisms of ethyl methanesulfonate-induced reversion in mammalian cells were studied by using as a target a gpt gene that was integrated chromosomally as part of a shuttle vector. Murine cells containing mutant gpt genes with single base changes were mutagenized with ethyl methanesulfonate, and revertant colonies were isolated. Ethyl methanesulfonate failed to increase the frequency of revertants for cell lines with mutant gpt genes carrying GC----AT transitions or AT----TA transversions, whereas it increased the frequency 50-fold to greater than 800-fold for cell lines with mutant gpt genes carrying AT----GC transitions and for one cell line with a GC----CG transversion. The gpt genes of 15 independent revertants derived from the ethyl methanesulfonate-revertible cell lines were recovered and sequenced. All revertants derived from cell lines with AT----GC transitions had mutated back to the wild-type gpt sequence via GC----AT transitions at their original sites of mutation. Five of six revertants derived from the cell line carrying a gpt gene with a GC----CG transversion had mutated via GC----AT transition at the site of the original mutation or at the adjacent base in the same triplet; these changes generated non-wild-type DNA sequences that code for non-wild-type amino acids that are apparently compatible with xanthine-guanine phosphoribosyltransferase activity. The sixth revertant had mutated via CG----GC transversion back to the wild-type sequence. The results of this study define certain amino acid substitutions in the xanthine-guanine phosphoribosyltransferase polypeptide that are compatible with enzyme activity. These results also establish mutagen-induced reversion analysis as a sensitive and specific assay for mutagenesis in mammalian cells.
PMCID: PMC365488  PMID: 3185546
18.  The SUMO Isopeptidase Ulp2p Is Required to Prevent Recombination-Induced Chromosome Segregation Lethality following DNA Replication Stress 
PLoS Genetics  2011;7(3):e1001355.
SUMO conjugation is a key regulator of the cellular response to DNA replication stress, acting in part to control recombination at stalled DNA replication forks. Here we examine recombination-related phenotypes in yeast mutants defective for the SUMO de-conjugating/chain-editing enzyme Ulp2p. We find that spontaneous recombination is elevated in ulp2 strains and that recombination DNA repair is essential for ulp2 survival. In contrast to other SUMO pathway mutants, however, the frequency of spontaneous chromosome rearrangements is markedly reduced in ulp2 strains, and some types of rearrangements arising through recombination can apparently not be tolerated. In investigating the basis for this, we find DNA repair foci do not disassemble in ulp2 cells during recovery from the replication fork-blocking drug methyl methanesulfonate (MMS), corresponding with an accumulation of X-shaped recombination intermediates. ulp2 cells satisfy the DNA damage checkpoint during MMS recovery and commit to chromosome segregation with similar kinetics to wild-type cells. However, sister chromatids fail to disjoin, resulting in abortive chromosome segregation and cell lethality. This chromosome segregation defect can be rescued by overproducing the anti-recombinase Srs2p, indicating that recombination plays an underlying causal role in blocking chromatid separation. Overall, our results are consistent with a role for Ulp2p in preventing the formation of DNA lesions that must be repaired through recombination. At the same time, Ulp2p is also required to either suppress or resolve recombination-induced attachments between sister chromatids. These opposing defects may synergize to greatly increase the toxicity of DNA replication stress.
Author Summary
DNA damage, arising from environmental stress or errors in DNA metabolism, can interfere with DNA replication. Cells respond by using homologous recombination to bypass the damage, resulting in DNA strand linkages between the replicated chromosomes. It is crucial to undo these linkages so chromosomes can segregate properly. Previously, a regulatory mechanism known as SUMO modification was shown to be important in controlling recombination following replication interference by the DNA damaging agent MMS. We show that mutations in a yeast enzyme called Ulp2p, which reverses SUMO modification, increase recombination and impose a requirement for recombination to maintain survival. MMS–treated ulp2 mutants also accumulate recombination intermediates and fail to separate their chromosomes, leading to a permanent block to cell division. Further analysis suggests this block may not simply be due to a failure to resolve recombination intermediates, but may reflect a role for Ulp2p in undoing additional chromosome attachments that accompany recombination. In sum, our data indicate that cells defective for Ulp2p develop a love/hate relationship with recombination, requiring recombination for viability while failing to resolve chromosome attachments induced by recombination repair. Identification of Ulp2p substrates that ensure chromosome separation following recombination will shed light on how SUMO modification maintains genome stability.
doi:10.1371/journal.pgen.1001355
PMCID: PMC3069114  PMID: 21483811
19.  Functional interactions between BLM and XRCC3 in the cell 
The Journal of Cell Biology  2007;179(1):53-63.
Bloom's syndrome (BS), which is caused by mutations in the BLM gene, is characterized by a predisposition to a wide variety of cancers. BS cells exhibit elevated frequencies of sister chromatid exchanges (SCEs), interchanges between homologous chromosomes (mitotic chiasmata), and sensitivity to several DNA-damaging agents. To address the mechanism that confers these phenotypes in BS cells, we characterize a series of double and triple mutants with mutations in BLM and in other genes involved in repair pathways. We found that XRCC3 activity generates substrates that cause the elevated SCE in blm cells and that BLM with DNA topoisomerase IIIα suppresses the formation of SCE. In addition, XRCC3 activity also generates the ultraviolet (UV)- and methyl methanesulfonate (MMS)–induced mitotic chiasmata. Moreover, disruption of XRCC3 suppresses MMS and UV sensitivity and the MMS- and UV-induced chromosomal aberrations of blm cells, indicating that BLM acts downstream of XRCC3.
doi:10.1083/jcb.200702183
PMCID: PMC2064734  PMID: 17923529
20.  Functional Specialization of Chlamydomonas reinhardtii Cytosolic Thioredoxin h1 in the Response to Alkylation-Induced DNA Damage 
Eukaryotic Cell  2005;4(2):262-273.
DNA damage occurs as a by-product of intrinsic cellular processes, like DNA replication, or as a consequence of exposure to genotoxic agents. Organisms have evolved multiple mechanisms to avoid, tolerate, or repair DNA lesions. To gain insight into these processes, we have isolated mutants hypersensitive to DNA-damaging agents in the green alga Chlamydomonas reinhardtii. One mutant, Ble-1, showed decreased survival when it was treated with methyl methanesulfonate (MMS), bleomycin, or hydrogen peroxide (H2O2) but behaved like the wild type when it was exposed to UVC irradiation. Ble-1 carries an extensive chromosomal deletion that includes the gene encoding cytosolic thioredoxin h1 (Trxh1). Transformation of Ble-1 with a wild-type copy of Trxh1 fully corrected the MMS hypersensitivity and partly restored the tolerance to bleomycin. Trxh1 also complemented a defect in the repair of MMS-induced DNA strand breaks and alkali-labile sites. In addition, a Trxh1-β-glucuronidase fusion protein translocated to the nucleus in response to treatment with MMS. However, somewhat surprisingly, Trxh1 failed to correct the Ble-1 hypersensitivity to H2O2. Moreover, Trxh1 suppression by RNA interference in a wild-type strain resulted in enhanced sensitivity to MMS and DNA repair defects but no increased cytotoxicity to H2O2. Thioredoxins have been implicated in oxidative-stress responses in many organisms. Yet our results indicate a specific role of Chlamydomonas Trxh1 in the repair of MMS-induced DNA damage, whereas it is dispensable for the response to H2O2. These observations also suggest functional specialization among cytosolic thioredoxins since another Chlamydomonas isoform (Trxh2) does not compensate for the lack of Trxh1.
doi:10.1128/EC.4.2.262-273.2005
PMCID: PMC549321  PMID: 15701788
21.  OA01.16. Effects of drakshavaleha on weight and crown-rump length in developing mice embryo 
Ancient Science of Life  2012;32(Suppl 1):S16.
Purpose:
Cyclophosphamide (CP) causes stunting in size and loss of body weight of the pups when injected intra-peritoneal (10 mg/kg) to pregnant mice on day 11 of gestation. Due to anti-anaemic properties and nutritional values, Drakshavaleha has been used as a Naimittika Rasayana (promoter of specific vitality in specific disease) by some of the Ayurvedic physicians in Rajasthan to a woman during her pregnancy expecting a good health of both mother and her offspring. The objective of the study was to investigate the protective effect of Drakshavaleha against CP induced growth retardation in mice pups in the terms of body weight and CR (crown-rump) length.
Method:
Group I (Control): Pregnant mice (n=10) received 0.2 ml of vehicle (distilled water) intra-peritoneal on day 11 of pregnancy. Group II (Drakshavaleha): Pregnant mice (n=10) received Drakshavaleha (16g/kg) orally from day ‘0’ to day ‘18’ of pregnancy. Group III (CP): Pregnant mice (n=10) received Cyclophosphamide (10mg/kg) intra-peritoneal on day 11 of pregnancy. Group IV (CP + Drakshavaleha): Pregnant mice (n=10) received CP (10mg/kg) intra-peritoneal on day 11 under cover of Drakshavaleha (16 g/kg) orally from day ‘0 to day 18’ of pregnancy.
Result :
Drakshavaleha (alone) increases the size and weight of the pups when given to mother mice during gestation period and the difference between the two groups (Group III and Group IV) is statistically significant (p<0.001).
Conclusion:
In the present context Drakshavaleha can be conceived to be a Naimittika Rasayana to a woman during her pregnancy to obtain a healthy progeny.
PMCID: PMC3800892
22.  A Novel Approach Using DNA-Repair–Deficient Chicken DT40 Cell Lines for Screening and Characterizing the Genotoxicity of Environmental Contaminants 
Environmental Health Perspectives  2009;117(11):1737-1744.
Background
Many bacterial or mammalian cell-based test systems, such as the Ames test, chromosomal aberration assays, or gene mutation assays, are commonly used in developed countries to detect the genotoxicity of industrial chemicals. However, the specificity is generally limited and the sensitivity is not sufficiently high. In addition, most assays cannot provide information on mechanisms of genotoxicity of a given chemical.
Objectives
We aimed to establish a sensitive and fast screening method that is also capable of characterizing mechanisms of genotoxicity.
Methods
We developed a novel bioassay employing gene-disrupted clones of the chicken DT40 B-lymphocyte line, which are designed to be deficient in several specific DNA repair pathways. Genotoxic chemicals can delay cellular proliferation in DNA-repair–deficient clones more significantly than in wild-type cells by interfering with DNA replication, thereby inducing DNA damage. In addition, we verified the validity of this assay by analyzing the genotoxicity of γ-rays, ultraviolet (UV) light, and sodium metaarsenite (NaAsO2). We also characterized DNA lesions induced by NaAsO2.
Results
Genotoxicity of given stressors was successfully screened based on a comparison of proliferation kinetics between wild-type and DNA-repair–deficient mutants in 48 hr. We also found that NaAsO2 apparently induces at least two types of damage: chromosomal breaks and UV photoproduct-like DNA lesions.
Conclusion
This bioassay is a reliable and sensitive screening tool for environmental mutagens as well as for further characterizing the nature of detected genotoxicity.
doi:10.1289/ehp.0900842
PMCID: PMC2801191  PMID: 20049126
alternative test methods development; arsenic; DNA repair; genotoxicity; high-throughput testing; UV radiation
23.  Roles of Vertebrate Smc5 in Sister Chromatid Cohesion and Homologous Recombinational Repair ▿ 
Molecular and Cellular Biology  2011;31(7):1369-1381.
The structural maintenance of chromosomes (Smc) family members Smc5 and Smc6 are both essential in budding and fission yeasts. Yeast smc5/6 mutants are hypersensitive to DNA damage, and Smc5/6 is recruited to HO-induced double-strand breaks (DSBs), facilitating intersister chromatid recombinational repair. To determine the role of the vertebrate Smc5/6 complex during the normal cell cycle, we generated an Smc5-deficient chicken DT40 cell line using gene targeting. Surprisingly, Smc5− cells were viable, although they proliferated more slowly than controls and showed mitotic abnormalities. Smc5-deficient cells were sensitive to methyl methanesulfonate and ionizing radiation (IR) and showed increased chromosome aberration levels upon irradiation. Formation and resolution of Rad51 and gamma-H2AX foci after irradiation were altered in Smc5 mutants, suggesting defects in homologous recombinational (HR) repair of DNA damage. Ku70−/− Smc5− cells were more sensitive to IR than either single mutant, with Rad54−/− Smc5− cells being no more sensitive than Rad54−/− cells, consistent with an HR function for the vertebrate Smc5/6 complex. Although gene targeting occurred at wild-type levels, recombinational repair of induced double-strand breaks was reduced in Smc5− cells. Smc5 loss increased sister chromatid exchanges and sister chromatid separation distances in mitotic chromosomes. We conclude that Smc5/6 regulates recombinational repair by ensuring appropriate sister chromatid cohesion.
doi:10.1128/MCB.00786-10
PMCID: PMC3135288  PMID: 21245390
24.  Requirement of the Saccharomyces cerevisiae APN1 Gene for the Repair of Mitochondrial DNA Alkylation Damage 
The Saccharomyces cerevisiae APN1 gene that participates in base excision repair has been localized both in the nucleus and the mitochondria. APN1 deficient cells (apn1Δ) show increased mutation frequencies in mitochondrial DNA (mtDNA) suggesting that APN1 is also important for mtDNA stability. To understand APN1-dependent mtDNA repair processes we studied the formation and repair of mtDNA lesions in cells exposed to methyl methanesulfonate (MMS). We show that MMS induces mtDNA damage in a dose-dependent fashion and that deletion of the APN1 gene enhances the susceptibility of mtDNA to MMS. Repair kinetic experiments demonstrate that in wild-type cells (WT) it takes 4 hr to repair the damage induced by 0.1% MMS, whereas in the apn1Δ strain there is a lag in mtDNA repair that results in significant differences in the repair capacity between the two yeast strains. Analysis of lesions in nuclear DNA (nDNA) after treatment with 0.1% MMS shows a significant difference in the amount of nDNA lesions between WT and apn1Δ cells. Interestingly, comparisons between nDNA and mtDNA damage show that nDNA is more sensitive to the effects of MMS treatment. However, both strains are able to repair the nDNA lesions, contrary to mtDNA repair, which is compromised in the apn1Δ mutant strain. Therefore, although nDNA is more sensitive than mtDNA to the effects of MMS, deletion of APN1 has a stronger phenotype in mtDNA repair than in nDNA. These results highlight the prominent role of APN1 in the repair of environmentally induced mtDNA damage.
doi:10.1002/em.20462
PMCID: PMC2858446  PMID: 19197988
base excision repair; mitochondrial DNA; alkylating agent
25.  Histone H3 Lysine 56 Acetylation and the Response to DNA Replication Fork Damage 
Molecular and Cellular Biology  2012;32(1):154-172.
In Saccharomyces cerevisiae, histone H3 lysine 56 acetylation (H3K56ac) occurs in newly synthesized histones that are deposited throughout the genome during DNA replication. Defects in H3K56ac sensitize cells to genotoxic agents, suggesting that this modification plays an important role in the DNA damage response. However, the links between histone acetylation, the nascent chromatin structure, and the DNA damage response are poorly understood. Here we report that cells devoid of H3K56ac are sensitive to DNA damage sustained during transient exposure to methyl methanesulfonate (MMS) or camptothecin but are only mildly affected by hydroxyurea. We demonstrate that, after exposure to MMS, H3K56ac-deficient cells cannot complete DNA replication and eventually segregate chromosomes with intranuclear foci containing the recombination protein Rad52. In addition, we provide evidence that these phenotypes are not due to defects in base excision repair, defects in DNA damage tolerance, or a lack of Rad51 loading at sites of DNA damage. Our results argue that the acute sensitivity of H3K56ac-deficient cells to MMS and camptothecin stems from a failure to complete the repair of specific types of DNA lesions by recombination and/or from defects in the completion of DNA replication.
doi:10.1128/MCB.05415-11
PMCID: PMC3255698  PMID: 22025679

Results 1-25 (1055360)