Analysis Of Polymerase Chain Reaction Products Research Articles

Multiplex PCR - RFLP Assay for Identification of Cryptococcus neoformans and Cryptococcus gattii Isolated from Birds’ Droppings and Eucalyptus Trees

Cryptococcus neoformans/ Cryptococcus gattii (C. neoformans/ C. gattii) species complex are encapsulated basidiomycetous yeasts, causing cryptococcosis which is a life-threatening fungal disease of the pulmonary and central nervous system of humans and animals. This study aimed to investigate the recovery rate of C. neoformans and C. gattii from bird droppings and Eucalyptus trees in Egypt as well as the performance of the phenotypic and molecular identification methods for Cryptococcus species identification. Overall, 27 Cryptococcus isolates (13.5%) were isolated from 200 examined samples including 70 pigeon droppings, 50 captive birds’ droppings, and 80 Eucalyptus trees samples. The recoveredisolates were phenotypically identified based on macro- and micro-morphological characters, urease test, and differentiation using cryptococcus differential agar media. Multiplex polymerase chain reaction (PCR) followed by restriction fragment length polymorphism (RFLP) analysis using EcoRIrestriction enzyme for confirmation of species identification. The molecular methods identified 20 C. neoformansfrom pigeon’s droppings (12/70, 17.14%) and captive birds’ droppings samples (8/50, 16%), as well as 7 C. gattii from Eucalyptus trees (7/80, 8.75%). Molecular identification results did not correspond with those of the phenotypic identification methods in three isolates (11.11%), as phenotypic methods identified only 4 C. gattii isolates and molecular methods identified 7 isolates. In conclusion, multiplex PCR and RFLP analysis of multiplex PCR products are rapid, sensitive, species-specific, and more reliable methods for identification of Cryptococcus species and may be used as a complementary to phenotypic methods to avoid false-negative and false-positive results.

Surface-enhanced Raman spectroscopy for analysis of PCR products of viral RNA of hepatitis C patients

In the current study, for a qualitative and quantitative study of Polymerase Chain Reaction (PCR) products of viral RNA of Hepatitis C virus (HCV) infection, surface-enhanced Raman spectroscopy (SERS) methodology has been developed. SERS was used to identify the spectral features associated with the PCR products of viral RNA of Hepatitis C in various samples of HCV-infected patients with predetermined viral loads. The measurements for SERS were performed on 30 samples of PCR products, which included three PCR products of RNA of healthy individuals, six negative controls, and twenty-one HCV positive samples of varying viral loads (VLs) using Silver nanoparticles (Ag NPs) as a SERS substrates. Additionally, on SERS spectral data, the multivariate data analysis methods including Principal Component Analysis (PCA) and Partial Least Squares Regression (PLSR) were also carried out which help to illustrate the diagnostic capabilities of this method. The PLSR model is designed to predict HCV viral loads based on biochemical changes observed as SERS spectral features which can be associated directly with HCV RNA. Several SERS characteristic features are observed in the RNA of HCV which are not detected in the spectra of healthy RNA/controls. PCA is found helpful to differentiate the SERS spectral data sets of HCV RNA samples from healthy and negative controls. The PLSR model is found to be 99% accurate in predicting VLs of HCV RNA samples of unknown samples based on SERS spectral changes associated with the Hepatitis C development.

Genetic identification and restriction fragment length polymorphism (RFLP) based analysis of Myxovirus resistant gene (Mx) of chicken in Bangladesh

The Myxovirus resistant gene (Mx) codes for Mx protein with antiviral activity. Mx gene has been found in yeast and vertebrates ranging from fish to humans. In the present study Mx gene and its diversity in chicken is reported. A total of 42 blood samples were collected from different groups of chicken and were analyzed by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP). The diversity of Mx gene was enumerated by RFLP of PCR product with RsaI and SspI restriction enzyme. Mx gene was amplified from all the tested samples (100%) with the primers used. The primers amplified specific 100bp and 300bp DNA fragments from Mx gene. RFLP analysis of PCR product obtained with mismatched primers revealed that three types of Mx gene allele are prevailing in the tested samples; these are homozygous resistant Mx allelic gene (R/R), heterozygous Mx allelic gene (R/S) and homozygous sensitive Mx allelic gene (S/S). The proportions of each gene allele in the sampled chicken were 42.86% R/R, 42.86% S/S and 14.29% R/S. Interestingly, variation in Mx gene was observed within and between the groups of chicken. Present study has limitations like number of sample, species of bird sampled, etc. However, the study provides the genetic basis to some extent of chicken about resistance or sensitivity to avian influenza. To the best of our knowledge this is the first report of Mx gene related study in chicken in Bangladesh.
 Bangladesh J. of Livestock Res. 20(1-2): 18-25, Jan-Dec 2013

Real-Time PCR and analysis of amplicon melting curves to assess the suitability of SSR loci of Scots pine for multiplexing

Nuclear microsatellite markers are considered to be among the most powerful tools for assessing genetic resources. To date, a great variety of primers for SSR loci of pines has been developed. As regards Scots pine, selection of neutral steadily amplifiable loci not containing null alleles and their multiplexing are high-priority tasks, as there are no generally accepted multiplex panels of loci for this species. Authors of published multiplexes tend not to use loci due to their unstable amplification or the presence of single nucleotide repeats. The aim of the paper was to create the new multiplexes of reliable previously published pine nSSR loci in view of preliminary data based on the analysis of melting curves of products after Real-Time polymerase chain reaction (PCR) for each locus separately. Initially, microsatellite multiplexes were created using Multiplex Manager 1.0. DNA was extracted by the CTAB method from samples of pine needles. Real-Time PCR was performed in CFX96 thermal cyclers (BIO-RAD, USA). Fragment analysis of PCR products labeled with FAM, HEX and ROX dyes was performed on a 3500 genetic analyzer (Applied Biosystems). GeneScanTM 500 LIZ size standard was used. As a result of the study, 3 multiplexes have been proposed.

First Report of Strawberry (Fragaria × ananassa) as a Host of a ‘Candidatus Phytoplasma americanum’-Related Strain in the United States

In June 2018, while conducting a survey for possible presence of phytoplasma pathogens in Pennsylvania production fields, a strawberry plant (Fragaria × ananassa) was observed with symptoms of stunting and unseasonal reddening and distortion of leaves. Only one out of 500 strawberry plants expressed the described symptoms in a farm in Perry County, PA. Several leaves and stems were collected from the symptomatic plant as well as from a few asymptomatic ones for further work. Total DNA was extracted from 100 mg of leaf midveins with a DNeasy Plant Mini Kit (Qiagen, Valencia, CA). All DNA samples were initially tested using a phytoplasma universal real-time polymerase chain reaction (PCR) assay (Hodgetts et al. 2009). Positive amplification results were obtained only with samples derived from the symptomatic strawberry plant. To detect and identify the suspected phytoplasmal pathogen strain(s), the DNA samples were used as a template in conventional PCRs for amplification of phytoplasma 16S rRNA, secY, secA, and tuf gene sequences as previously described (Dickinson and Hodgetts 2013; Lee et al. 2004, 2010; Makarova et al. 2012). All of the obtained amplicons were of expected sizes, and no amplification was observed from the asymptomatic strawberry samples. PCR products were purified with a QIAquick PCR Purification Kit (Qiagen) and sequenced. Nucleotide sequences of the PCR products were deposited in the GenBank database under accession numbers MN227133 to MN227136. The nucleotide sequences were analyzed using Geneious software (Biomatters, Auckland, NZ) for sequence alignments and using iPhyClassifier (Zhao et al. 2009) for group-subgroup and ‘Candidatus Phytoplasma’ species assignments. The classification into 16Sr groups and subgroups was established by virtual restriction fragment length polymorphism (RFLP) analysis of PCR products compared with reference strains. The phytoplasma, termed strain SRL1-PA (Strawberry Red Leaf1-PA), was found to share 99.9% similarity with that of the ‘Candidatus Phytoplasma americanum’ reference strain (GenBank accession DQ174122). The virtual RFLP pattern derived from the query 16S rDNA F2nR2 fragment is most similar to the reference group XVIII, subgroup A (GenBank accession DQ174122), with a pattern similarity coefficient of 0.98. Another sample from the same strawberry plant was independently determined positive for ‘Ca. P. americanum’ by CPHST Beltsville Lab using nucleotide sequence analysis of 16S rRNA gene sequences amplified in end point PCR. Alignments and phylogenetic analyses of secY, secA, and tuf gene sequences confirmed the close relatedness of the Pennsylvania SRL1-PA strain with the reference strains of ‘Ca. P. americanum’. ‘Ca. P. americanum’ was previously reported (Lee et al. 2006) in Texas and Nebraska on potato and associated with potato purple top wilt disease. In 2019, the Pennsylvania Department of Agriculture team revisited the same farm and collected additional samples including some from potato but was not able to detect any phytoplasma. To our knowledge, this report provides the first evidence for the presence of a ‘Ca. P. americanum’-related strain in Pennsylvania and more importantly describes strawberry (Fragaria × ananassa) as a new host for this phytoplasma. With only one single positive strawberry plant in a single year, the true extent of disease spread on strawberries remains undetermined.

Sequencing and Phylogenetic Analysis of the Salmonella Enterotoxin (stn) Gene of Salmonella spp. Isolated from Egyptian Broiler Breeder Chickens Farms

Salmonella is a member of Enterobacteriaceae family that found to be pathogenic to domestic and wild animals and humans. Salmonellae were isolated from three distinct governorates, Giza, Monofia and Qaluobia from broiler breeder chicken farms. Molecular characterization of the Salmonella isolates using polymerase chain reaction (PCR) assay as well as Sequencing and phylogenetic analysis of PCR products were conducted to distinguish the collected Salmonellae species. The nucleotide sequence of 617 bp PCR products representing the amplified fragment of stn gene of seven isolates of Salmonella enteritidis has been sequenced. Furthermore, the nucleotide sequence was submitted to the gene bank. The obtained sequences were blasted with the highly similar sequences and the multiple sequence alignments were conducted. Neighbor-joining tree was constructed for the Egyptian Salmonella isolates against 30 Salmonella spp. from the Gene bank database representing maximum similarity with stn gene when subjected to multiple sequence alignment, and the phylogenetic tree was constructed based on the comparative analysis of related sequences at the nucleotide level.

Cloning and Expression of Immunogenic Regions of EMA-1 Gene of Theileria equi From Infected Horses.

Diversity among the pathogenic strains of Theileria equi (T. equi), a major agent of equine piroplasmosis, can affect the appropriate detection of parasite and host immunization. Production of recombinant surface proteins from an infected horse in natural endemic area provides a reliable tool for immunodiagnosis of parasite. Regarding this, the present study was targeted toward the cloning, expression, and purification of the immunogenic regions of equine merozoite antigen 1 (EMA-1 gene), as one of the most important immunodominant surface proteins in T. equi, from naturally infected horses in Iran. The immunogenic region of EMA-1 gene was amplified using the blood of infected horses. EMA-1 gene was cloned into pET26b vector. Then, recombinant plasmids (pET 26b-EMA-1) were transformed into competent E. coli BL21 (DE3) cells. Cloning was confirmed by polymerase chain reaction (PCR), restriction enzyme assays, and DNA sequence analysis. The recombinant protein was expressed using isopropyl β-D-1-thiogalactopyranoside as an inducer, purified using nickle-nitrilotriacetic acid column, and then confirmed by 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and dot blot analysis utilizing Anti-His Tag antibody. Furthermore, the immunoreactivity of recombinant protein against the serum of the infected horses was evaluated using dot blot analysis. The PCR product analysis showed a 750-bp band belonging to immunogenic regions of EMA-1 gene. Sequence analysis revealed that cloned EMA-1 and protein had 94% and 97% homology to EMA-1 sequences submitted to GenBank from different countries, respectively. Restriction enzyme and sequence analyses confirmed the subcloning and correction of the orientation of inserted gene. The SDS-PAGE analysis confirmed the expression of EMA-1 protein with a 28-kDa band. The results of the dot blot analysis revealed that the horse serum containing antibody against T. equi could react with the purified recombinant protein. Purified EMA-1 protein can be used as a reliable tool for the future development of diagnostic tests or vaccines.

Systematic evaluation of the early access applied biosystems precision ID Globalfiler mixture ID and Globalfiler NGS STR panels for the ion S5 system

Systematic evaluation of the early access applied biosystems precision ID Globalfiler mixture ID and Globalfiler NGS STR panels for the ion S5 system

Molecular Evaluation of High Fluoroquinolone Resistant Genes in Endemic Cases of Shigellosis, Northeast Part of Karnataka, India

ObjectivesShigellosis is an acute infection of the intestine caused by bacteria in the genus Shigella and also an important cause of diarrhea in developing countries. This study was carried out to find the extent and nature of the emerging resistance in north part of Karnataka, India, and surrounding region with huge population, and also focused on the molecular mechanism of development of resistance against different generations of fluoroquinolones and explored the diversity of restriction endonucleases; we also tried to establish the significance of reduced minimal inhibitory concentrations (MIC) values. MethodsA total of 32 multidrug-resistant Shigella species (isolated from infants’ stools) were subjected to MICs of fluoroquinolone-resistant isolates done by both broth dilution and E-test method. The genes implicated in resistance to fluoroquinolone generations ciprofloxacin, ofloxacin, and gatifloxacin (gyrA, gyrB, parC, and parE) were amplified using polymerase chain reaction (PCR) method and restriction digestion analysis of PCR product were performed using PvuI and HaeII enzymes. FindingsFluoroquinolone-resistant Shigella species (n = 32) comprising S dysenteriae, S flexneri, and S sonnei were selected for MIC; 90.6% (29/32), 93.75% (30/32), and 93.75% (30/32) of isolates were ciprofloxacin, ofloxacin, and gatifloxacin resistant and showed the MIC range from 4-128 μg/mL. The PCR amplification results were positive for all species and asserted the presence of gyrA, gyrB, parC, and pare and sizes of the amplified products. The restriction banding patterns of amplified resistant genes were employed to detect differences among the Shigella species. ConclusionsThe present study found that the genetic basis and its characterization of fluoroquinolone resistance in Shigella isolates was considered for the common resistant genes, namely, gyrA, gyrB, parC, and pare, and had mutations at position 83 of gyrA and at position 80 of parC of the quinolone-resistant determining regions and associated molecular mechanism. Our study beneficial in identification of the causative agents of the infections, careful control and cautions use of antibiotics must be promoted, particularly to monitor the emergence of isolates that are fully resistant to fluoroquinolones.

Parallel-processing continuous-flow device for optimization-free polymerase chain reaction.

A parallel-processing four-station polymerase chain reaction (PCR) device has been developed, which performs continuous-flow PCR without optimization of the annealing temperature. Since the annealing temperature of each station can be controlled independently, the device covers an annealing temperature range of 50-68°C, which is wide enough to perform PCR for any DNA fragment regardless of its optimum annealing condition. This arrangement lets us continuously obtain an amplified amount of a DNA fragment at least from one of the stations. The device consists of four identical cylindrical stations (diameter 20mm, height 55mm). A polytetrafluoroethylene capillary reactor (length 2m, I.D. 100μm, O.D. 400μm) is wound helically up around each station. The whole assembly is designed to minimize the number of heating blocks (for providing temperatures of denaturation, annealing, and extension) to be seven and to shape a compact cube (height 55mm, base 60mm × 60mm). The reproducibility for continuous-flow PCR is reasonably high (run-to-run and station-to-station relative standard deviation of their amplification is lower than 6% and about 4%, respectively). Performance on the optimization-free DNA amplification has been evaluated with four DNA samples with different annealing conditions and product sizes (323, 608, 828, and 1101bp), which has demonstrated that in all cases, PCR is successful at least on one station. In addition, three DNA fragments with different lengths (323, 1101, and 2836 bp) have been successfully amplified in a segmented-flow mode without the carry-over contamination between segments. This result suggests that this device could serve as the PCR module of a continuous-flow high-throughput on-line total DNA analysis system integrating all necessary modules from cell lysis/DNA extraction to PCR product analysis.

Platinum nanoparticles on reduced graphene oxide as peroxidase mimetics for the colorimetric detection of specific DNA sequence.

In this work, we developed a simple and sensitive colorimetric detection platform for specific DNA sequences by using peroxidase mimetics of platinum nanoparticles supported on reduced graphene oxide. This nanocomposite possessed the combined advantages of platinum nanoparticles (superior peroxidase-like activity) and reduced graphene oxide (π-stacking interaction with single-stranded but not double-stranded DNA). The catalytic activity was strongly dependent on the chloroplatinic acid-to-graphene oxide mass ratio during the synthesis step, with an optimum ratio of 7 : 1. Unlike natural peroxidase, the nanocomposite had excellent stability over wide ranges of temperature (4-90 °C) and pH (1-13). For DNA detection, the nanocomposite had higher affinity for the single-stranded probe (in the absence of target) than the probe-target duplex. The probe-bound nanocomposite was stabilized against salt-induced aggregation and thus upon the addition of 3,3',5,5'-tetramethylbenzidine and hydrogen peroxide to the supernatant, an intense blue color was generated. The linear range and limit of detection of this assay platform were 0.5-10 nM and 0.4 nM, respectively. Moreover, this platform featured high specificity that 3-base-mismatched sequence could be distinguished with the naked eye and 1-base-mismatched sequence with absorbance measurement. Furthermore, the applicability for real sample detection was demonstrated by polymerase chain reaction product analysis. Taken together, this new platform is well suited for point-of-care and on-site nucleic acid testing.

Isolation and Characterization of Lytic Properties of Bacteriophages Specific for M. haemolytica Strains.

Aim of StudyThe objective of this study was isolation and morphological characterization of temperate bacteriophages obtained from M. haemolytica strains and evaluation of their lytic properties in vitro against M. haemolytica isolated from the respiratory tract of calves.Material and MethodsThe material for the study consisted of the reference strain M. haemolytica serotype 1 (ATCC®) BAA-410™, reference serotypes A1, A2, A5, A6, A7, A9 and A11, and wild-type isolates of M. haemolytica. Bacteriophages were induced from an overnight bacterial starter culture of all examined M. haemolytica strains treated with mitomycin C. The lytic properties and host ranges were determined by plaque assays. The morphology of the bacteriophages was examined in negative-stained smears with 5% uranyl acetate solution using a transmission electron microscope. The genetic analysis of the bacteriophages was followed by restriction analysis of bacteriophage DNA. This was followed by analysis of genetic material by polymerase chain reaction (PCR).ResultsEight bacteriophages were obtained, like typical of the families Myoviridae, Siphoviridae and Podoviridae. Most of the bacteriophages exhibited lytic properties against the M. haemolytica strains. Restriction analysis revealed similarities to the P2-like phage obtained from the strain M. haemolytica BAA-410. The most similar profiles were observed in the case of bacteriophages φA1 and φA5. All of the bacteriophages obtained were characterized by the presence of additional fragments in the restriction profiles with respect to the P2-like reference phage. In the analysis of PCR products for the P2-like reference phage phi-MhaA1-PHL101 (DQ426904) and the phages of the M. haemolytica serotypes, a 734-bp phage PCR product was obtained. The primers were programmed in Primer-Blast software using the structure of the sequence DQ426904 of reference phage PHL101.ConclusionsThe results obtained indicate the need for further research aimed at isolating and characterizing bacteriophages, including sequence analysis of selected fragments. Moreover, standardization of methods for obtaining them in order to eliminate M. haemolytica bacteria involved in the etiopathogenesis of BRDC is essential.

Mycobacterium tuberculosis complex identification by polymerase chain reaction from positive culture in patients from Jamot and Mbalmayo district hospitals

mycobacteria (NTM) such as Para nitro benzoic acid (PNB) inhibition tests are often time consuming. This study aim at using PCR amplification of specific markers (hupB, IS6110, IS1081, oxyR and rpoB) for more rapid detection of MTBC in positive cultures. The study was conducted in Jamot Hospital, the largest urban treatment center for tuberculosis in Cameroon and in Mbalmayo District Hospital, a small rural district hospital. Mycobacterial culture was performed on all smear positive sputa. All positive cultures were subjected to drug susceptibility testing (DST) using the indirect proportion method. On the same way, MTBC were differentiated from other mycobacreia using the PNP inhibition test. DNA extracted from positive cultures was subjected to PCR amplification using specific primers (hupB, IS6110, IS1081, oxyR and rpoB). Analysis of PCR products was done by agarose gel electrophoresis. A total of 79 smear positive pulmonary tuberculosis patients were enrolled at the two sites. Drug susceptibility carried out showed that among the samples analyzed, 68 (86.08%) were susceptible to all TB drugs tested, while 11 (13.92%) were resistant to at least one of them. Resistance to streptomycin was the most frequent (8.86%), followed by resistance to isoniazid (5.06%). Identification by PCR using specific markers as hupB, IS6110, IS1081, oxyR and rpoB revealed that the mycobacterium strains belonged to the MTBC.In short, identification by PCR using these specific makers revealed that mycobacterium species responsible for pulmonary tuberculosis in patients from Jamot and Mbalmayo District Hospital belonged to the MTBC. Also PCR technique is more rapid compared to the PNP inhibition test. Key words : Mycobacterium tuberculosis complex, polymerase chain reaction (PCR), Cameroon.

Investigation of the presence of class 1, 2, 3 integrons and their relationships with antibiotic resistance in clinical Stenotrophomonas maltophilia isolates

Stenotrophomonas maltophilia is an opportunistic emergent pathogen causing hospital-acquired infections. It is resistant to majority of the broad spectrum antibiotics due to several mechanisms which significantly limit the treatment options. Although the relationship between integrons, mobile genetic elements which play role in transferring resistance genes, and the antibiotic resistance in different gram-negative bacteria have been investigated, the data are limited in Turkey especially for S.maltophilia. The aims of this study were to detect the presence of different classes of integrons and plasmids in clinical isolates of S.maltophilia and to investigate the antibiotic resistance profiles of those isolates. One hundred S.maltophilia strains isolated from various clinical samples (32 sputum, 25 tracheal aspirates, 9 urine and blood, 7 exudates and catheters, 4 sterile body fluids and wounds, 2 CSF, 1 conjunctiva) in our microbiology laboratory during January 2011-September 2012, were included in the study. The isolates were identified by VITEK2 Compact (BioMerieux, France) or Phoenix 100 (BD, USA) automatized systems, and the susceptibilities of the strains to levofloxacin, chloramphenicol, ceftazidime and trimethoprim/sulfamethoxazol (SXT) were evaluated via broth microdilution method according to the CLSI recommendations. Class 1 (intI-1), class 2 (intI-2), class 3 (intI-3) integron gene cassettes and integron 5'-3' conserved gene regions (intI-5'-3'CS) were investigated by polymerase chain reaction (PCR) using specific primers in all of the strains. Nucleotide sequence analysis of PCR products was performed in case of positive result, and the presence and size of plasmids were further investigated. The susceptibility rates of S.maltophilia strains to ceftazidime, chloramphenicol, SXT and levofloxacin were found as 24%, 66%, 93% and 95%, respectively, while MIC(50) and MIC(90) values were 64-128 µg/ml, 8-16 µg/ml, 1/19-2/38 µg/ml and 1-2 µg/ml, respectively. In PCR amplification with intI-1, intI-2 and intI-3 primers, 12%, 2% and 10% of the isolates yielded expectative bands, respectively. DNA sequence analysis of the amplified products revealed five isolates to harbour intI-1 gene, while intI class 2 and class 3 genes were not detected in any of the strains. Furthermore in PCR amplification with intI-5'CS and 3'CS primers, 20% of the strains yielded expected bands. Sequence analysis of these amplicons revealed the presence of quaternary ammonium compound resistance protein genes (qacL) in two, aminoglycoside adenyltransferase gene (aadA) in one and integron-associated recombination site (attI1) genes in five strains. Additionally, the presence of plasmids have been detected in 9 (9%) of the strains, however all of them was integron-negative. The sizes of plasmids were 2340, 1350, 2760, 18600, 20000, 3570-2540, 2510 and 5000-2540 base pairs, respectively. When the antibiotic susceptibility patterns of strains were compared with the presence of intI gene regions, no statistically significant relationship was observed (p> 0.05). In conclusion, the demonstration of integron class 1 genes and plasmids among clinical S.maltophilia strains is regarded as a warning data to indicate the potential for spread of those resistant strains in our hospital.

Severe Congenital Toxoplasmosis: A Case Report and Strain Characterization

We report a fatal congenital toxoplasmosis case in an Iranian woman in the south of Iran. A pregnant mother had been admitted at the 15th week of her pregnancy on account of a febrile illness, symptoms of common cold, and enlargement of submandibular lymph nodes. Serological testing of the mother's serum revealed positive IgG and IgM anti-Toxoplasma antibodies. Amniotic fluid was taken and evaluated by polymerase chain reaction (PCR) assay with a direct amplification of the Toxoplasma URPT gene which was found to be positive. Sequencing and analysis of PCR product revealed that the isolate has the most similarity with type I of Toxoplasma gondii. Fetal scan showed anomaly in fetus including mild hydrocephaly. Termination of the pregnancy was suggested by the physician and pregnancy was terminated 178 days after conception.

First record of Ixodes arboricola (Ixodida: Ixodidae) from Turkey with presence of Candidatus Rickettsia vini (Rickettsiales: Rickettsiaceae).

Birds are the specific hosts of many tick species and may contribute to the dissemination of ticks and tick-borne pathogens throughout the world. Determination of ticks infesting birds and their pathogens are important for the detection of natural foci of human pathogens. Unfortunately, there is very limited information about the occurrence of ticks on birds and associated pathogens in Turkey. We performed a tick survey on three passerine bird species; Parus major, Sylvia atricapilla, and Turdus merula. Ticks collected from these birds were identified to species and tested for the presence of Borrelia, Ehrlichia, and Rickettsia species. Ixodes arboricola Schulze & Schlottke, Ixodes frontalis Panzer, and Ixodes ricinus L. were found on the birds. This is the first study reporting the presence of I. frontalis and I. arboricola on S. atricapilla and P. major, respectively, in Turkey. In addition, the results of polymerase chain reaction (PCR) with primers specific for gltA and ompA genes and DNA sequence analysis of positive PCR products indicated the presence of Candidatus Rickettsia vini in I. arboricola ticks. In conclusion, this is the first record of both I. arboricola and Candidatus Rickettsia vini in Turkey. Therefore, future studies needed to be conducted on the ticks infesting birds and their pathogens to elucidate the role of birds in the dispersal of tick species and tick-borne pathogens in Turkey.

Genetic properties of blaCTX-M and blaPER β-lactamase genes in clinical isolates of Enterobacteriaceae by polymerase chain reaction.

blaCTX-M and blaPER are two genes that encode class A extended-spectrum β-lactamases (ESBLs) and can be responsible for therapeutic problems. This study was carried out to evaluate the molecular properties of these genes in clinical isolates of Enterobacteriaceae by polymerase chain reaction (PCR), restriction digestion and sequencing. During six months, starting from January 2012, one hundred clinical isolates of Enterobacteriaceae were collected from urinary samples. The ESBL-producing isolates were detected by phenotypic confirmation test. After plasmid extraction, blaPER and blaCTX-M genes were detected using PCR by specific primers. The blaCTX-M PCR products were digested with Taq1, and two of the blaCTX-M genes were sequenced. Phenotypic tests showed that 27 (27%) isolates were ESBL producers with the highest frequency for Klebsiella pneumoniae (47.4%) and Escherichia coli (17.9%). Twenty six (26%) of Enterobacteriaceae isolates harbored the blaCTX-M gene, and none of them had blaPER . The restriction analysis of PCR products showed that all blaCTX-M amplified products had the same patterns. Both sequenced bacteria were CTX-M-15 type ESBL carriers. The results of this study showed the blaCTX-M-15 gene in Enterobacteriaceae isolates for the first time in Mashhad, Iran. High degrees of associated resistance to co-trimoxazole and gentamicin were found in ESBL producers. Therefore, an integrated and regular management of antibiotic prescription need to be trained in our society.

Molecular characterisation of phytoplasmas infecting roses in Poland

Symptoms of shoot dieback and leaf yellowing followed by leaf chlorosis were observed in naturally infected roses 'Frisco' and 'Suela', cultivated in a commercial greenhouse in Poland. The presence of phytoplasma was demonstrated in affected plants by nested polymerase chain reaction (PCR) with R16Fl/RO and Pl/P7 primer pairs in the first round followed by a second one with R16F2n/R2, fA/rA, Pc399/P1694, R16(I)Fl/Rl and Pl/fArev primer pairs. Restriction fragment length polymorphism (RFLP) analysis of PCR products (primed with primers R16F2n/R2) was done using enzymes AluI, MseI, RsaI and HpaII. Restriction profiles obtained with these enzymes were identical to those of reference strain AY1 belonging to aster yellows phytoplasma group, subgroup I-B (16SrI-B). Nested PCR products from roses 'Frisco' and 'Suela' were sequenced. Analysis of sequences confirmed that the phytoplasma infecting those roses could be classified to aster yellows phytoplasma group, subgroup B.

A Comparative Histopathology, Serology and Molecular Study, on Experimental Ocular Toxocariasis byToxocara catiin Mongolian Gerbils and Wistar Rats

The aim of this study was to compare the performance of three in-house diagnostic tests, that is, histopathology, enzyme-linked immunosorbent assay (ELISA), and polymerase chain reaction (PCR), for the diagnosis after experimental infection with Toxocara cati. Twenty Mongolian gerbils and Wistar rats were divided into ten groups (n = 2/group). Toxocara cati infections were established in Mongolian gerbils and Wistar rats by administering doses of 240 and 2500 embryonated Toxocara cati eggs by gavage, respectively. Tissue sections were stained with Haematoxylin and Eosin and observed under the light microscope. Sera and vitreous fluid collected from separate infected groups were tested against Toxocara cati antigens, for 92 days postinfection. Genomic DNA was extracted from formalin-fixed paraffin-embedded (FFPE) blocks, and aqueous fluids belong to the animals. The histopathology test gave negative results among the groups of animals examined between 5 and 92 days postinfection. The ELISA results showed that anti-Toxocara antibodies have risen between 7 and 61 days postinfection in sera and vitreous fluid in the animals infected, respectively. Analysis of PCR products revealed positive band (660 bp) in the orbital tissue infected Mongolian gerbils at 5 days postinfection. Of the three evaluated methods, the PCR could be recommended for scientific and laboratory diagnoses of toxocariasis in experimentally infected animals.

Entire DAX1 Gene Deletion in an Indian Boy with Adrenal Hypoplasia Congenita

To report a case of Adrenal hypoplasia congenita (AHC) in an Indian boy presenting with adrenal failure in the neonatal period. Molecular diagnosis demonstrated absence of the entire DAX1 gene sequence region. Real-time SYBR Green Polymerase Chain Reaction (PCR) amplification followed by melt curve analysis was the molecular analytical method used. Analysis of the PCR products by Agarose gel electrophoresis was also performed. Real-time SYBR Green PCR amplification carried out on a 240 bp region of Exon 1 and 320 bp region of Exon 2 of DAX1 gene did not result in any amplification for two independent DNA extractions of the patient sample. The melt curve analysis also failed to show the characteristic melt peaks. Additional analysis of the PCR products performed by Agarose gel electrophoresis of the patient samples did not reveal any DNA bands. Inability to amplify two distinct regions located on two distinct exons of the DAX1 gene of the patient sample point to the possible absence of the entire DAX1 gene sequence region in the index patient. Such molecular diagnostic techniques may prove very useful in making a diagnosis as well as for genetic counseling.