DNA Fragment Probe Research Articles

微生物叢ゲノム断片をプローブとするアイソトープアレイによる基質特異的微生物検出手法の開発

A method for the specific detection of microorganisms that assimilate radioactive substrates was combined with the use of membrane arrays consisting of random genomic DNA fragment probes prepared from the original microbial community.The feasibility of this combined method was investigated in terms of specificity, sensitivity and the applicability to the analysis of environmental samples. DNA fragment probes prepared from pure cultures exhibited specific signals to their cognate targets although one probe derived from the rRNA gene was found to be cross-hybridized. Strong correlations of signal intensity with both the amount of probe spotted and the concentration of 14C-labeled DNA in the hybridization buffer were observed after hybridization with a membrane array using whole genomic DNA as probes. A membrane array was fabricated from an activated sludge sample and hybridized with 14C-DNA extracted from the same sample grown on either 14C-acetate or 14C-methanol. One out of 48 spots was detected for each target and the positions of the two spots were found to be Identical, thus indicating the specific detection of 14C-assimilating microorganisms and a microorganism capable of assimilating both acetate and methanol.

Glyceraldehyde-3-phosphate dehydrogenase-encoding gene as a useful taxonomic tool for Staphylococcus spp.

The gap gene of Staphylococcus aureus, encoding glyceraldehyde-3-phosphate dehydrogenase, was used as a target to amplify a 933-bp DNA fragment by PCR with a pair of primers 26 and 25 nucleotides in length. PCR products, detected by agarose gel electrophoresis, were also amplified from 12 Staphylococcus spp. analyzed previously. Hybridization with an internal 279-bp DNA fragment probe was positive in all PCR-positive samples. No PCR products were amplified when other gram-positive and gram-negative bacterial genera were analyzed using the same pair of primers. AluI digestion of PCR-generated products gave 12 different restriction fragment length polymorphism (RFLP) patterns, one for each species analyzed. However, we could detect two intraspecies RFLP patterns in Staphylococcus epidermidis, Staphylococcus hominis, and Staphylococcus simulans which were different from the other species. An identical RFLP pattern was observed for 112 S. aureus isolates from humans, cows, and sheep. The sensitivity of the PCR assays was very high, with a detection limit for S. aureus cells of 20 CFU when cells were suspended in saline. PCR amplification of the gap gene has the potential for rapid identification of at least 12 species belonging to the genus Staphylococcus, as it is highly specific.

Rab6c, a new member of the Rab gene family, is involved in drug resistance in MCF7/AdrR cells

A new Rab6 homolog cDNA, Rab6c, was discovered by a hypermethylated DNA fragment probe that was isolated from a human multidrug resistant (MDR) breast cancer cell line, MCF7/AdrR, by the methylation sensitive-representational difference analysis (MS-RDA) technique. Rab6c was found to be under-expressed in MCF7/AdrR and MES-SA/Dx5 (a human MDR uterine sarcoma cell line) compared with their non-MDR parental cell lines. MCF7/AdrR cells expressing the exogenous Rab6c exhibited less resistance to several anti-cancer drugs, such as doxorubicin (DOX), taxol, vinblastine, and vincristine, than the control cells containing the empty vector. Flow cytometry experiments confirmed that the transfectants' diminished resistance to DOX was caused by increased drug accumulation induced by the exogenous Rab6c. These results indicate that Rab6c is involved in drug resistance in MCF7/AdrR cells.

Rapid identification and typing of Staphylococcus aureus by PCR-restriction fragment length polymorphism analysis of the aroA gene.

The Staphylococcus aureus aroA gene, which encodes 5-enolpyruvylshikimate-3-phosphate synthase, was used as a target for the amplification of a 1,153-bp DNA fragment by PCR with a pair of primers of 24 and 19 nucleotides. The PCR products, which were detected by agarose gel electrophoresis, were amplified from all S. aureus strains so far analyzed (reference strains and isolates from cows and sheep with mastitis, as well as 59 isolates from humans involved in four confirmed outbreaks). Hybridization with an internal 536-bp DNA fragment probe was positive for all PCR-positive samples. No PCR products were amplified when other Staphylococcus spp. or genera were analyzed by using the same pair of primers. The detection limit for S. aureus cells was 20 CFU when the cells were suspended in saline; however, the sensitivity of the PCR was lower (5 x 10(2) CFU) when S. aureus cells were suspended in sterilized whole milk. TaqI digestion of the PCR-generated products rendered two different restriction fragment length polymorphism patterns with the cow and sheep strains tested, and these patterns corresponded to the two different patterns obtained by antibiotic susceptibility tests. Analysis of the 59 human isolates by our easy and rapid protocol rendered results similar to those of other assays.

DNA polymorphism among Fusarium oxysporum f.sp. elaeidis populations from oil palm, using a repeated and dispersed sequence ``Palm''

A worldwide collection, of 76 F. oxysporum f.sp. elaeidis isolates (Foe), and of 21 F. oxysporum isolates from the soil of several palm grove was analysed by RFLP. As a probe, we used a random DNA fragment (probe 46) from a genomic library of a Foe isolate. This probe contains two different types of sequence, one being repeated and dispersed in the genome "Palm", the other being a single-copy sequence. All F. oxysporum isolates from the palm-grove soils were non-pathogenic to oil palm. They all had a simple restriction pattern with one band homologous to the single-copy sequence of probe 46. All Foe isolates were pathogenic to oil palm and they all had complex patterns due to hybridization with "Palm". This repetitive sequence reveals that Foe isolates are distinct from the other F. oxysporum palm-grove soils isolates. The sequence can reliably discriminate pathogenic from non-pathogenic oil palm isolates. Based on DNA fingerprint similarities, Foe populations were divided into ten groups consisting of isolates with the same geographic origin. Isolates from Brazil and Ecuador were an exception to that rule as they had the same restriction pattern as a few isolates from the Ivory Coast, suggesting they may originated from Africa.

Identification of Bordetella avium using the polymerase chain reaction

A DNA fragment from Bordetella pertussis, encoding the fim2 fimbrial subunit gene with adjacent sequences, was used as a probe for the detection of homologous sequences in chromosomal DNA of Bordetella avium. A 1.8 kb Sa1I- PstI fragment from the genome of B. avium, which hybridized with the probe, was isolated and sequenced. No fimbrial subunit gene was located on the B. avium DNA fragment. Two regions could be distinguished in the sequence of the fragment. Region 1, which was 80% identical to the sequence upstream of the fim2 gene of B. pertussis and region 2, which had no identity with any known sequence. A 491 bp EagI DNA fragment (probe A) within region 1 and a 650 bp Eag I DNA fragment (probe B) within region 2 were used as DNA probes on restriction endonuclease digests of chromosomal DNA from various bacterial species. This hybridization experiment showed that the region 2 sequence was specific for B. avium. A polymerase chain reaction (PCR) with specific primers within region 2 resulted in the amplification of a 500 bp DNA fragment with B. avium DNA only. This PCR is a useful method for the rapid detection of B. avium and appeared useful to discriminate B. avium from other Bordetella species and also from Alcaligenes faecalis.

Enzyme-labeled oligonucleotide probes for detection of the genes for thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH) of Vibrio parahaemolyticus.

Alkaline phosphatase conjugated oligonucleotide probes were developed to detect the genes (tdh and trh) coding for the thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH) of Vibrio parahaemolyticus. Using dot blot hybridization, probes were tested with 94 clinical isolates of V. parahaemolyticus. Results agreed well with those obtained using radio-labeled recombinant DNA probes for the genes tdh and trh. Specificity and sensitivity of enzyme tdh probes for detection of the trh gene were 100 and 93%, respectively, and those of the trh probes for trh gene detection were 93 and 86%, respectively. The tdh probes also hybridized with tdh-like genes processed by all strains of V. hollisae, and some strains of V. mimicus and V. cholerae non-O1, but neither tdh nor trh probes reacted with other bacterial species isolated from diarrheal stools. However, some V. parahaemolyticus strains that were negative with the enzyme trh probe hybridized weakly with a radio-labeled trh DNA fragment probe at medium stringency, and a few strains that were negative in high stringency conditions with a radio-labeled trh DNA fragment probe hybridized with the enzyme trh probe. This suggests that some strains of V. parahaemolyticus may carry another gene resembling trh.

Digoxigenin labelled DNA probes for rapid detection of enterotoxigenic, enteropathogenic and Vero cytotoxin producing Escherichia coli in faecal samples

Detection of diarrhoeagenic Escherichia coli in stool specimens cannot be performed easily in most routine laboratories. This study describes a rapid hybridization assay for identification of enterovirulent Escherichia coli in faecal samples. DNA fragment probes specific for enterotoxigenic Escherichia coli, Vero cytotoxin producing Escherichia coli and enteropathogenic Escherichia coli were labelled with digoxigenin and produced in large quantities by polymerase chain reaction. Stool samples were cultured overnight, replica-plated and hybridized with five different probes. This method gives satisfactory results, requires a minimum number of bacteria subcultures and may be used routinely in the laboratory.

Coexistence of GP195 Alleles of Plasmodium Falciparum in a Small Endemic Area

Dimorphic variations in the genotype of the precursor to Plasmodium falciparum major merozoite surface antigens or gp195, among wild isolates in a small malaria parasite population were examined using Southern blot hybridization techniques. Hybridization, with DNA fragment probes and oligonucleotide probes derived from variable blocks of known gp195 alleles against 18 wild isolates from Mae Sod district in Thailand, revealed the existence of seven gp195 alleles, two of which were newly identified in this study. In four out of 17 patients, two different alleles coexisted in the circulation. It was furthermore noted that the seven alleles did not occur at the same frequency, but rather several alleles predominated in the population of P. falciparum in this small malaria field.

Characterization of herpes simplex virus type 2 transcription during latent infection of mouse trigeminal ganglia

Using a cornea trigeminal ganglion model, we have investigated transcription by herpes simplex virus type 2 (HSV-2) during latency in mice. Latency was verified 2 months postinoculation by reactivation of HSV-2 after explant cocultivation of trigeminal ganglia from the majority of mice (83%). Transcription during latent HSV-2 infection was limited to the repeat regions of the viral genome as determined by in situ hybridization using restriction fragment probes representing 100% of the HSV-2 genome. Further mapping of the positively hybridizing region by using subfragments showed that transcription occurred from approximately 11.5 kb of contiguous DNA fragments. A 1.0-kb PvuI-BamHI fragment within the BamHI F fragment and a 0.3-kb BamHI-SalI fragment and a 3.4-kb SalI-BamHI fragment within the BamHI P fragment hybridized more strongly than other subfragments in in situ hybridization experiments. All positive signals were confined to the nucleus. The RNA that hybridized to the 3.4-kb SalI-BamHI DNA fragment probe by in situ hybridization corresponded to a 2.3-kb transcript on Northern (RNA) blots. Under our conditions for Northern blot hybridization, the 3.4-kb SalI-BamHI probe of HSV-2 hybridized to a limited degree with the latency-associated transcripts of HSV-1. Shorter spliced species of latency-associated transcript RNA, which are seen during HSV-1 latency, have not been detected in latent HSV-2 RNA. However, viral gene expression during HSV-2 latency appears to be very similar to that during HSV-1 latency.

Enteropathogenic Escherichia coli serotype O111:HNT isolated from preterm neonates in Nairobi, Kenya

This investigation was initiated as a consequence of several cases of diarrhea in a nursery ward for preterm babies in Nairobi, Kenya. Ten lactose-positive colonies were isolated from the stools of each of 30 neonates, regardless of whether they had diarrhea; 229 strains were identified as Escherichia coli and 65 strains were identified as Klebsiella pneumoniae. Six strains were lost during laboratory handling. No other bacterial, viral, or parasitic enteropathogens were identified. Using synthetic alkaline phosphatase-labeled probes, the bacterial isolates were found to be negative for the presence of genes coding for heat-stable and heat-labile enterotoxins. Seventy-eight E. coli strains isolated from a total of 13 neonates possessed the E. coli enteropathogenic adhesion factor (EAF) gene, as demonstrated by the use of a cloned radiolabeled DNA fragment probe. These strains possessed similar plasmid profiles constituting a core plasmid profile, and while all adhered to HeLa cells, none produced Vero cell cytotoxins. The EAF gene was located on a 65-megadalton plasmid. Serotyping showed the strains to be of serogroup O111 and serotype H nontypable, a well known enteropathogenic type. Five neonates died during the outbreak, and the fatality rate was 30.7% (4 of 13) for neonates infected with EAF-positive E. coli strains compared with 7.7% (1 of 13) for neonates from whom only EAF-negative E. coli strains were isolated. K. pneumoniae only was isolated from five neonates.

The distribution and divergence of DNA sequences related to the Tn21 and Tn501 mer operons.

The mercury resistance (mer) operons of the Gram-negative bacterial transposons, Tn21 and Tn501, are phenotypically indistinguishable and have extensive DNA identity. However, Tn21 mer has an additional coding region (merC) in the middle of the operon which is lacking in Tn501 and there is also a discrete region of the mercuric ion reductase gene (merA) which differs markedly between the two operons. DNA fragment probes were used to determine the distribution of specific mer coding regions in two distinct collections of mercury-resistant (Hgr) Gram-negative bacteria. Colony blot hybridization analysis showed that merC-positive operons occur almost exclusively in Escherichia, although merC-negative operons can also be found in this genus. The merC-negative operons were found in Citrobacter, Klebsiella, and Enterobacter and in some Pseudomonas. Most of the Pseudomonas did not hybridize detectably with either of the two operons studied, indicating that they harbor an unrelated or more distantly related class of mercury resistance locus. Southern hybridization patterns demonstrated that the merC-positive mer operon is well conserved at the DNA level, whereas the merC-negative operons are much less conserved. The presence of merC also correlated with conservation of a specific variant region of the merA gene and with an antibiotic resistance pattern similar to that of Tn21. Tn501 appears to be an atypical example of the merC-negative subgroup of Hgr loci.

Acute leukemias associated with the 4;11 chromosome translocation have rearranged immunoglobulin heavy chain genes

Studies of acute leukemia with the 4;11 translocation have yielded conflicting results regarding the lineage of the cell of origin in this disease. To investigate this issue further, we have examined the state of immunoglobulin genes in tumor cells from two affected patients, immunophenotyped their leukemic cells using a number of monoclonal antibody reagents with specificities for lymphoid or myelomonocytic antigens, and examined the malignant cells by electron microscopy. DNA was extracted from leukemic bone marrow cells and hybridized with radiolabeled DNA fragment probes specific for the constant region of immunoglobulin heavy chain and kappa and lambda light chain genes. Autoradiographs revealed rearrangement of both allelic heavy chain genes, but a germline configuration of light chain genes in both cases. Surface marker analysis showed that blasts from both patients expressed HLA-DR and the myeloid antigens Leu-M1, 1C2, 2D1, and 4B3, but lacked common acute lymphocytic leukemia antigen or T antigens. Furthermore, they did not have sheep erythrocyte receptors nor did they express surface or cytoplasmic immunoglobulin or B cell precursor determinants. Electron microscopy analysis showed that blast cells from patient 1 exhibited numerous monoribosomes, polyribosomes, and isolated strands of rough endoplasmic reticulum in their cytoplasm. These ultrastructural features are characteristic for both common acute lymphocytic leukemia and pre-B-ALL cells, but not for T-ALL or acute myelogenous leukemia cells. Peroxidase was undetectable in cells from both patients. Our study suggests that this disorder represents a unique subtype of leukemia. The cell of origin may be an early B cell progenitor that shares certain surface antigens with myeloid cells or a stem cell with the potential for both lymphoid and myelomonocytic differentiation.

Acute Leukemias Associated With the 4;11 Chromosome Translocation Have Rearranged Immunoglobulin Heavy Chain Genes

Studies of acute leukemia with the 4;11 translocation have yielded conflicting results regarding the lineage of the cell of origin in this disease. To investigate this issue further, we have examined the state of immunoglobulin genes in tumor cells from two affected patients, immunophenotyped their leukemic cells using a number of monoclonal antibody reagents with specificities for lymphoid or myelomonocytic antigens, and examined the malignant cells by electron microscopy. DNA was extracted from leukemic bone marrow cells and hybridized with radiolabeled DNA fragment probes specific for the constant region of immunoglobulin heavy chain and kappa and lambda light chain genes. Autoradiographs revealed rearrangement of both allelic heavy chain genes, but a germline configuration of light chain genes in both cases. Surface marker analysis showed that blasts from both patients expressed HLA-DR and the myeloid antigens Leu-M1, 1C2, 2D1, and 4B3, but lacked common acute lymphocytic leukemia antigen or T antigens. Furthermore, they did not have sheep erythrocyte receptors nor did they express surface or cytoplasmic immunoglobulin or B cell precursor determinants. Electron microscopy analysis showed that blast cells from patient 1 exhibited numerous monoribosomes, polyribosomes, and isolated strands of rough endoplasmic reticulum in their cytoplasm. These ultrastructural features are characteristic for both common acute lymphocytic leukemia and pre-B-ALL cells, but not for T-ALL or acute myelogenous leukemia cells. Peroxidase was undetectable in cells from both patients. Our study suggests that this disorder represents a unique subtype of leukemia. The cell of origin may be an early B cell progenitor that shares certain surface antigens with myeloid cells or a stem cell with the potential for both lymphoid and myelomonocytic differentiation.

Immunoglobulin gene rearrangements in hairy cell leukemia

Studies of hairy cell leukemia have yielded conflicting data about the cell of origin in this disease. To investigate this issue, we have examined the state of immunoglobulin genes in the cells of 11 randomly selected spleens showing histologic involvement with hairy cell leukemia. DNA was extracted from splenic tissue samples and digested with restriction endonucleases. Following agarose gel electrophoresis and transfer to nitrocellulose filters or activated nylon membranes, splenic DNA was hybridized with radiolabeled DNA fragment probes specific for the constant regions of the immunoglobulin heavy chain and kappa and lambda light chain genes. Autoradiograms of the hybridized DNA in each case revealed rearrangements of a heavy chain gene and at least one light chain gene. In addition, immunophenotyping of cellular immunoglobulin polypeptides was carried out on frozen tissue sections from all but one case. In each case in which an immunoglobulin polypeptide could be detected, a rearrangement was present in the DNA of the corresponding immunoglobulin gene. These studies offer strong evidence for endogenous immunoglobulin synthesis in hairy cells and for the B lymphocytic character of this leukemia.

Immunoglobulin Gene Rearrangements in Hairy Cell Leukemia

Studies of hairy cell leukemia have yielded conflicting data about the cell of origin in this disease. To investigate this issue, we have examined the state of immunoglobulin genes in the cells of 11 randomly selected spleens showing histologic involvement with hairy cell leukemia. DNA was extracted from splenic tissue samples and digested with restriction endonucleases. Following agarose gel electrophoresis and transfer to nitrocellulose filters or activated nylon membranes, splenic DNA was hybridized with radiolabeled DNA fragment probes specific for the constant regions of the immunoglobulin heavy chain and kappa and lambda light chain genes. Autoradiograms of the hybridized DNA in each case revealed rearrangements of a heavy chain gene and at least one light chain gene. In addition, immunophenotyping of cellular immunoglobulin polypeptides was carried out on frozen tissue sections from all but one case. In each case in which an immunoglobulin polypeptide could be detected, a rearrangement was present in the DNA of the corresponding immunoglobulin gene. These studies offer strong evidence for endogenous immunoglobulin synthesis in hairy cells and for the B lymphocytic character of this leukemia.