Comparison of karyotype analysis and RT-PCR for AML1/ETO in 204 unselected patients with AML

Clinical isolates of Microsporum canis and M. gypseum from humans, dogs and cats were examined by random amplification of polymorphic DNA (RAPD) and Southern hybridization analyses. The RAPD band patterns of six clinical isolates of M. canis were identical to those of standard strains of Arthroderma otae. Of nine clinical isolates of M. gypseum seven and two isolates showed RAPD patterns identical to those of standard strains of A. gypseum and A. incurvatum respectively. Southern blot analysis using a probe (C3) obtained from A. otae DNA revealed that six clinical isolates of M. canis showed specific bands identical to those detected in the standard strains of A. otae. Of nine clinical isolates of M. gypseum, seven and two isolates showed bands hybridized by the C3 probe identical to those detected in A. gypseum and A. incurvatum respectively. Furthermore, the results from mating experiments on these nine clinical isolates of M. gypseum showed complete agreement with the results from RAPD and Southern hybridization analyses. These findings clearly indicate that RAPD and Southern hybridization analyses are very useful in the identification of clinical isolates of M. canis and M. gypseum.     

Phylogenetic analysis of 8 dermatophyte species using chitin synthase 1 gene sequences

Nucleotide sequences of chitin synthase 1 (CHS1) gene of eight species of dermatophytes, Arthroderma benhamiae, A. fulvum, A. grubyi, A. gypseum, A. incurvatum, A. otae, A. simii and A. vanbreuseghemii were obtained and analysed for their phylogenetic relationship. A 600-bp genomic DNA fragment of the CHS1 gene was amplified from these dermatophytes by polymerase chain reaction (PCR) and sequenced. The CHS1 nucleotide sequences of these eight dermatophyte species showed more than 85% similarity between the species. The phylogenetic analysis of their sequences revealed three clusters, the first cluster consisting of A. benhamiae, A. simii and A. vanbreuseghemii, the second cluster consisting of A. fulvum, A. gypseum and A. incurvatum, and the third cluster consisting of A. grubyi and A. otae. The phylogenetic analysis of CHS1 gene in this study will provide useful information for classification and understanding the evolution of these dermatophyte species.     

Distribution of genes conferring combined resistance to tetracycline and minocycline among group B streptococcal isolates from humans and various animals

Forty-nine tetracycline and minocycline resistant streptococci of serological group B isolated from humans, cattle, pigs and nutrias were investigated for the presence of genes conferring this combined resistance. Southern blot hybridization of EcoRI-digested chromosomal DNA of the bacteria revealed for 39 of the cultures a hybridization signal with tet(M), for four of the cultures a hybridization signal with tet(O) and for none of the cultures a hybridization signal with the tet(Q) gene probe. The restriction endonuclease digested and blotted DNA of six tetracycline and minocycline resistant group B streptococci did not hybridize with any of the available gene probes. The tet(M) gene probes recognized complementary sequences of EcoRI fragments of approximately 10.5 kb and 21.5 kb, the tet(O) gene probe hybridized with fragments of approximately 19 kb. The hybridization of the tet(M) gene probe in two different patterns appeared to be related to the origin of the cultures.     

Human cutaneous leishmaniasis caused by Leishmania (Viannia) braziliensis in Santiago del Estero, Argentina: identification of parasites by monoclonal antibodies and isoenzymes

Bacteroides forsythus is a fastidious anaerobic Gram-negative organism associated with active periodontal disease. The ability of random amplified polymorphic DNA (RAPD) fingerprinting to generate species-specific markers was exploited towards the construction of a polymerase chain reaction (PCR)-DNA probe assay specific for B. forsythus. The strategy included the four following steps: (1) construction of a first generation DNA probe based on a 507-bp RAPD species-specific marker; (2) cloning and sequencing the 507-bp RAPD marker; (3) design of the primer pair Bf 392-1/Bf 392-2 flanking a 392-bp specific internal sequence; and (4) synthesis of quantities of a 392-bp second generation DNA probe by PCR amplification. The PCR-DNA probe assay includes a PCR amplification of a 392-bp specific sequence in the genomic DNA of B. forsythus strains followed by hybridization with the 392-bp digoxigenin-labelled second generation probe. We observed strong, specific hybridization with the amplified DNAs from 11 stains of B. forsythus and no cross-hybridization with the PCR products from 22 foreign species. The PCR-DNA probe assay must be seen as a highly specific and sensitive method for the detection of B. forsythus in mixed infections.     

Hourly activity of Lutzomyia ovallesi and L. gomezi (Diptera:Psychodidae), Vectors of cutaneous leishmaniasis in northcentral Venezuela

Random amplified polymorphic DNA (RAPD) analysis was used to amplify the genome of black tiger prawns (Penaeus monodon) to detect DNA markers and assess the utility of the RAPD method for investigating genetic variation in wild P. monodon in Thailand. A total of 200 ten-base primers were screened, and 84 primers yielded amplification products. Six positive primers that gave highly reproducible RAPD patterns were selected for the analysis of three geographically different samples of Thai P. monodon. A total of 70 reproducible RAPD fragments ranging in size from 200 to 2000 bp were scored, and 40 fragments (57%) were polymorphic. The RAPD analysis of broodstocks from three different locales, Satun-Trang, Trat, and Angsila, revealed different levels of genetic variability among the samples. The percentages of polymorphic bands were 48% and 45% in Satun-Trang and Trat, respectively, suggesting a high genetic variability of the two samples to be used in selective breeding programs. Only 25% polymorphic bands were found in the Angsila sample, indicating the lowest polymorphic level among the three samples examined. Primer 428 detected a RAPD marker that was found only in P. monodon originating from Satun-Trang, suggesting the potential use of this marker as a population-specific marker in this species.     

Distribution of transposable elements in neotropical species of Drosophila

The phylogenetic distribution of transposable families, P, gypsy, hobo, I, and mariner has been analyzed in 33 species of 11 groups of neotropical Drosophila and a Drosophilidae species Zygotrica vittimaculosa, using squash blot and dot blot. Genomic DNA of almost all neotropical species tested hybridized with gypsy probe and some species showed a particularly strong hybridization signal, as D. gaucha, D. virilis, and species of flavopilosa group. The hobo element was restricted to melanogaster group and some strains of D. willistoni. Only D. simulans DNA showed hybridization to mariner probe in all species tested and D. simulans and D. melanogaster showed hybridization with I element probe. P element homologous sequence was present in D. melanogaster and all species and strains of the willistoni and saltans groups tested. The presence of at least one P-homologous sequence was detected in Drosophila mediopunctata. This one was the only P-bearing species of all six tested from the tripunctata group. Four different pairs of primers homologous to segments of the canonical sequence of D. melanogaster's P were used to amplify specific sequences from D. mediopunctata DNA, showing the occurrence of seemingly well-conserved P-homologous sequences.     

Gene transfer via pollen-tube pathway for anti-fusarium wilt in watermelon

In order to obtain transgenic fusarium wilt resistant watermelon plants, squash DNA was introduced into the ovaries of watermelon plants via the pollen-tube pathway. The introduction of foreign genes into ovaries was accomplished using co-transformation with the CaMV35S-GUS as a marker. Transformed watermelon plants contained integrated copies of the GUS activity and the seeds of transformed progeny produced a blue color when stained with 5-bromo-4-chloro-3-indolyl glucuronide, whereas seeds from untransformed control plants did not. Of 200 transformed seedlings, ten were wilt resistant. The presence of the GUS activity in the genome of stable transgenic seedlings was confirmed by Southern blot analysis. Furthermore, the generation of random amplified polymorphic DNA (RAPD) fingerprints using primers with embedded restriction sites showed amplification products unique to these transgenic plants. Primers OPA-1 and OPA-9 gave distinct band patterns of genomic DNA using the polymerase chain reaction.     

No evidence of HTLV-I proviral integration in lymphoproliferative disorders associated with cutaneous T-cell lymphoma

Several recent studies have reported detection of HTLV-I genetic sequences in patients with cutaneous T-cell lymphoma (CTCL) including mycosis fungoides and Sezary syndrome. The purpose of this study was to determine whether HTLV-I was detectable in lesional tissues of patients suffering from diseases known to be associated with CTCL. Thirty-five cases were obtained from diverse geographical locations including Ohio, California, Switzerland, and Japan. Six of them had concurrent CTCL. Cases were analyzed using a combination of genomic polymerase chain reaction (PCR)/ Southern blot, dot blot, and Southern blot analyses. All assays were specific for HTLV-I provirus. Sensitivity ranged from approximately 10(-6) for PCR-based studies to 10(-2) for unamplified genomic blotting. Lesional DNA from patients with lymphomatoid papulosis (fourteen cases), Hodgkin's disease (twelve cases), and CD30+ large-cell lymphoma (nine cases) was tested for the HTLV-I proviral pX region using a genomic PCR assay followed by confirmatory Southern blot analysis with a nested oligonucleotide pX probe. All cases were uniformly negative. All of the Hodgkin's disease cases, eight of the large-cell lymphoma cases, and six of the lymphomatoid papulosis cases were then subjected to dot blot analysis of genomic DNA using a full-length HTLV-I proviral DNA probe that spans all regions of the HTLV-I genome. Again, all cases were negative. Finally, eleven of the Hodgkin's disease cases were also subjected to Southern blot analysis of EcoRI-digested genomic DNA using the same full-length HTLV-I probe. Once again, all cases were negative. These findings indicated that, despite utilization of a variety of sensitive and specific molecular biological methods, HTLV-I genetic sequences were not detectable in patients with CTCL-associated lymphoproliferative disorders. These results strongly suggest that the HTLV-I retrovirus is not involved in the pathogenesis of these diseases.     

Application of random amplified polymorphic DNA analysis for detection of Salmonella spp. in foods

The random amplified polymorphic DNA (RAPD) band patterns from 23 Salmonella spp. produced by use of an oligonucleotide primer (called du primer) designed on the basis of the N-terminal sequence of dulcitol 1-phosphate dehydrogenase (5'-GTGGTGACCCAGGATGGCCAGGTG-3') were different from those from 16 non-Salmonella spp. The bands at 460 and 700 bp were produced in all Salmonella strains tested. These RAPD fragments obtained from Salmonella typhimurium strongly hybridized with the corresponding RAPD bands from the other strains of Salmonella, but not with those from non-Salmonella spp. in Southern blot analysis. The RAPD bands were detected by ethidium bromide staining even when genomic DNA prepared from as few as 2.8 x 10(3) cells was used. The minimum detectable cell number in the initial inoculum of S. typhimurium was 4 x 10(-1) CFU/25 g of raw beef after the preenrichment in Enterobacteriaceae enrichment mannitol (EEM) broth for 6 h and the selective enrichment in dulcitol-magnesium chloride-pyridinesulfonic acid-brilliant green-novobiocin (DMPBN) medium for 18 h at 42 degrees C. Seven raw foods inoculated with S. typhimurium at numbers from 4 x 10(-1) to 2.6 x 10(2) CFU/25 g of food were positive in both the RAPD analysis and the conventional culture method.     

Identification of Aeromonas hydrophila hybridization group 1 by PCR assays

Synthetic oligonucleotide primers of 24 and 23 bases were used in a PCR assay to amplify a sequence of the lip gene, which encodes a thermostable extracellular lipase of Aeromonas hydrophila. A DNA fragment of approximately 760 bp was amplified from both sources, i.e., lysed A. hydrophila cells and isolated DNA. The amplified sequence was detected in ethidium bromide-stained agarose gels or by Southern blot analysis with an internal HindIII-BamHI 356-bp fragment as a hybridization probe. With A. hydrophila cells, the sensitivity of the PCR assay was < 10 CFU, and with the isolated target, the lower detection limit was 0.89 pg of DNA. Primer specificity for A. hydrophila was determined by the PCR assay with cells of 50 strains of bacteria, including most of the 14 currently recognized DNA hybridization groups of Aeromonas spp. as well as other human and environmental Aeromonas isolates. Detection of A. hydrophila by PCR amplification of DNA has great potential for rapid identification of this bacterium because it has proved to be highly specific.     

The mouse C1q genes are clustered on chromosome 4 and show conservation of gene organization

Mouse complement component C1q is a serum glycoprotein which consists of six A chains, six B chains and six C chains. The three polypeptides are 223, 228, and 217 residues long, respectively, and are encoded by three genes. DNA probes for mouse C1q A, B, and C chains were hybridized to Southern blots of DNA obtained from various inbred mouse strains. On the basis of fragment length polymorphisms, two different alleles of each of the genes could be identified. The distribution of these alleles was determined in the BXD and LXPL recombinant inbred strain series. Comparison with previously reported strain distribution patterns shows that the genes encoding mouse C1q map to the same locus on distal chromosome 4. Overlapping clones spanning the entire gene cluster of C1q were isolated from genomic libraries using specific cDNA probes. The three genes C1qA, C1qB, and C1qC are closely arranged on a 19 kilobase stretch of DNA in the 5' to 3' orientation A-C-B. Each gene consists of two exons separated by one intron. Sequence comparison of C1q from three different species have shown that the B chains have the strongest similarity. Southern blot analysis of chromosomal DNA from 14 vertebrate species demonstrated highest similarity between the C1qB genes, followed by C1qC and finally C1qA.     

Activation of latent HIV-1 by Mycobacterium tuberculosis and its purified protein derivative in alveolar macrophages from HIV-infected individuals in vitro

A chromosome-specific satellite DNA from the South American fish species Leporinus obtusidens has been isolated and characterized. Sequence analysis and Southern hybridization studies indicate that the cloned 483-bp fragment is 60% AT rich and appears to comprise two diverged monomers. A highly variable low-copy number polymorphism was detected and, thus, this satellite DNA may serve as a valuable genetic marker. Using a Southern blot approach, the cloned satellite DNA cross-hybridized strongly to the DNA of Leporinus elongatus but failed to detect homologous sequences in the genomes of other closely related Leporinus species and higher vertebrates. Using fluorescence in situ hybridization to mitotic metaphase spreads of L. obtusidens and L. elongatus, this satellite DNA was located to the (peri)centromeric region of one single chromosome pair in both species. As the cloned satellite DNA sequence clearly evolved along a chromosomal lineage and is highly variable, it may serve as a very useful marker in further genetic, molecular and cytogenetic studies of the genus Leporinus.     

Variability of mitochondrial subgenomic molecules in the meristematic cells of higher plants

MtDNAs from BY-2 cells and rice root were analyzed by random amplified polymorphic DNA (RAPD) assay and Southern hybridization analysis. A number of differences were observed in the RAPD patterns amplified from mtDNAs sampled at different phases of the BY-2 cell culture. RAPD fragments also varied with the template DNAs derived from various areas of rice root tip. When a RAPD fragment was hybridized to restriction fragments of whole DNAs, isolated from the distal area of the apical meristem and differentiated elongation zone of a root, two distinct stoichiometric differences were observed in the hybridization signals. This suggests that the organization of mt-genome in prototypic cells in the root apical meristem differs from that found in the differentiated cells.     

Occurrence of homologs of the Escherichia coli lytB gene in gram-negative bacterial species

The Escherichia coli LytB protein regulates the activity of guanosine 3',5'-bispyrophosphate synthetase I (RelA). A Southern blot analysis of chromosomal DNA with the E. coli lytB gene as a probe revealed the presence of lytB homologs in all of the gram-negative bacterial species examined but not in gram-positive species. The lytB homologs from Enterobacter aerogenes and Pseudomonas fluorescens complemented the E. coli lytB44 mutant allele.     

AM1 theoretical study, synthesis and biological evaluation of some benzofuran analogues of anti-inflammatory arylalkanoic acids

To evaluate different methods for strain differentiation, 10 isolates of Aspergillus terreus from Germany and two epidemiologically unrelated strains were investigated. The sources of the isolates were patients with cystic fibrosis (4), immunosuppression (2), otitis externa (2), sinusitis (1) and endocarditis (1). Environmental isolates were obtained from a contaminated cell culture and from soil. The isolates did not differ in their macroscopic and microscopic morphology, in their protein patterns analysed by SDS-PAGE and in their susceptibility to amphotericin B and itraconazole. The RFLP analysis of total genomic DNA digested by EcoRI resulted in patterns that were too faint for interpretation. However, after hybridisation of the digested DNA with a short DNA probe of repetitive sequence, six different patterns were found. Based on the patterns of the randomly amplified polymorphic DNA (RAPD) with three primers, nine different genotypes were discriminate. RAPD patterns discriminated the epidemiologically unrelated reference strains (endocarditis isolate from Thailand, soil isolate from the USA) and the isolates from Germany. It is concluded that, in contrast to the phenotypic methods, the analysis of RAPD patterns is useful for strain differentiation of A. terreus.     

Multiplex PCR for simultaneous detection of the most frequent T cell receptor-delta gene rearrangements in childhood ALL

A rapid and simple multiplex polymerase chain reaction (PCR) is described that is capable of identifying the six most frequent rearrangements of the T cell receptor (TCR)-delta gene segments in childhood acute lymphoblastic leukemia (ALL). The PCR products amplified in a single reaction are of different size for each TCR-delta gene rearrangement. Therefore, they are readily and unambiguously distinguished after agarose gel electrophoresis and assigned to a specific V-D-J gene rearrangement. There is no need for labor-intensive and time-consuming Southern blot hybridization or nested PCR. To evaluate the multiplex assay we chose 45 DNA samples of childhood ALL analyzed beforehand for TCR-delta gene rearrangements by Southern blot and single PCR of which 30 showed TCR-delta gene rearrangements. The multiplex PCR results corresponded to the Southern blot and single PCR analyses. The described multiplex PCR enables the detection of clonal markers in about 50% of patients in order to monitor minimal residual disease (MRD) in prospective studies with a high turnover of samples.     

Soil dermatophytes in Madras, India, in relation to human ringworm

A total of 269 soil samples collected from different habitats in Madras, India, were screened for the presence of dermatophytes by the hair-baiting technique. Three strains of Trichophyton mentagrophytes and 16 strains of Microsporum gypseum complex were isolated. These strains were subjected to the mating experiment. 2/3 soil isolates of Trichophyton mentagrophytes belonged to Arthroderma vanbreuseghemii (+) mating type, and 1/3 was Arthroderma vanbreuseghemii (-) mating type. Similarly 6/70 clinical strains of Trichophyton mentagrophytes isolated in our previous study also belonged to Arthroderma vanbreuseghemii (+) mating type. These 6 strains were isolated from severe cases of tinea capitis in children belonging to rural Madras. The teleomorphic and mating type homology between the clinical and soil isolates of T. mentagrophytes suggest that soil may act as reservoir for these organisms. The incompatible clinical strains of T. mentagrophytes var. interdigitale and A. vanbreuseghemii showed DNA homology, thereby establishing the epidemiologic link which supports the above findings.     

Detection of HeLa cell contamination--presence of human papillomavirus 18 DNA as HeLa marker in JTC-3, OG and OE cell lines

There are warnings of the contamination of cell cultures with HeLa cells in many laboratories in the world. The cell lines JTC-3, OG and OE that were established in Okayama in 1959, 1969 and 1971, respectively, were examined for human papillomavirus (HPV) 18 DNA by Southern blot hybridization. The HPV 18 DNA detected in these three cell lines showed hybridization patterns characteristic of the HPV 18 DNA in the HeLa cell line established in 1951. Southern hybridization patterns of HPV 18 DNA in the cellular DNA of the C4-II cervical cancer cell line that was established in the USA in 1962 was different from that of HeLa cells. These results suggest that the JTC-3, OG and OE cell lines have been contaminated by HeLa cells.     

Presence of Streptococcus anginosus DNA in esophageal cancer, dysplasia of esophagus, and gastric cancer

We recently reported cloning of Streptococcus anginosus (S. anginosus) DNA fragments containing the 16S ribosomal gene from DNA samples of surgical specimens of gastric cancers. To investigate the specificity of S. anginosus infection, Southern blot analysis with S. anginosus 16S ribosomal DNA probe and PCR analysis with S. anginosus-specific primers were performed in DNA samples prepared from 15 esophageal cancers, 43 gastric cancers, 16 lung cancers, 10 cervical cancers, 14 renal cell carcinomas, 10 colorectal cancers, and 19 bladder cancers. We frequently found S. anginosus DNA sequences in DNA samples from esophageal cancer and gastric cancer tissues, as well as in those from dysplasia of the esophagus of esophageal cancer patients. No S. anginosus DNA bands were detected by Southern blot analysis on DNAs from the noncancerous portions of the esophagus or the stomach. By PCR analysis with 35 cycles, only 7% of the noncancerous portion of the esophagus was shown to contain S. anginosus sequences. No S. anginosus sequences were found in DNAs from cancers in lung, cervix, and kidney, but they were found in 1 of 10 colon cancers.