Random Amplified Polymorphic DNA Profiles Research Articles

Use of random amplified polymorphic DNA (RAPD) to detect DNA damage induced by Prangos ferulacea (Umbelliferae) essential oil against the Mediterranean flour moth Ephestia kuehniella Zeller (Lepidoptera: Pyralidae)

DNA damage detection in Ephestia kuehniella by RAPD-PCR Abstract - The random amplified polymorphic DNA (RAPD) assay is a useful method for detecting genotoxin-induced DNA damage. In the present study, this assay was evaluated to measure the essential oil of Prangos ferulacea-induced DNA changes in Ephestia kuehniella Zeller larvae. The third instar larvae of E. kuehniella were exposed to 500 μl L-1 essential oil for 24 h. Forty random primers were used for RAPD-PCR of which eleven produced unique polymorphic band patterns. In comparison with control larvae, the essential oil-treated larvae showed greater changes in RAPD profiles. This is the first report of an analysis of the genotoxic effect of P. ferulacea essential oil against E. kuehniella larvae using RAPD-PCR.

Genotoxicity of Thermopsis turcica on Allium cepa L. roots revealed by alkaline comet and random amplified polymorphic DNA assays.

This study was undertaken to evaluate genotoxic potential of Thermopsis turcica aqueous extracts on the roots of onion bulb (Allium cepa L.) by comet assay and random amplified polymorphic DNA technique. The Allium root growth inhibition test indicated that the EC50 and 2×EC50 values were 8 and 16mg/ml concentrations of T. turcica aqueous extracts, respectively. The negative control (distilled water), positive control (methyl methane sulfonate, 10mg/l) and 8 and 16mg/ml concentrations of T. turcica extracts were introduced to the roots of onion bulbs for 24 and 96h. The root growth, DNA damage in root cells and randomly amplified polymorphic DNA (RAPD) profiles of root tissue were used as endpoints of the genotoxicity. The comet assay clearly indicated that dose-dependent single strand DNA breaks in the root nuclei of onions were determined for the treatment concentrations of T. turcica extracts. In comparison to RAPD profile of negative control group, RAPD polymorphisms became evident as disappearance and/or appearance of RAPD bands in treated roots. The diagnostic and phenetic numerical analyses of RAPD profiles obviously indicated dose-dependent genotoxicity induced by Thermopsis extracts. In conclusion, the results clearly indicated that water extract of T. turcica has genotoxic potential on the roots of onion bulbs as shown by comet assay and RAPD technique.

Aroclor 1254 May Induce Common DNA Effects in Developing Paralichthys olivaceus Embryos and Larvae

Polychlorinated biphenyls (PCBs) are persistent pollutants in aquatic environments, often causing the decline or disappearance of wild populations. In this study, we used a random amplified polymorphic DNA (RAPD) assay to evaluate the effects on the genom ic DNA of olive flounder embryo and larval stages of exposure to Aroclor 1254 at concentrations of 1, 5, 10, 20, and 40 μg/L. We compared RAPD fingerprints of exposed and non-exposed samples. Polymorphisms were revealed as the presence and/or absence of DNA fragments between the two samples. A dose-dependent increase in the number of polymorphic bands was observed with Aroclor 1254 treatment. Also, RAPD profiles of animals exposed to Aroclor 1254 exhibited an increase in the frequency values (FV) compared to the control. A phenogram constructed using neighbor-joining method indicated that genomic template stability in developing embryo and larval stages was significantly affected at ≥ 5 μg/L. This study suggested that DNA polymorphisms detected by RAPD analysis could be used as an investigative tool for environmental toxicology and as a useful biomarker in early life stages for the detection of potential genotoxicants.

Evaluation of arsenic trioxide genotoxicity in wheat seedlings using oxidative system and RAPD assays.

Arsenic is a metalloid that is toxic to living organisms. It is known that high concentration of arsenic causes toxic damage to cells and tissues of plants. While the toxic effect of arsenic is known, limited efforts have been made to study its genotoxic effect on the crops. In the present study, effects of arsenic trioxide (As2O3) on seed germination, root length, reactive oxygen species (ROS), lipid peroxidation (malondialdehyde (MDA)), and activities of antioxidant enzymes, as well as DNA in wheat seedlings were investigated. Seedlings were exposed to different (10 to 40 mg/L) As2O3 concentrations for 7 days. Seed germination and root elongation decreased with increase of As2O3 concentration. The values of hydrogen peroxide (H2O2), superoxide anion (O2 (·-)), and MDA contents significantly increased by As2O3 concentrations. The highest values for H2O2, O2 (·-), and MDA were obtained in 40 mg/L treated wheat seedling. A significant increase of peroxidase (POX) and catalase (CAT) activity in seedlings were observed with increased concentration of As2O3, then decreased when reaching a value of 40 mg/L, whereas the activities of superoxide dismutase (SOD) were gradually enhanced with increasing As2O3 concentration. Alterations of DNA in wheat seedlings were detected using randomly amplified polymorphic DNA (RAPD) technique. The changes occurring in RAPD profiles of seedlings following As2O3 treatment included loss of normal bands and appearance of new bands in comparison to that of control seedlings. The results of our study showed that As2O3 induced DNA damage in a dose-dependent meaner, and the root cells of wheat studied showed a defense against As2O3-induced oxidative stress by enhancing their antioxidant activities.

Paradevosia shaoguanensis gen. nov., sp. nov., isolated from a coking wastewater.

A Gram staining negative, rod-shaped, aerobic bacterial strain J5-3(T) with a single polar flagellum was isolated from coking wastewater collected from Shaoguan, Guangdong, China. It was motile and capable of optimal growth at pH 6-8, 30 °C, and 0-2 % (w/v) NaCl. Its predominant fatty acids were 11-methyl C18:1 ω7c (29.2 %), C16:0 (20.6 %), C19:0 cyclo ω8c (18.2 %), C18:0 (11.0 %), and C18:1 ω7c/C18:1 ω6c (10.9 %) when grown on trypticase soy agar. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unknown glycolipids (GL1, GL2), and two unknown phospholipid (PL1, PL2). The predominant ubiquinone was Q-10, and the genome DNA G+C content was 61.7 mol %. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain J5-3(T) belonged to the family Hyphomicrobiaceae in Alphaproteobacteria. It shared the 16S rRNA gene sequence similarities of 93.8-96.1 % with the genus Devosia, 94.5-94.8 % with the genus Pelagibacterium, and <92.0 % with all the other type strains in family Hyphomicrobiaceae. It can be distinguished from the closest phylogenetic neighbors based on several phenotypic and genotypic features, including α-galactosidase activity, tetracycline susceptibility, major fatty acid composition, polar lipid profile, DNA gyrase B subunit (gyrB) gene sequence, and random-amplified polymorphic DNA profile. Therefore, we consider strain J5-3(T) to represent a novel species of a novel genus within the family Hyphomicrobiaceae, for which the name Paradevosia shaoguanensis gen. nov., sp. nov. is proposed. The type strain of Paradevosia shaoguanensis is J5-3(T) (=CGMCC 1.12430(T) =LMG 27409(T)).

Genotoxic Effects of Heavy Metal Mixture in Drosophila melanogaster: Expressions of Heat Shock Proteins, RAPD Profiles and Mitochondrial DNA Sequence

The genotoxic effects of four heavy metal mixtures on Drosophila melanogaster were investigated with reference to gene expressions of heat shock proteins (HSP26, HSP60, HSP70 and HSP83), DNA profiles, and mitochondrial NADH dehydrogenase sequence. Adult D. melanogaster flies were treated with a mixture of four (Fe, Cu, Cd and Pb) heavy metals (HMs) in three different concentrations, which were selected based on one higher dose (HM3) and one lower dose (HM1) relative to the permitted limits (HM2) in drinking water at 1st, 5th and 10th days. It was determined that the amount of the accumulated heavy metals and the expressions of the HSP genes were changed with increasing exposure time. The accumulations of Cd and Pb were increased with increasing exposure time; additionally, the HSP expression patterns were determined as HSP70 > HSP60 > HSP26 > HSP83 HM1 (5th day), HM2 (5th day and 10th day), and HM3 (all exposure times). It was also determined that the application of the heavy metal mixture affected the random amplified polymorphic DNA (RAPD) profiles and the mitochondrial NADH dehydrogenase sequence of D. melanogaster. The highest base pair changes (9 bp) were determined at the HM2 concentration (permissible limits in drinking water) on the 1st day of treatment. Therefore, it was shown that mixture of four heavy metals caused a genotoxic effect and D. melanogaster is a useful model organism for heavy metal-induced genotoxicity studies.

Random amplified polymorphic DNA reveals that TiO2 nanoparticles are genotoxic to Cucurbita pepo

Titanium dioxide nanoparticles (TiO2 NPs) are used in cosmetics, sunscreens, paints, and toothpaste, among other applications. These NPs are very stable and can be transported and dispersed in wastewater and biosolids. Animal species have shown negative reactions to TiO2 NPs. However, little is known about their toxicity in plants, specifically the possibility of gen- otoxic effects. In this study, we used a random amplified polymorphic DNA (RAPD) technique to study the genotoxic effects of TiO2 NPs on hydroponically cultivated zucchini (Cucurbita pepo) plants. Seeds were allowed to germinate for 7 d and plants were selected at random for individual and population studies. Four plants were selected for the individual study and 18 for the popu- lation study. RAPD profiles of TiO2 NPs treated plants showed differences in band intensity, loss of bands, or appearance of new bands, compared to untreated plants. To the authors' knowledge, this is the first report of the genotoxic potential of TiO2 NPs in zucchini.

Assessment of arsenic-induced DNA damage in goldfish by a polymerase chain reaction-based technique using random amplified polymorphic DNA markers.

Arsenic is a groundwater contaminant of global concern. It is a potent human carcinogen, and its marked genotoxic effects have been reported in several human and animal studies. The present work investigates the applicability of the random amplified polymorphic DNA (RAPD) assay to study the DNA-damaging effects of arsenic at low-level exposure in goldfish Carassius auratus. Four experimental groups of fish, A, B, C and D, were exposed to 0, 10, 50, and 1,000 µg L(-1) of arsenic, respectively, in aquaria water for 15 consecutive days. Genomic DNA extraction was followed by RAPD-polymerase chain reaction amplification for each fish separately. One arbitrary decamer primer (PUZ-19) of 33 primers used appeared as the most informative and was capable of exhibiting marked alterations in RAPD profiles between arsenic-exposed and unexposed (control) samples. Different sets of 11 loci were amplified in various experimental groups with four clear polymorphic bands by the primer PUZ-19. The X and XIII amplification loci, which were prominent in the unexposed group, failed to appear in the arsenic-exposed groups. In contrast, the I and XI RAPD bands appeared as new amplification loci in all of the exposed groups. Such alterations in genomic DNA, however, did not exhibit a clear dose-dependent tendency. The RAPD assay, because of its efficacy to unmask alterations in genomic DNA induced by arsenic at low exposure level of 10 µg L(-1), appears to be a sensitive and potential tool for detecting arsenic genotoxicity.

Development of an efficient protocol for plant regeneration from nodal explants of recalcitrant bamboo (Bambusa arundinacea Retz. Willd) and assessment of genetic fidelity by DNA markers

The present study describes an efficient method for in vitro plant regeneration in B. arundinacea through axillary shoot bud proliferation. Nodal explants were excised, cultured on MS medium containing different concentrations of 6-benzylaminopurine (BAP), kinetin (KIN) (0.5–5.0 mg l−1) alone and/or in combinations with KIN/BAP (0.5 mg l−1). The highest frequency (91.5 %) of multiple shoot bud induction with maximum number of shoots (85 shoots/explant) was noticed on MS medium + 3.0 mg l−1 BAP + 0.5 mg l−1 KIN. The regenerated multiple shoots were elongated on MS medium + 4.0 mg l−1 KIN + 2.0 mg l−1 gibberellic acid (GA3) with maximum shoot length (4.9 cm). The elongated shoots were transferred to MS medium containing indole-3 butyric acid (IBA; 0.5–5.0 mg l−1) alone and/or in combination with 0.5 mg l−1 KIN and BAP. Highest frequency of rooting (75 %) was obtained on half-strength MS medium + 2.0 mg l−1 IBA + 0.5 mg l−1 KIN. After hardening, the plantlets were shifted to the green house and subsequently established in the field conditions with 90 % survival rate. random amplified polymorphic DNA (RAPD) markers were used to evaluate the genetic stability of the regenerants. RAPD profiles generated from the regenerated plants were found to be monomorphic, similar to the control. Results confirmed that the regenerated plants were true-to-type in nature and the developed micropropagation protocol could be used for large scale plant production of B. arundinacea.

English

Random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) was applied to analyze the genetic variation among Channa striatus collected from four geographically distant locations in India. After initial PCR screening, nine random oligodecamers viz. OPA10, OPA11, OPA15, OPAC01, OPAC03, OPAC05, OPAC07, OPAC09 and OPAC19 which generated the RAPD profile for the four C. striatus populations were selected. Amplification using these nine primers resulted in fragments ranging in length between 309-3029 bp assigned to 87 loci. Estimates of Nei&rsquo;s (1978) unbiased genetic distance (D) values ranged from 0.3242-0.6320. Unweighted pair group method with arithmetic mean (UPGMA) dendrogram constructed on the basis of genetic distance revealed very close genetic relationship among C. striatus populations of river Tamirabarani (Tamil Nadu) and river Periyar (Kerala). Both populations from river Tamirabarani and Periyar were found to be genetically closer to fish populations from Kolleru Lake (Andhra Pradesh) whereas C. striatus population from Brahmani River (Orissa) was found to be genetically distant from the rest of the populations. Key words: Indian snakehead, Channa striatus, genetic diversity, random amplified polymorphic DNA (RAPD).

Genetic Diversity and Pathogenicity of Fusarium oxysporum f.sp. melonis Races from Different Areas of Italy

AbstractFusarium wilt caused by Fusarium oxysporum f.sp. melonis (FOM) is a devastating disease of melon worldwide. Pathogenicity tests performed with F. oxysporum isolates obtained from Italian melon‐growing areas allowed to identify thirty‐four FOM isolates and the presence of all four races. The aims of this work were to examine genetic relatedness among FOM isolates by race determination and to perform phylogenetic analyses of identified FOM races including also other formae speciales of F. oxysporum of cucurbits. Results showed that FOM race 1,2 was the most numerous with a total of eighteen isolates, while six and nine isolates were identified as race 0 and 1, respectively, and just one isolate was assigned to race 2. Phylogenetic analysis was performed by random amplified polymorphic DNA (RAPD) profiling and by translation elongation factor‐1α (TEF‐1α) sequencing. The analysis of RAPD profiles separated FOM races into two distinct clades. Clade 1, which included races 0, 1 and 1,2, was further divided into ‘subclade a’ which grouped almost all race 1,2 isolates, and into ‘subclade b’ which included race 0 and 1 isolates. Clade 2 comprised only race 2 isolates. The phylogenetic analysis based on TEF‐1α separated FOM from the other formae speciales of F. oxysporum. Also with TEF‐1α analysis, FOM races 0, 1 and 1,2 isolates grouped in one single clade clearly separated from FOM race 2 isolates which grouped closer to F. oxysporum f.sp. cucumerinum. RAPD technique was more effective than TEF‐1α in differentiating FOM race 1,2 isolates from those belonging to the closely related races 0 and 1. Both phylogenetic analyses supported the close relationship between the three different FOM races which might imply the derivation from one another and the different origin of FOM race 2.

Halophilic bacteria are colonizing the exhibition areas of the Capuchin Catacombs in Palermo, Italy.

The Capuchin Catacombs of Palermo, Italy, contain over 1800 mummies dating from the 16th to 20th centuries AD. Their environment is not conducive to the conservation of the remains due to, among other factors, water infiltration, which is producing salt efflorescences on the walls. A multiphasic approach was applied to investigate the halophilic microbiota present in the Catacombs. Enrichment cultures were conducted on media containing different NaCl concentrations, ranging from 3 to 20 %. For screening of the strains, the following two PCR-based methods were used and compared: fluorescence internal transcribed spacer PCR (f-ITS) and random amplification of polymorphic DNA (RAPD) analyses. Results derived from RAPD profiles were shown to be slightly more discriminative than those derived from f-ITS. In addition, the proteolytic and cellulolytic abilities were screened through the use of plate assays, gelatin agar and Ostazin Brilliant Red H-3B (OBR-HEC), respectively. Many of the strains isolated from the wall samples displayed proteolytic activities, such as all strains belonging to the genera Bacillus, Virgibacillus and Arthrobacter, as well as some strains related to the genera Oceanobacillus, Halobacillus and Idiomarina. In addition, many of the strains isolated from materials employed to stuff the mummies showed cellulolytic activities, such as those related to species of the genera Chromohalobacter and Nesterenkonia, as well as those identified as Staphylococcus equorum and Halomonas sp. Furthermore, many of the strains were pigmented ranging from yellow to a strong pink color, being directly related to the discoloration displayed by the materials.

New Plant Type Mutants in Jute (Corchorus olitorius L.)

Three macromutants namely, 'pigmented stem', 'viridis' and 'lax branching', of jute (Corchorus olitorius L. - JRO 524; commercial fibre yielding crop) were induced at M2 following gamma irradiations and EMS (Ethyl Methane Sulphonate) treatments. The true breeding mutants (selfed seeds of a single phenotypically stable plant forwarded in each generation from M4) are assessed considering different attributes like germination, survivability, meiotic chromosome behavior, pollen fertility and viability and quantitative traits across the generations (M5, M6 and M7) in relation to control under a uniform field condition(s). Further, genetic variations between/among the mutants and between mutant(s) and control is also analyzed from seed protein (SDS-PAGE - sodium dodecyl sulphate-polyacrylamide gel electrophoresis), RAPD (Random Amplification of Polymorphic DNA) and ISSR (inter-simple sequence repeat) profiles. Pigment profiles following TLC (Thin Layer Chromatography) have been studied in 'viridis' and control. Inheritance of the mutant trait(s) has also been assessed from reciprocal crossings performed between control and mutants. Results suggest that the mutants are true breeding, stable and significant and may enrich genetic resources in the species.

Outbreak of Achromobacter xylosoxidans in an Italian Cystic fibrosis center: genome variability, biofilm production, antibiotic resistance, and motility in isolated strains.

Cystic fibrosis (CF) patients have chronic airway infection and frequent exposure to antibiotics, which often leads to the emergence of resistant organisms. Achromobacter xylosoxidans is a new emergent pathogen in CF spectrum. From 2005 to 2010 we had an outbreak in A. xylosoxidans prevalence in our CF center, thus, the present study was aimed at deeply investigating virulence traits of A. xylosoxidans strains isolated from infected CF patients. To this purpose, we assessed A. xylosoxidans genome variability by randomly amplified polymorphic DNA (RAPD), biofilm production, antibiotic resistances, and motility. All A. xylosoxidans strains resulted to be biofilm producers, and were resistant to antibiotics usually employed in CF treatment. Hodge Test showed the ability to produce carbapenemase in some strains. Strains who were resistant to β-lactamics antibiotics, showed the specific band related to metal β-lactamase (blaIMP-1), and some of them showed to possess the integron1. Around 81% of A. xylosoxidans strains were motile. Multivariate analysis showed that RAPD profiles were able to predict Forced Expiratory Volume (FEV1%) and biofilm classes. A significant prevalence of strong biofilm producers strains was found in CF patients with severely impaired lung functions (FEV1% class 1). The outbreak we had in our center (prevalence from 8.9 to 16%) could be explained by an enhanced adaptation of A. xylosoxidans in the nosocomial environment, despite of aggressive antibiotic regimens that CF patients usually undergo.

Draft Genome Comparison of Representatives of the Three Dominant Genotype Groups of Dairy Bacillus licheniformis Strains

The spore-forming bacterium Bacillus licheniformis is a common contaminant of milk and milk products. Strains of this species isolated from dairy products can be differentiated into three major groups, namely, G, F1, and F2, using random amplification of polymorphic DNA (RAPD) analysis; however, little is known about the genomic differences between these groups and the identity of the fragments that make up their RAPD profiles. In this work we obtained high-quality draft genomes of representative strains from each of the three RAPD groups (designated strain G-1, strain F1-1, and strain F2-1) and compared them to each other and to B. licheniformis ATCC 14580 and Bacillus subtilis 168. Whole-genome comparison and multilocus sequence typing revealed that strain G-1 contains significant sequence variability and belongs to a lineage distinct from the group F strains. Strain G-1 was found to contain genes coding for a type I restriction modification system, urease production, and bacitracin synthesis, as well as the 8-kbp plasmid pFL7, and these genes were not present in strains F1-1 and F2-1. In agreement with this, all isolates of group G, but no group F isolates, were found to possess urease activity and antimicrobial activity against Micrococcus. Identification of RAPD band sequences revealed that differences in the RAPD profiles were due to differences in gene lengths, 3' ends of predicted primer binding sites, or gene presence or absence. This work provides a greater understanding of the phylogenetic and phenotypic differences observed within the B. licheniformis species.

English

Cucurbita pepo ssp. pepo; zucchini group is a widely grown and economically important group belonging to genus Cucurbita, and being one of the easiest groups to cultivate in temperate climate with overwhelming production. Since, RAPD analysis provides a fast and reliable method for molecular characterization and investigation of the intraspecific genetic relationships; it had been used in this study to discriminate and clarify the genetic diversity between seven cultivars of C. pepo ssp. pepo originated worldwide. Seven out of 20 decamer arbitrary primers showed polymorphism in the RAPD profile. The polymorphism was investigated by 87 consistent amplification products. Some of those fragments were uniquely amplified in single cultivar. Thus, they can be used as molecular markers for cultivar identification. The results of Jaccard similarity and the phenogram ascertained the wide genetic base of the Egyptian landrace El-Escandrani with the lowest loading component of 0.400. Therefore, it could be recommended as a reservoir of alleles useful for breeding programs in parental crosses. The multivariate analysis using the principle component analysis separated all the cultivars on the first component indicating the high correlation between them. The strongest correlation was confirmed between the two MHTSQ hybrids with Mansoura cultivar from Italy, with a loading component of 0.85. &nbsp; Key words: Genetic diversity, Cucurbita pepo, cluster analysis, random amplified polymorphic DNA (RAPD).

English

Genetic diversity within&nbsp;Gerbera jamesonii Bolus&nbsp;is the key to genetic improvement of this important ornamental species. In the present study, genetic diversity of 12 accessions of gerbera was assessed through random amplified polymorphic DNA (RAPD) markers. A total of 40 RAPD primers belonging to OPD, OPE, OPF and OPG series of universal primers set were used out of which, only 10 primers produced clear, reproducible and scorable bands. Ten (10) decamer RAPD primers produced a total of 49 scorable bands from 12 genotypes of G. jamesonii Bolus, out of which 42 were polymorphic and seven were monomorphic. The percentage of polymorphism ranged from a maximum of 100.00% by OPE-02, OPE-14, OPF-18, OPG-18, OPG-16 and OPG-17 to a minimum of 50.00% by OPE-08. The RAPD profiles generated were further evaluated for studying the Jaccard&rsquo;s similarity coefficient. The average genetic similarity coefficient for the 12 accessions evaluated by Jaccard index was 0.66 ranging from 0.35 to 0.86. The RAPD amplification data were used to obtain similarity matrix and for generation of dendrogram using unweighted pair group method with arithmetic averages (UPGMA) method. Based on the dendrogram, all 12 genotypes could be distinctly divided into two clusters and the accession CF Orange was found most dissimilar from other accessions. This study shows that DNA based molecular marker RAPD is a powerful, less time consuming and cost effective molecular technique for assessment of genetic diversity among different genotypes of&nbsp;G. jamesonii Bolus. The availability of these gerbera RAPD markers would facilitate the use of molecular markers in gerbera breeding and genetic studies. &nbsp; Key words: Gerbera jamesonii Bolus, molecular markers, genetic diversity, RAPD.

Emergence of Third Generation Cephalosporin Resistance and Typing by Randomly Amplified Polymorphic DNA (RAPD) among Clinical Salmonella Isolates from Lagos, Nigeria

Aims: To investigate emergence of cephalosporin resistance and clonal relatedness among clinical Salmonella isolates recovered from patients in Lagos, Nigeria. Study Design: It is an investigative study. A total of 300 patients who presented with various types of medical conditions at prominent referral public hospitals were recruited. Place and Duration of Study: Department of Microbiology, Lagos State University, Ojo, Lagos and Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria from July 2011 to May 2012. Methodology: Salmonella identification was done using standard methods. The isolates were subjected to antimicrobial susceptibility by disk diffusion method. The isolates were further screened for plasmid DNA and blaCTX-M carriage on plasmid using alkaline lysis and PCR methods. Clonal relatedness of the isolates was assessed by RAPD PCR using genomic DNA as template for three RAPD primers (784, 1254 and OPA4). The resulting Original Research Article British Microbiology Research Journal, 4(6): 668-677, 2014 669 RAPD types were determined by visualization and discrimination index was measured using a discriminating index calculator. Results: Sixty three Salmonella isolates were recovered made up of five serovars. In all 49% of the isolates were resistant to cefuroxime, 46% to cefoxitin, 37% to cefriazone and 35% to ceftazidine. Interestingly 28(87.5%) of the 32 ESBL producing Salmonella isolates possessed at least one or more plasmids from five distinct sizes recorded 2.5; 4; 9; 15;23.5kb. Four distinct RAPD profiles were exhibited by the test strains. The total discriminatory power among the isolates was 0.77 (77%). Conclusion: Third generation cephalosporin resistance involving blaCTX-M has emerged among clinical Salmonella isolates in Lagos. RAPD elicits potential as a cost-effective and time saving tool for local discrimination of clinical Salmonella isolates for epidemiological purposes.

Heavy metal accumulation and genotoxicity indicator capacity of the lichen species Ramalina pollinaria collected from around an iron steel factory in Karabük, Turkey

In the present work, Ramalina pollinaria (Westr.) Ach. specimens collected from around an iron steel factory in Karabük were analyzed due to their heavy metal accumulation by atomic absorption spectrometry. The specimens were also evaluated for pollution-induced DNA damage by random amplified polymorphic DNA (RAPD) assay. Genomic template stabilities were calculated from the changes in RAPD profiles and compared with heavy metal content in R. pollinaria. The results obtained from chemical analysis suggest that R. pollinaria is a particularly suitable lichen species for the detection of air quality. Results of RAPD assay showed significant differences in band patterns in R. pollinaria as compared to the control sample with respect to disappearance and appearance of bands. In this study, we have assessed the potential of RAPD assay as an application tool for detecting the genotoxic effect of air pollutants according to the changes in DNA band patterns in R. pollinaria.

CYTOGENOTOXICITY EVALUATION OF WATER CONTAMINATED WITH SOME TEXTILE AZO DYES USING RAPD MARKERS AND CHROMOSOMAL ABERRATIONS OF ONION (Allium cepa) ROOT CELLS

The Allium cepa assay is an efficient test for chemical screening and in situ monitoring for genotoxicity of environmental contaminants. This test has been used widely to study genotoxicity of many chemicals pollutions revealing that these compounds can induce chromosomal aberrations in root meristems of Allium cepa. In this study, we aimed to determine genotoxic effects of some textile azo dyes by using the Allium cepa chromosome aberrations test and random amplification of polymorphic DNA (RAPD) analyses. The onion (Allium cepa L.) roots were exposed to different concentrations of three textile azo dyes. The mitotic index of samples exposed to EC50 (500 μg/ml) of selected azo dyes for RLB, RN and SGL was 10.8, 10.3 and 8.8, respectively. The results indicated that the root length of Allium cepa reduced with an increasing azo dye concentration. A random amplification of polymorphic DNA (RAPD) analysis from the extracted DNA was carried out using ten 10-base pair random primers. Ten primers produced 54 bands between 100-1600 base pairs in gel electrophoresis. The number of disappearing bands in profiles was differenced from one to five bands of azo dyes treatment compared to total bands in control and new bands were appeared in treatments. Obtained results from this study revealed that the total chromosomal aberrations and RAPD profiles were performed as useful tool for detection and biomarker assays for the evaluation of genotoxic effects on textile azo dyes polluted plants.