PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “DNA analysis”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 919 records · Page 51Linked to original sources
PubMed2004

Trichomonas vaginalis: random amplified polymorphic DNA analysis of isolates from symptomatic and asymptomatic women in India.

Trichomonas vaginalis, the causative agent for human trichomoniasis, is a protozoan parasite. Trichomoniasis is the most common non-viral sexually transmitted disease. The infection in women may be asymptomatic or may lead to severe vaginitis, cervicitis and severe sequelae. Despite its high prevalence, the genetic variability and factors leading to symptomatic infection have been poorly understood. One thousand women in childbearing age group were screened for the presence of T vaginalis. Thirty-eight women were found positive for T vaginalis and out of these 22 (57.9%) were having symptomatic infection and 16 (42%) were asymptomatic. Fresh isolates from 15 symptomatic and 15 asymptomatic women were axenised and subjected to random amplified polymorphic DNA (RAPD) analysis with the use of five different random primers (OPD 1-OPD 5). The isolates with similar banding pattern were assigned as a single type. OPD 3 indicated least (nine types) while OPD 4 indicated highest typing (18 types) ability. Phylogenetic analysis using RAPD distance software indicated two distinct lineages; upper branch consisting of only seven symptomatic isolates while lower branch consisting of all the 15 asymptomatic isolates the other eight symptomatic isolates were recorded in separate cluster. The study indicated that RAPD technique might be helpful to delineate the pathogenic mechanism(s) for its virulence; however, further studies on large number of isolates are desired to elucidate the findings.

Animals↗
PubMed2006

Drug resistance and random amplified polymorphic DNA analysis of Photobacterium damselae ssp. piscicida isolates from cultured Seriola (yellowtail, amberjack and kingfish) in Japan.

AIMS: To investigate the antimicrobial susceptibility and genetic characteristics of Photobacterium damselae ssp. piscicida isolates obtained from cultured Seriola in Japan. METHODS AND RESULTS: Minimal inhibitory concentrations of 14 antimicrobials for 74 isolates from Seriola in Japan in 2002 were determined. Isolates showed high frequencies of resistance to sulfamonomethoxine (SMMX) (97.3%), oxytetracycline (OTC) (77.0%), flumequine (FMQ) (77.0%), chloramphenicol (CP) (75.7%), kanamycin (KM) (63.5%) and oxolinic acid (OA) (62.0%), but low to ampicillin (ABPC) (2.8%). All isolates were susceptible to bicozamycin (BCM), fosfomycin (FOM) and florfenicol (FF). Of these isolates, 45 (60.8%) showed same resistance pattern (SMMX-OTC-FMQ-OA-CP-KM). In random amplified polymorphic DNA (RAPD) analysis, no difference was observed among our 74 field isolates and ATCC51736 isolated from Seriola in 1974 in Japan, but different from ATCC 17911 isolated from white perch in USA. CONCLUSIONS: FF, BCM, FOM and ABPC were useful antimicrobials for treating pseudotuberculosis. However, the frequency of multidrug resistance was high. RAPD analysis showed homogeneity of isolates from Seriola in Japan. SIGNIFICANCE AND IMPACT OF THE STUDY: This study demonstrates that some antimicrobials were still useful for treating pseudotuberculosis and that P. damselae ssp. piscicida strains of same origin might have spread among Seriola in Japan since 1974.

Animals↗
PubMed1997

Mitochondrial DNA analysis of Phialophora verrucosa.

Restriction fragment length polymorphism (RFLP) of mitochondrial DNA (mtDNA) was examined in 32 isolates of Phialophora verrucosa (eight isolates from Japan, 10 from China, four from the USA, six from Venezuela and four from Colombia) and in three of Phialophora americana using five restriction enzymes. P. verrucosa isolates were divided into 10 mtDNA types based on RFLP patterns. Phylogeny constructed on sequence divergence of mtDNA indicated that P. verrucosa is a single species and isolates are clustered into three groups. Japan and the USA contained Group A and Group B isolates, China Group B isolates and South America Group B and Group C isolates. RFLP patterns of P. americana mtDNA were identical to those of Type 1 or Type 4 of P. verrucosa mtDNA, suggesting that both are identical. RFLP patterns of P. verrucosa were distinct from those of other dematiaceous fungi including Exophiala jeanselmei, E. moniliae, E. dermatitidis, E. spinifera, Cladophialophora (Cladosporium) carrionii, Fonsecaea pedrosoi, and Hortaea werneckii. These results indicate that RFLP analysis of mtDNA is a useful method for the identification, taxonomy, typing, epidemiology and phylogeny of P. verrucosa.

DNA, Fungal↗
PubMed1990

Typical and atypical carcinoid tumors of lung: a clinicopathologic and DNA analysis of 20 tumors.

Twelve typical carcinoid tumors (TCT) and eight atypical (malignant) carcinoid tumors (ACT) of the lung were studied for quantitative DNA content by image analysis in order to identify prognostic features. No correlation of any histologic variables of the TCTs and ACTs with abnormal DNA content were noted. Furthermore, it was concluded that although abnormalities of DNA content, particularly aneuploidy, are common in ACTs, DNA ploidy cannot be used independently to assess malignant potential.

Adult↗
PubMed1999

Identification by 16S rDNA fragment amplification and determination of genetic diversity by random amplified polymorphic DNA analysis of Pasteurella pneumotropica isolated from laboratory rodents.

Pasteurella pneumotropica is an opportunistic bacterium frequently isolated from colonies of various laboratory rodents. Identification of this species, including its differentiation into two distinct biotypes (Jawetz and Heyl), is usually based on the use of conventional bacteriologic methods. In this study, a 16S rDNA fragment amplification procedure was developed for use as an alternative method for identification and differentiation of P. pneumotropica. Polymerase chain reaction (PCR) products were two distinctive fragments of 937 and 564 bp specific for biotypes Jawetz and Heyl, respectively. Specificity of PCR products could be achieved by EcoRI cleavage, leading to 596 plus 341-bp and 346 plus 218-bp fragments for each of the amplification products. Use of this procedure confirmed identification of 34 field isolates and allowed definitive identification of some strains that could not have been done by use of bacteriologic examinations. Field isolates subjected to random amplified polymorphic DNA (RAPD) analysis had high genetic diversity among biotype Jawetz strains in contrast to biotype Heyl strains. In conclusion, RAPD could represent an additional means for identification of ambiguous strains of biotype Heyl and a valuable epidemiologic tool for identification of biotype Jawetz strains of P. pneumotropica.

Animals↗
PubMed2002

Microbial diversity in an in situ reactor system treating monochlorobenzene contaminated groundwater as revealed by 16S ribosomal DNA analysis.

A molecular approach based on the construction of 16S ribosomal DNA clone libraries was used to investigate the microbial diversity of an underground in situ reactor system filled with the original aquifer sediments. After chemical steady state was reached in the monochlorobenzene concentration between the original inflowing groundwater and the reactor outflow, samples from different reactor locations and from inflowing and outflowing groundwater were taken for DNA extraction. Small-subunit rRNA genes were PCR-amplified with primers specific for Bacteria, subsequently cloned and screened for variation by restriction fragment length polymorphism (RFLP). A total of 87 bacterial 16S rDNA genes were sequenced and subjected to phylogenetic analysis. The original groundwater was found to be dominated by a bacterial consortium affiliated with various members of the class of Proteobacteria, by phylotypes not affiliated with currently recognized bacterial phyla, and also by sporulating and non-sporulating sulfate-reducing bacteria. The most occurring clone types obtained from the sediment samples of the reactor were related to the beta-Proteobacteria, dominated by sequences almost identical to the widespread bacterium Alcaligenes faecalis, to low G+C gram-positive bacteria and to Acidithiobacillus ferrooxidans (formerly Thiobacillus ferrooxidans) within the gamma subclass of Proteobacteria in the upper reactor sector. Although bacterial phylotypes originating from the groundwater outflow of the reactors also grouped within different subdivisions of Proteobacteria and low G+C gram-positive bacteria, most of the 16S rDNA sequences were not associated with the sequence types observed in the reactor samples. Our results suggest that the different environments were inhabited by distinct microbial communities in respect to their taxonomic diversity, particular pronounced between sediment attached microbial communities from the reactor samples and free-living bacteria from the groundwater in- and outflow.

Bacteria↗
PubMed2004

Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa).

This study presents the first 18S rRNA multi-library environmental PCR survey of a single protozoan phylum, Cercozoa Cavalier-Smith 1998, from a range of different habitats. Phylogenetic analysis reveals at least nine novel clades within the phylum, several possibly at the level of order or above. Further experiments are described to ascertain the true ecological and geographical distributions of some clades that might be inferred from the tree to be restricted in either or both ways. These results suggest that the diversity of cercozoan taxa may run into thousands of lineages, making it comparable in diversity to the largest better-characterized protozoan phyla, e.g. Ciliophora (ciliates and suctorians) and Foraminifera. New sequences of cultured Spongomonas, Metromonas and Metopion are also presented. In the light of these additions, and the increased taxon sampling from the environmental libraries, some revisions of cercozoan classification are made: the transfer of Spongomonadea from Reticulofilosa to Monadofilosa; the removal of Metopiida from Sarcomonadea; and the creation of the new order Metromonadida, currently containing the single genus Metromonas. Although Metromonas groups with weak to moderate support with Chlorarachnea, it is here placed in superclass Monadofilosa, to which it is morphologically more similar.

Animals↗
PubMed1996

DNA analysis in the study of fungal infections in the immunocompromised host.

Fungal infections, most of which are caused by the Candida species, are an increasing problem in the immunocompromised host. The clinical manifestations of Candida infections include disseminated candidiasis, oral and esophageal infections, focal hepatic infections, peritoneal urinary tract infections, and wound infections. DNA methods, which include pulse field electrophoresis and restriction enzyme analysis of genomic DNA, have been used to increase understanding of the epidemiology of these infections. These techniques have shown that most Candida infections are endogenous or acquired from one's own flora. Recent outbreaks have provided evidence for exogenous acquisition of some isolates. Better methods for differentiation of colonization versus infection and identifying infection in the absence of positive cultures are under investigation.

Adult↗
PubMed1994

Speciation in the Artemia genus: mitochondrial DNA analysis of bisexual and parthenogenetic brine shrimps.

From the cloned mitochondrial DNAs (mtDNAs) isolated from two bisexual species, one Mediterranean, Artemia salina, and one American, Artemia franciscana, and two parthenogenetic (diploid and tetraploid) strains of Artemia parthenogenetica collected in Spain, physical maps have been constructed and compared. They are extremely different among themselves, much more than the differences between Drosophila melanogaster and D. yakuba and in the same range of different mammalian species such as mouse/rat or man/cow. The nucleotide sequences of two regions of mtDNA encoding parts of the cytochrome c oxidase subunit I (COI) and cytochrome b (Cytb) genes have been determined in the two bisexual species and the two parthenogenetic strains. Comparisons of these sequences have revealed a high degree of divergence at the nucleotide level, averaging more than 15%, in agreement with the differences found in the physical maps. The majority of the nucleotide changes are silent and there is a strong bias toward transitions, with the C<==>T substitutions being highly predominant. The evolutionary distance between the two Artemia parthenogenetica is high and there is no clear relationship with any of the bisexual species, including the one present nowadays in Spain. Using a combination of molecular (mtDNA) and morphological markers it is possible to conclude that all of these Artemia isolates should be actually considered as belonging to different species, even the two Artemia parthenogenetica diploidica and tetraploidica.

Amino Acid Sequence↗
PubMed2000

Sandhoff disease in Cyprus: population screening by biochemical and DNA analysis indicates a high frequency of carriers in the Maronite community.

In the last 15 years, four patients with the infantile form of Sandhoff disease were diagnosed in four different families in Cyprus (population 703,000, birth rate 1.7%). Three of these cases came from the Christian Maronite community (less than 1% of the population) and one from the Greek community (84% of the population). This relatively large number of patients prompted us to initiate an epidemiological study in order to establish the frequency of the mutant allele in Cyprus. Carrier detection was initially based on the measurement of beta-hexosaminidase A and B in both leucocytes and serum. Using the enzyme test, 35 carriers were identified among 244 random Maronite samples and 15 among 28 Maronites with a family history of Sandhoff disease, but only one carrier was found out of 115 random samples from the Greek community. In parallel to the biochemical screening, DNA studies were undertaken in one of the three Maronite patients and in a Greek carrier related to the Greek patient. These studies resulted in the identification of two novel mutations, a deletion of A at nt76 and a G to C transversion at position 5 of the 5'-splice site of intron 8, which have been published. We subsequently screened the carriers detected in the biochemical study for these two mutations using PCR-based tests. Of 50 Maronite carriers examined, 42 were found to have the nt76 deletion. Eight Maronite samples, designated carriers from the biochemical results, were negative for both mutations. It is possible that these individuals were incorrectly classified as carriers since their enzyme values are equivocal, although the presence of another mutation has not been excluded. Two Greek Cypriot carriers and two obligate Lebanese carriers were negative for both mutations. We conclude that there is a high frequency of Sandhoff disease carriers in the Maronite community of Cyprus, approximately 1 in 7, and that a single mutation predominates in this population.

Cyprus↗
PubMed1997

Oropharyngeal or gastric colonization and nosocomial pneumonia in adult intensive care unit patients. A prospective study based on genomic DNA analysis.

Colonization of the digestive tract has been supposed to be the source of many hospital-acquired infections, especially nosocomial pneumonia. To assess the relationship between oropharyngeal and gastric colonization and subsequent occurrence of nosocomial pneumonia, we prospectively studied 86 ventilated, intensive care unit (ICU) patients. Oropharyngeal or gastric colonizations were detected and quantified on admission and twice weekly during ICU stay. When nosocomial pneumonia was suspected on clinical grounds (new chest X-ray infiltrate and purulent tracheal secretions), diagnosis was assessed on fiberoptic bronchoscopy with quantitative cultures of a protected specimen brush sampling and/or a plugged telescoping catheter sampling yielding > or = 10(3) cfu/ml of at least one microorganism. Bacterial strains responsible for colonization and infection (Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacteriaceae, and Staphylococcus aureus) were compared using pulsed-field electrophoresis. A total of 31 cases (36%) of pneumonia were diagnosed. Oropharyngeal colonization, detected either on admission or from subsequent samples, was a predominant factor of nosocomial pneumonia as compared with gastric colonization. For instance, oropharyngeal colonization with A. baumannii yielded a 7.45-fold estimated increased risk of pneumonia as compared with patients not yet or not identically colonized (p = 0.0004). DNA genomic analysis demonstrated that an identical strain was isolated from oropharyngeal or gastric samples and bronchial samples in all but three cases of pneumonia, due to S. aureus. These findings provide better knowledge of the pathophysiology of nosocomial pneumonia in mechanically ventilated patients.

Adult↗
PubMed1996

Role of immunocytochemistry, electron microscopy, and DNA analysis in fine-needle aspiration biopsy diagnosis of Wilms' tumor.

We reviewed the cytologic features and results of ancillary studies in eight fine-needle aspiration biopsies (FNAB) performed by posterior approach in 8 patients with unresectable Wilms' tumor (WT). Chemotherapy was given following the FNAB diagnosis of WT, which was confirmed subsequently by histologic examination of surgically resected specimens. Indications for FNAB included: unresectable tumor, bilateral disease, initial presentation with metastatic disease, uncertainty regarding tumor site, and documentation of recurrence. Cytologic examination revealed blastemal cells (8/8 aspirates), spindle cells (3/8 aspirates), and epithelial differentiation or tubules (3/8 aspirates). There was no cytologic evidence of anaplasia in any of the cases. Immunocytochemical studies on cell blocks and/or smears showed cytokeratin positivity in 5/8 and vimentin positivity in 5/5 of the aspirates in which these studies were performed. Focal positivity for neuron-specific enolase (NSE) was seen in 3/3 aspirates. Stains for actin and leukocyte-common antigen were negative (0/3 and 0/2 aspirates, respectively). DNA ploidy analysis of the aspiration material by flow cytometry revealed near-diploid populations in three aspirates. Electron microscopic findings helpful for diagnosis included: cell junctions, microvilli, flocculent basement membrane-like material, cilia, autophagolysosomes, and lack of neuroectodermal differentiation. Diagnostic morphologic pitfalls for an incorrect diagnosis of neuroblastoma included nuclear molding (all aspirates), pseudorosette formation (one aspirate), and focal NSE positivity (3/3 aspirates). None of the tumors showed anaplasia on histologic examination. Cytologic recognition of the triphasic cellular components of WT (blastemal cells, spindle cells, and epithelial cells) can be helpful for a correct diagnosis; however, in 5/8 aspirates in this study, only the blastemal component was present. In these cases, immunocytochemical stains and electron microscopy proved useful in arriving at a correct FNAB diagnosis of WT. However, NSE positivity can be a pitfall for a diagnosis of neuroblastoma if the radiologic, clinical, and other cytologic features are not clearly delineated. Presence of cytokeratin and vimentin positivity would be helpful in the diagnosis of WT in such instances.

Biopsy, Needle↗
PubMed2004

DNA analysis from mixed biological materials.

At the crime scene a mixture of biological samples from more than one individual often happens and since generally different contributors may give in the mixture a different contribution of biological material, in this study we have evaluated this effect on STRs analysis.

DNA↗
PubMed2002

Complementary DNA analysis, expression and subcellular localization of hnRNP E2 gene in Xenopus laevis.

The cloning and sequencing of complementary DNAs corresponding to the two copies (a and b) of the Xenopus laevis gene for hnRNP E2 is presented. Comparison of the two sequences reveals that while they are somewhat divergent at the nucleotide level, they are very conserved at the amino acid level. The analysis also showed two transcripts of different length (alpha and beta), likely generated by alternative processing. There are indications that either gene copy can generate both type of transcripts. Northern blot analysis in oocytes and developing embryos showed that hnRNP E2 RNA is constantly present and that increases in amount at tadpole stage. A semiquantitative reverse transcriptase polymerase chain reaction analysis performed with RNA from developing embryos showed that long (alpha) transcript accumulation is constant during development, whereas the short one (beta) accumulation increases at later stages, thus determining the observed increase in total RNA. Nucleo-cytoplasm localization experiments indicated that in oocyte hnRNP E2 is exclusively cytoplasmic, whereas in somatic cells it is distributed in both compartments. Comparison of the amino acid sequence of the two X. laevis hnRNP E2 with the corresponding mammalian sequences shows a high homology along the molecule except for the region subjected to alternative splicing, which is completely different. Moreover, there are indications that the homologous of mammalian hnRNP E1 gene, very related to and derived from hnRNP E2 by retrotransposition, is not expressed or even not present in X. laevis, suggesting that mammalian hnRNP E1 gene may have originated after mammal/amphybia divergence.

Amino Acid Sequence↗
PubMed1996

Cytophotometric DNA-analysis of bone-tumors. A new method for preparing formalin-fixed tissue and the regarding of DNA-malignancy grade and its prognostic value.

78 benign and malign, formalin-fixed bone or bone-associated tumors of different origin were prepared for image-cytophotometric measuring with a new method of preparing. The DNA-content of the tumors and the so resulting malignancy-grade were determined and compared with the corresponding measurements of unprepared fresh tumors respectively paraffin-embedded tissue sections. Regarding the comparison of the fresh material with the formalin-fixed material, no significant difference (p < or = 0.01) of the data could be found. There was also no significant difference (p < or = 0.01) concerning the comparison of the data obtained from the formalin-fixed material and the data from the tissue sections. The criterium aneuploidy showed a sensitivity of 86% and a specificity of 100% in regards to identifying a malignant tumor, irrespective of the preparation method. A strong correlation could be found (p < 0.001) between the DNA-malignancy grade and the survival rate of the patients.

Age Factors↗
PubMed2003

Random amplified polymorphic DNA analysis of Anopheles nuneztovari (Diptera: Culicidae) from Western and northeastern Colombia.

Random amplified polymorphic DNA (RAPD) markers were used to analyze 119 DNA samples of three Colombian Anopheles nuneztovari populations to study genetic variation and structure. Genetic diversity, estimated from heterozygosity, averaged 0.34. Genetic flow was greater between the two populations located in Western Colombia (F ST: 0.035; Nm: 6.8) but lower between these two and the northeastern population (F ST: 0.08; Nm: 2.8). According to molecular variance analysis, the genetic distance between populations was significant (phi ST 0.1131, P < 0.001). The variation among individuals within populations (phi ST 0.8869, P < 0.001)was also significant, suggesting a greater degree of population subdivision, not considered in this study. Both the parameters evaluated and the genetic flow suggest that Colombian An. nuneztovari populations are co-specific.

Animals↗
PubMed1992

Flow cytometric DNA analysis in Japanese colorectal cancer. A multivariate analysis.

Using Cox's proportional hazard model, we performed a multivariate analysis of survival data from 126 patients who underwent curative resection for colorectal cancer from 1971 to 1985. Flow cytometric DNA measurements were carried out using paraffin wax-embedded tissue blocks. Fifty-four per cent of the cases were found to be aneuploid and 46% were diploid. The depth of invasion of the tumor, nodal status, liver metastasis, peritoneal dissemination, DNA ploidy pattern, histology, macroscopic classification of the tumor, age, sex and site were tested in a survival analysis. The initial seven factors were found to be the significant prognostic variables in a univariate analysis. A multivariate analysis shows liver metastasis, DNA ploidy pattern and peritoneal dissemination as being the significant discriminants of survival (P = 0.0001, 0.0022, 0.0119, in this order). Therefore, nuclear DNA ploidy pattern in colorectal cancer is considered to be an independent prognostic factor.

Adult↗