Random Amplified Polymorphic DNA Patterns Research Articles

Impact of Iron Nanoparticles Application on Date Palm In-vitro Regeneration Stability

The use of nanoparticles is critical in a number of industries, including manufacturing, healthcare, and agriculture. Iron nanoparticles (Fe NPs) are one of the main sources of plant nutrition because they are effective in releasing a variety of pH values. To study the effect of different concentrations of Fe NPs (0, 0.5, 1.0, 2.0, 4.0 ml/l) on the regeneration and rooting of Bartamoda cv. date palm, as well as to ascertain the content of carbohydrates and chlorophyll in shoots, an experiment was conducted at the Central Laboratory for Research and Development of Date Palm, Agricultural Research Center Giza, Egypt. Adding treatments of Fe NPs at 1.0 and 2.0 ml/l to MS medium containing BA at 2.0 mg/l and NAA at 0.5 mg/l significantly enhanced growth (number of shoots/cluster, number of leaves/cluster, and leaf length), according to Results. MS medium supplemented with NAA at 1.0 mg/l and Fe NPs at 1.0 ml/l showed the highest rooting percentage (89.0%). Treating the shoots with varying doses of iron nanoparticles led to a significantly higher iron content compared to the untreated control shoots. The carbohydrate content improved steadily and significantly with increasing Fe NP concentration. Compared with the control group, treatments with Fe NPs at 1.0 and 2.0 ml/l enhanced the levels of chlorophyll a, chlorophyll b, and carotenoids.
 Through the use of random amplified polymorphic DNA (RAPD) profiles, the somaclonal variation in shoots that can be caused by Fe NPs during the multiplication stage was examined. To amplify DNA from various shoots, seven random 10-mer primers were applied. The shoots' RAPD patterns matched those of the original plant mother, proving that Fe NPs did not cause somaclonal variation that could be seen using the RAPD method.

Intracellular presence and genetic relationship of Helicobacter pylori within neonates' fecal yeasts and their mothers' vaginal yeasts.

Helicobacter pylori are transmissible from person to person and among family members. Mother-to-child transmission is the main intrafamilial route of H. pylori transmission. However, how it transmits from mother to child is still being determined. Vaginal yeast often transmits to neonates during delivery. Therefore, H. pylori hosted in yeast might follow the same transmission route. This study aimed to detect intracellular H. pylori in vaginal and fecal yeasts isolates and explore the role of yeast in H. pylori transmission. Yeast was isolated from the mothers' vaginal discharge and neonates' feces and identified by internal transcribed spacer (ITS) sequencing. H. pylori 16S rRNA and antigen were detected in yeast isolates by polymerase chain reaction and direct immunofluorescence assay. Genetic relationships of Candida strains isolated from seven mothers and their corresponding neonates were determined by random amplified polymorphic DNA (RAPD) fingerprinting and ITS alignment. The Candida isolates from four mother-neonate pairs had identical RAPD patterns and highly homologous ITS sequences. The current study showed H. pylori could be sheltered within yeast colonizing the vagina, and fecal yeast from neonates is genetically related to the vaginal yeast from their mothers. Thus, vaginal yeast presents a potential reservoir of H. pylori and plays a vital role in the transmission from mother to neonate.

Molecular Variability in Phaeoisariopsis personata Causing Late Tikka Leaf Spot of Ground Nut in Cuddalore District of Tamil Nadu

An experiment was carried out at Department of plant pathology, Annamalai University, Tamil Nadu, India. To test the five isolates of Phaeoisariopsis personata from different regions of groundnut Vridhachalam-2 (VRI-2) variety that showed typical symptoms of late tikka leaf spot disease from Cuddalore district viz., Shivapuri (LT1), Srimushnam (LT2), Chaithiram (LT3), Parangipettai (LT4), and Kammapuram (LT5) were collected. Random Amplified Polymorphic DNA (RAPD) analysis was used to detect the variations among the isolates of P. personata. Pair wise genetic similarities between the different isolates of P. personata were estimated by DICE similarity coefficient. The Dendrogram results revealed that these five isolates showed 66 per cent to 80 per cent similarity coefficient. There is no congruence between the RAPD pattern and the virulence pattern of test isolates. The clustering in the RAPD dendrogram was not associated with the virulence.

Bacterial community analysis of infant foods obtained from Chinese markets by combining culture-dependent and high-throughput sequence methods

In this study, twenty-two baby foods including cereal-based products and powdered infant formula (PIF) obtained from local markets were comprehensively investigated for their bacterial contamination using culture-dependent and high-throughput sequence (HTS) methods. In addition, the genetic diversity and biofilm-forming capacity of the most abundant species were analyzed using random amplified polymorphic DNA (RAPD) and crystal violet staining assay, respectively. Results showed that 170 mesophilic isolates collected from 22 samples were clustered into 15 genera and 41 species. Bacillus (77.65%) was the most prevalent genus, followed by Paenibacillus (7.06%), Alkalibacillus (3.53%), and Lysinibacillus (2.35%). Bacillus licheniformis (49.41%) proved to be the most dominant species in infant foods, and a high genetic diversity with six different RAPD profiles was observed. A total of 87.5% of B. licheniformis isolates were identified as strong biofilm formers, and heterogeneous biofilm-forming ability was observed among the isolates sharing the same RAPD pattern. HTS analysis revealed an 18-fold higher biodiversity at the genus level, and a significantly different bacterial community of infant foods was dominated by Lactococcus, Streptococcus, and Bifidobacterium. Foodborne pathogens including Bacillus cereus, and potentially pathogenic microorganisms such as Acinetobacter baumannii, were identified in infant foods by HTS. The current results could expand the crucial information about bacterial contamination of baby foods.

Microbial biodiversity of raw milk collected from Yangzhou and the heterogeneous biofilm‐forming ability of Pseudomonas

This study aimed to reveal microbial populations in Chinese raw milk using both 16S rRNA sequencing and high‐throughput sequence (HTS) methods. Psychrotrophic isolates were clustered into 23 genera and 57 species, and the abundant genera in raw milk were Pseudomonas, Acinetobacter and Lactococcus. Genetic diversity and biofilm‐forming capacity of Pseudomonas isolates were analysed using random amplified polymorphic DNA (RAPD) and crystal violet staining assay, respectively. Heterogeneous biofilm‐forming ability of Pseudomonas isolates with the same RAPD patterns was observed. HTS analysis revealed a 33‐fold higher diversity at the genus level, and a different bacterial population was predominated by Flavobacterium, Pseudomonas and Acinetobacter. The results provide insight into the microbial contamination of raw milk.

Genotoxicity Evaluation of Metformin in Freshwater Planarian Dugesia japonica by the Comet Assay and RAPD Analysis.

Objective To investigate the genotoxicity of metformin on planarian with different concentrations and exposure times. Methods The planarians were treated, respectively, with 10 mmol/L and 50 mmol/L metformin for 1, 3, and 5 days, and then, the comet assay and random amplified polymorphic DNA (RAPD) analysis were performed. 13 random primers were used for PCR amplification with the genomic DNAs as templates. Planarians cultured in clear water were used as the control. Genomic template stability (GTS) was calculated by comparing and analyzing the RAPD patterns of the control group and the treatment groups. Results In the comet assay, DNA damage of planarians treated with 10 mmol/L metformin for 1, 3, and 5 days was 10.2%, 25.4%, and 36.8%, respectively, and that of planarians treated with 50 mmol/L metformin was 40.6%, 62.8%, and 65.4%, respectively. GTS values of planarians exposed to 10 mmol/L metformin for 1, 3, and 5 days were 64.1%, 62.8%, and 52.6%, respectively, and those of planarians exposed to 50 mmol/L metformin for 1, 3, and 5 days were 52.6%, 51.3%, and 50%, respectively. DNA damage increased and GTS values decreased with the increasing metformin exposure concentration and exposure time. Conclusion Metformin has certain genotoxicity on planarian in a dose- and time-related manner. The comet assay and RAPD analysis are highly sensitive methods for detecting genotoxicity with drugs.

Iron toxicity-induced DNA damage, DNA methylation changes, and LTR retrotransposon polymorphisms in Zea mays

The impact of Fe2+ (iron)toxicity on genomic instability, DNA methylation status, and Long Terminal Repeat Retrotransposons (LTR RTs) polymorphisms on Zea mays is unknown. We investigated the toxicity of Fe2+ using Random Amplified Polymorphic DNA (RAPD), Coupled Restriction Enzyme Digestion-Random Amplification (CRED-RA) and Inter Retrotransposon Amplified Polymorphism (IRAP) assays in Zea mays seedlings, respectively. The results indicated that each dose of FeSO4 (50, 100, 200, and 300 mg/L) had a reducing effect on Genomic Template Stability (GTS) and increasing in RAPD pattern changes (DNA damage). The value of DNA methylation rised gradually depending on FeSO4 doses. Moreover, five LTR RTs (Wltr2105, Nikita-N57, Sukkula, Nikita-E2647, and Stowaway) of the maize genome revealed polymorphism in all FeSO4 doses. Furthermore, the present study indicated that there is a relationship between DNA methylation alterations and LTR RTs mobilization. It was concluded that iron caused DNA methylation changes as well as genotoxic damage in the maize genome. Also, considering the increase in some LTR RTs polymorphism we can say that it may be a part of the defense mechanism of the plant during stress

Biotyping of isolates of Pseudomonas aeruginosa isolated from human infections by RAPD and ERIC-PCR

Pseudomonas aeruginosa is a significant mortality factor due to nosocomial infections in humans. P. aeruginosa has been known with severe infections, high incidence, and multiple drug resistance. The present study aims to rapidly diagnose and biotype the isolates of P. aeruginosa isolated from human infections in Shiraz hospitals and health centers. Ninety six different isolates were collected from skin, urine, sputum, blood, wound, central vein blood, body fluids and burn wounds between January 2016 and February 2017. After phenotypic confirmation, isolates were examined by PCR for molecular confirmation. Ninety three isolates were verified as P. aeruginosa in molecular analysis. Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR and Random Amplified Polymorphic DNA (RAPD) were done for 67 isolates. In ERIC-PCR, the patterns obtained included 2–11 bands. The RAPD patterns obtained with primers 272 and 208 consisted of 3–11 and 1–12 bands respectively. Based on dice similarity coefficient of greater than 80%, 38, 45 and 38 groups were identified in ERIC, RAPD 272 and RAPD 208 respectively. The results showed that the isolates of P. aeruginosa have a high polymorphism apparently because of the high genetic variation.

Molecular identification and analysis of Psidium guajava L. from indigenous tribes of Taiwan

Psidium guajava L. is a perennial fruit tree in subtropical and tropical areas. In Taiwan, P. guajava has been used as anthro-pharmacological plants by aboriginal people to treat acute diarrhea, cough and intestinal spasmodic diseases. The classification and functional identification of P. guajava remains unsolved these days. In this study, molecular markers 18S rRNA, internal transcribe spacer (ITS) region of ribosomal DNA, trnL intron and trnL-trnF intergenic spacer (IGS) of chloroplast DNA (cpDNA), and random amplified polymorphic DNA (RAPD) were used for the molecular identification of 18 P. guajava samples from different indigenous tribes, 2 from non-indigenous tribe, and 12 commercial cultivars from markets in Taiwan. Molecular methods restricted fragment length polymorphism (RFLP) and denatured gradient gel electrophoresis (DGGE) are found time-consuming and less efficient as compared to RAPD, thus are not suitable for samples of high homology. In this study, 18S rDNA, ITS and cpDNA trnL intron and trnL-trnK intergenic spacer were also tested molecular marker; however, results analyzed by molecular algorithm UPGMA, Neighbor-Joining, Parsimony or Maximum likelihood showed no discriminations (data not shown). On the other side, ten 10-mer oligonucleotide primers were used in RAPD to amplify the specific genes from 32 guava samples. Four primers, OPB 17, OPG 6, OPY 15 and OPY 18, were able to direct the amplification and yielded a total of 82 polymorphic RAPD patterns. Thirty-two genotypes on the dendrogram were identified and were divided into two major groups, the uncultivated and commercial cultivars. Based on the cluster analysis, the red-flesh Psidium samples that were believed to have high medical function were grouped independently. The results suggest that RAPD is useful for the discrimination of uncultivated, cultivars and potential Psidium of high economy.

Morphological, Chemical, and Genetic Characteristics of Korean Native Thyme Bak-Ri-Hyang (Thymus quinquecostatus Celak.).

Bak-ri-hyang (Thymus quinquecostatus Celak.) is an important medicinal and aromatic plant in Korea. T. quinquecostatus population and is always mixed with other thyme cultivars during cultivation and marketing. Hence, this study aimed to determine the genetic variability and the essential oil composition of three Korean native thyme, T. quinquecostatus cultivars collected from the Wolchul, Jiri, and Odae mountains, in comparison with six commercial thyme cultivars (T. vulgaris), to distinguish Bak-ri-hyang from other thyme cultivars. The composition of essential oils obtained from nine individuals was analyzed by gas chromatography–mass spectrometry (GC–MS). The random amplified polymorphic DNA (RAPD) analysis was accomplished using 16 different primers. The GC–MS analysis revealed that Wolchul, creeping, golden, and orange cultivars belong to the geraniol chemotype. Whereas the Odae, lemon, and silver cultivars belong to the thymol chemotype. Further, linalool was the most abundant component in carpet and Jiri cultivars. The RAPD analysis demonstrated that all thyme cultivars showed characteristic RAPD patterns that allowed their identification. In total, 133 bands were obtained using 16 primers, and 124 bands were polymorphic, corresponding to 93.2% polymorphism. Cluster analysis of RAPD markers established the presence of clear separation from nine thyme cultivars. The highest dissimilarity and similarity coefficient of the RAPD markers were 0.58 and 0.98, respectively. According to the RAPD patterns, the nine thyme cultivars could be divided into two major clusters. Among three Korean cultivars, the Wolchul and Odae cultivars were placed into the same cluster, but they did not show identical clustering with their essential oil compositions. The findings of the present study suggest that RAPD analysis can be a useful tool for marker-assisted identification of T. quinquecostatus from other Thymus species.

Corneal ulcer/keratitis derived Aspergillus flavus &Aspergillus tamarii and their RAPD-PCR typing

The aim of the study was investigate the DNA polymorphisms of Aspergillus flavus and Aspergillus tamarii isolated from regional fungal keratitis cases based on random amplified polymorphic DNA (RAPD) analyses. Thirty-two A. flavus and six A. tamarii isolates were identified using conventional macroscopic and microscopic features. Five decamer primers were used to amplify the genomic DNA sequences of the test isolates, and 140 total RAPD patterns were generated among them. From each of the 38 isolates, a range of 15–30 RAPD types were revealed. All of these were isolated from male farmers from Tamil Nadu. In the future, RAPD analyses could be employed as a reliable and rapid technique to differentiate among keratitis isolates of fungal pathogens.

Molecular typing of Staphylococcus aureus from different sources by RAPD-PCR analysis

Staphylococcus aureus is an opportunistic bacterium which is carried as a normal flora organism but has a major role in the epidemiology and pathogenesis of different staphylococcal infections in humans and animals. Fifty S. aureus isolated from banknotes, foods, human infections and bovine mastitis were subjected to DNA fingerprinting by randomly amplified polymorphic DNA (RAPD) analysis to examine their genotypic polymorphism and investigate the amount of genetic relatedness among these various isolates. At 100% RAPD profile similarity level, isolates were classified into four, five and seven groups of the same clone, according to the RAPDPCR with OLP6, OLP11 and OLP13 primers, respectively. Amplification of the isolates resulted in several polymorphic bands ranged from >50 to >1500 bp in size. Maximum number of bands was obtained by primer OLP13 which produced seven bands in bovine mastitis isolates. Most polymorphisms were observed in isolates of bovine mastitis and the lowest were associated with human infections isolates. There was no relationship between the RAPD patterns and the sources of isolates, except the three clusters which showed host specificity and only included the strains from the same sources. The results confirm the wide genotypic diversity of the studied S. aureus strains. RAPD-PCR technique can be a valuable tool for assessing the genetic relationship, detection of polymorphism in S. aureus and tracing the sources and management of S. aureus infections.

Genetic Diversity of Salmonella enterica Strains Isolated from Sewage Samples of Different Hospitals in Bangladesh

The degree of salmonellosis is associated with the genetic diversity of the Salmonella enterica. Here, the genetic diversity of Salmonella enterica isolated from hospital sewage samples of Bangladesh were analyzed to elucidate the prevalence of S. enterica by random amplification of polymorphic DNA (RAPD) and amplified ribosomal DNA restriction analysis (ARDRA). Twenty six isolates were identified as S. enterica by cultural and biochemical methods as well as 16srDNA sequencing. These isolates showed two types of ARDRA and eight distinct RAPD patterns. All of these isolates possessed invA gene. However, agfA and fliC genes were found in 21 isolates and 16 isolates respectively. All of the isolates were resistant to rifamycin but most of them were sensitive to ceftriaxone and streptomycin. The study indicated that the genetic diversity is very high among the S. enterica isolates of Bangladesh. Therefore, such diversity may contribute to the future outbreak of salmonellosis in Bangladesh.
 Bangladesh J Microbiol, Volume 35 Number 1 June 2018, pp 57-60

Studies on the Genetic Variations between Field Strains of Pectinophora gossypiella (SAUNDERS) using Polymerase Chain Reaction (PCR) Technique

Five different strains of the pink bollworm, Pectinophora gossypiella (Saunders) were used in the present study.The laboratory strain was used as a baseline in the molecular biology assays. Four strains were selected from natural popoulations, fields located in Qalubia, Gharbia, Menoufia and Kafr-Elsheikh Governorates. The molecular studies included the analysis of the plod genomic DNA of the tested strains under this study by using Random Amplified Polymorphic DNA (RAPD) method. A battery of five primers was used to evaluate the mutagenic differentiation among the five strains. The primer S4 generated the highest numbers of fragments (32 fragments). Both primers K15 and S8 generated 23 fragments. The lowest number of fragments appeared in primer C15 and primer P8, (18 fragments). The molecular sizes of fragments ranged between 180 and 1182bp. The RAPD patterns resulted from amplification of DNA of the field colony strains and laboratory strain of the pink bollworm P. gossypiella revealed that the lowest value of similarity index (0.0%), which reflects the highest degree of change in DNA structure and sequences between the genomes of laboratory pink bollworm and those exposed to a wide spread of different insecticides for controlling the pest in the fields. On the other hand, there is no compilitily similarity index between field strains and laboratory strain of pink bollworm. The highest similarity index between field strains and laboratory strain of the pink bollworm appeared in primer P8, while the lowest similarity index between field strains and laboratory strain of the pink bollworm appeared in primer K15. The primer S4 recorded that is no similarity index between Qalubia strain and each of laboratory and field strains. It is interrest to note that the less damaging effect to pink bollworm DNA could be attributed to a good detoxifying mechanism developed by the insect as a result of wide spread and long term exposure of insect larvae in additional to different thermal degrees in the fields

Nosocomial outbreak of Candida parapsilosis sensu stricto fungaemia in a neonatal intensive care unit in China

Candida parapsilosis is a common agent of fungaemia, but few outbreaks of Candida parapsilosis infection have been reported in China. To elaborate an outbreak of nosocomial Candida parapsilosis sensu stricto fungaemia in a neonatal intensive care unit (NICU) of a comprehensive hospital in China from July to October 2017. Epidemics and characteristics of fungaemia cases were investigated. Surveillance samples were collected. Vitek 2 Compact System, internal transcribed spacer sequencing, and random amplified polymorphic DNA (RAPD) typing were conducted to identify the isolates. Antifungal susceptibility test was performed for all bloodstream isolates. Sixteen neonates were diagnosed as Candida parapsilosis sensu stricto fungaemia during this period. Presenting symptoms included leucopenia, thrombocytopenia, and respiratory crackles. Fifteen cases were cured whereas one case who suffered from severe concomitant diseases died. The isolates were susceptible to fluconazole, amphotericin B, itraconazole, voriconazole, and 5-fluorocytosine. A total of 313 surveillance samples were collected, and Candida parapsilosis sensu stricto was identified from 16 environmental samples and one sample from an ultrasonographer's hand. The colonized locations included wiping cloths, faucets, sinks, operating table, puddles in the bathroom, a ventilator, and an ultrasonic probe. The RAPD patterns of all the Candida parapsilosis sensu stricto isolates from bloodstream and surveillance samples were identical. The outbreak was controlled after a series of infection control measures. Contaminated environment was associated with this outbreak. Close attention to immunocompromised patients, thorough environmental disinfection and hand hygiene should be strengthened in NICU.

Tracking Multidrug-Resistant Klebsiella pneumoniae from an Italian Hospital: Molecular Epidemiology and Surveillance by PFGE, RAPD and PCR-Based Resistance Genes Prevalence.

Antimicrobial-resistant Klebsiella pneumoniae represent a global public health concern. K. pneumoniae strains isolated during 2010 and 2014-2016 within a single hospital of Molise Region, Central Italy, were analyzed testing antimicrobial susceptibility, clonality by pulsed-field gel electrophoresis (PFGE) and random amplified polymorphic DNA (RAPD)-PCR, and prevalence of carbapenem resistance genes by PCR. Forty isolates (23 wild-type in 2010 and 17 non-wild-type in 2014-2016) were collected from hospitalized patients (65.2 ± 18.1years old, 75% male, 80% from intensive care unit-ICU). K. pneumoniae showed multidrug-resistant profiles and 15 resistotypes were identified (discriminatory power D = 0.88). The 69.6 and 17.4% of isolates in 2010 resulted intermediate and resistant to imipenem, respectively, and 91.3% was sensitive to meropenem, while 88.2% of isolates of 2014-2016 were resistant to both antibiotics. PFGE identified 16 clusters versus 23 by RAPD, 26 pulsotypes versus 33 RAPD patterns (D ≥ 0.97). PFGE separated strains according to isolation period and identified an outbreak occurred in the ICU during December 2014 and January 2015. No strains harbored blaGES, blaIMP, blaNDM-1, and blaOXA-48 genes, as well as AmpC plasmid-mediated beta-lactamases genes. Only K. pneumoniae isolated during 2014-2016 were blaKPC positive. Prevalence of blaVIM was 87 and 76.5% during 2010 and 2014-2016, respectively. No strains colistin-resistant harbored mcr-1 plasmid-mediated resistance gene. The study findings underline an increased circulation of multidrug-resistant K. pneumoniae within the hospital, and the acquisition of carbapenem resistance mechanism. The implementation of surveillance and molecular characterization of isolates are needed to identify outbreaks, reduce the spread of resistance, and guide empirical therapy.

Phenotypic and Genotypic Characterization of Serratia marcescens from Clinical and Environmental Sources

S.marcescens is opportunistic pathogens that cause nosocomical infections. There have been many reports concerning the identification, antibiotic susceptibility, pathogenicity, epidemiological investigations and typing of this organism. Accurate identification is important in defining outbreaks. In the present study, S. marcescens have been selected from the natural sources and were then confirmed with 16S rRNA identification method with cultures of MTCC. To investigate these S. marcescens isolates, random amplification of polymorphic DNA (RAPD) was used in conjunction with the specific primers. The RAPD patterns for each isolate were identified on the basis of identical numbers and sizes of the bands. And by using dendrogram we can able to show, that the pattern of the primers to separate isolates was closely related to their sequence homology with the genome and their amount of guanine and cytosine nucleotide content. S. marcescens as a pathogen shows a tissue-damaging capacity. The cytotoxic activity is mainly elicited by the secreted hemolysin/cytotoxin ShlA. Here, the isolates were tested for hemolytic activity. S. marcescens is known to be frequently resistant to various antibiotics and our results also showed such a tendency.

SCAR MARKER DEVELOPMENT FOR THE CORRECT IDENTIFICATION OF IRIS ENSATA

Objective: The objective of this research was to develop the RAPD based SCAR marker for the correct identification of the Iris ensata Thunb. (I. ensata) plant from its adulterants.Methods: Five samples of I. ensata. from the different geographical area were used in this study. The plant genomic DNA was isolated with the CTAB method with some modification (as dried samples were also used). After that, polymorphism was checked with the help of the 10-mer random primers of OPAA and BG series. Then, the bands of interest were eluted and cloned into pGEMT easy vector for the sequencing. Finally, the sequence is used to develop the SCAR primers (Ir-f andIr-R) specific for I. ensata and the developed primers also validated with respect to the market samples.Results: A putative 580 bp sequence specific for Iris ensata was identified from the randomly amplified polymorphic DNA (RAPD) analysis. To overcome the main limitation of RAPD it has been converted into SCAR markers. So that, this specific band was then eluted, cloned and sequenced. After that, SCAR primers (Ir-F and Ir-R) were synthesized by using this sequence. For the validation of the synthesized SCAR primers, they were tested with respect to the market samples. The amplicon of 260 bp was produced by the SCAR primers in the authentic I. ensata but market samples did not produce any bands with the synthesized SCAR primers.Conclusion: The results of this study show a high level of polymorphism in the RAPD pattern of the different accessions of the plant. Furthermore, this study results in the successful development of the RAPD based SCAR marker for the identification of the I. ensata.

Characterization of Ornithobacterium rhinotracheale field isolates from Hungary

ABSTRACTOrnithobacterium rhinotracheale is a widely distributed rod-shaped Gram-negative bacterium that infects several avian species including chickens and turkeys. It is associated with respiratory signs, growth retardation, mortality, and reduced egg production, thus causing severe economic losses to the poultry industries. In this study, 37 field isolates of O. rhinotracheale, collected from various locations in Hungary between 1997 and 2015, were identified and characterized by the analysis of partial 16S rRNA gene sequences, enterobacterial repetitive intergenic consensus (ERIC)-PCR, and random amplified polymorphic DNA (RAPD) PCR assays with the OPG11, OPH19, and M13 primers. Most of the field isolates were serotype A, one was serotype B, and four were serotype D. One isolate could not be typed with antisera against serotypes A–E. In a phylogenetic analysis of the 16S rRNA sequences, the isolates formed two clusters. Thirteen distinct patterns were identified with ERIC-PCR, and the RAPD assay with the M13 primer assigned the isolates to 10 different patterns. The other two RAPD assays were unsuitable for distinguishing and grouping the isolates. Neither ERIC type nor RAPD pattern correlated with the place or year of isolation. However, the strains isolated from chickens were more heterogeneous on ERIC-PCR than the isolates recovered from turkeys. In this study, ERIC-PCR was the most discriminatory method for investigating the genetic diversity of O. rhinotracheale isolates.

Genotoxicity Evaluation of an Urban River on Freshwater Planarian by RAPD Assay.

The aim of this study was to evaluate the genotoxic potential of an urban river - the Wei River in Xinxiang, China using randomly amplified polymorphic DNA (RAPD) assay in planarians. The results showed that the total number of polymorphic bands and varied bands in RAPD patterns of treated planarians decreased with the water sample site far away from the sewage outlet of a factory. In addition, the genome template stability of treated groups decreased and the degree of the decline was negatively related to the distance between the sample site and the sewage outlet, suggesting that the Wei River water had genotoxicity effects on planarians and strengthening the management of the Wei River was necessary. Furthermore, this work also indicated that RAPD assay in planarians was a very promising test for environmental monitoring studies.