Probes In Hybridization Experiments Research Articles

Purification of Labeled Oligonucleotides by Precipitation with Ethanol.

If labeled oligonucleotides are to be used only as probes in hybridization experiments, complete removal of unincorporated label is generally not necessary. However, to reduce background to a minimum, the bulk of the unincorporated label should be separated from the labeled oligonucleotide. Most of the residual unincorporated precursors can be removed from the preparation by differential precipitation with ethanol, as described in this protocol, if the oligonucleotide is >18 nt in length.

Expanded-spectrum β-Lactamase and Plasmid-mediated Quinolone Resistance

Expanded-spectrum β-Lactamase and Plasmid-mediated Quinolone Resistance

Molecular analysis of and identification of antibiotic resistance genes in clinical isolates of Salmonella typhi from India.

A representative sample of 21 Salmonella typhi strains isolated from cultures of blood from patients at the Christian Medical College and Hospital, Vellore, India, were tested for their susceptibilities to various antimicrobial agents. Eleven of the S. typhi strains possessed resistance to chloramphenicol (256 mg/liter), trimethoprim (64 mg/liter), and amoxicillin (>128 mg/liter), while four of the isolates were resistant to each of these agents except for amoxicillin. Six of the isolates were completely sensitive to all of the antimicrobial agents tested. All the S. typhi isolates were susceptible to cephalosporin agents, gentamicin, amoxicillin plus clavulanic acid, and imipenem. The antibiotic resistance determinants in each S. typhi isolate were encoded by one of four plasmid types. Plasmid-mediated antibiotic resistance genes were identified with specific probes in hybridization experiments; the genes responsible for chloramphenicol, trimethoprim, and ampicillin resistance were chloramphenicol acetyltransferase type I, dihydrofolate reductase type VII, and TEM-1 beta-lactamase, respectively. Pulsed-field gel electrophoresis analysis of XbaI-generated genomic restriction fragments identified a single distinct profile (18 DNA fragments) for all of the resistant isolates. In comparison, six profiles, different from each other and from the resistance profile, were recognized among the sensitive isolates. It appears that a single strain containing a plasmid conferring multidrug-resistance has emerged within the S. typhi bacterial population in Vellore and has been able to adapt to and survive the challenge of antibiotics as they are introduced into clinical medicine.

Phenotypic and genetic diversity of Paenibacillus azotofixans strains isolated from the rhizoplane or rhizosphere soil of different grasses

Fifty-three strains identified as Paenibacillus azotofixans were isolated from the rhizoplane and rhizosphere of different grasses and from soil. To study the diversity within this species, four approaches were used: assessment of homology with a nifKDH probe in hybridization experiments; use of a selected 20-mer primer to produce RAPD profiles and of BOX- PCR to generate genomic fingerprintings; and phenotypic tests using the API50CH system. The API tests performed with the 53 P. azotofixans strains showed that all strains produced acid from 15 carbohydrates; using six other carbohydrates (sorbitol, dulcitol, tagarose, starch, glycogen and D- arabitol), the strains could be divided in five groups of related strains. All strains tested showed homology to Klebsiella pneumoniae nifKDH genes, resulting in 14 different hybridization patterns with this probe. Using RAPD- fingerprinting with one appropriate primer, 23 different amplification patterns were observed. The BOX-PCR approach confirmed the grouping suggested by the RAPD fingerprinting. A comparison of the 53 strains by similarity matrix analysis using the data obtained in all approaches resulted in a phenogram, grouping them into five broad groups at 74% similarity and into 27 subgroups at 94% similarity. At 100% similarity, 31 groups of strains could be formed, indicating a high degree of diversity among the strains tested. Overall, the diversity was independent from the origin of strains, since a variety of different groups was isolated from each plant studied. However, some clusters were dominant in wheat and sugarcane samples. The results indicated that the methods used here are sensitive indicators of diversity among the strains studied and can be applied as efficient and reliable means for further ecological and biogeographical studies.

Genetic validity of RAPD markers at the intra- and inter-specific level in wild Brassica species with n=9

The sequence homology of co-migrating RAPD markers within a genus, across species, and among populations of a species was investigated. DNA was isolated from ten wild Brassica species with n=9 and the RAPD patterns were established using three random primers. Five RAPD markers which appeared to be characteristic for the n=9 species (genus level), four markers which appeared to be species specific, and one population-specific marker were isolated from agarose gels and hybridized to the RAPD profiles of the ten Brassica species. Two RAPD markers were cloned for comparison with gel-isolated RAPD fragment probes in hybridization experiments. Non-specific and background hybridization, occurring when gel-isolated fragments were used as probes, disappeared when cloned fragments were used. A total of 250 RAPD-marker hybridizations were scored according to visual presence or absence in a gel lane. All except three markers hybridized as expected, resulting in an error rate of 1.2%. The deviating results included a lack of hybridization although a band was visible in the gel, a length polymorphism for one marker, and a dual hybridization signal for two single-band markers.

Trypanosoma cruzi: Parasite Detection and Strain Discrimination in Chronic Chagasic Patients from Northeastern Brazil Using PCR Amplification of Kinetoplast DNA and Nonradioactive Hybridization

Blood samples from 172 individuals from northeastern Brazil were subjected to PCR amplification of Trypanosoma cruzi-specific kDNA sequences. This method enabled us to detect parasite DNA in 21 of 47 patients that were serologically positive, In addition, 1 patient that gave doubtful results with chagasic serology was confirmed as positive by PCR. We applied the same PCR detection method to the feces of wild triatomines captured in the same region, obtaining three positive results that were confirmed by microscopic examination. The 25 amplified products obtained in this study were then reamplified with primers that gave a final amplicon containing sequences from the most variable region of kDNA minicircles. These were used as probes in hybridization experiments aimed at defining the degree of relatedness between the strains infecting humans and insects based on kDNA homologies. We found that the amplification products from the three triatomines were related and showed no crosshybridization with those obtained from human infections. Eight amplified products from human infections showed no cross-hybridization and did not hybridize with products from other patients. This indicates that the strains of T. cruzi circulating in the region present a high level of genetic heterogeneity. Finally, a number of amplified products hybridized with amplicons that did not hybridize with each other, indicating that infections with a parasite population presenting a mixed kDNA content (either due to different strains of T. cruzi or to a hybrid parasite) are a more frequent event than previously thought.

Isolation and identification of fimbriae and toxin production by Escherichia coli strains from cows with clinical mastitis

A total of 20 Escherichia coli strains isolated from cases of bovine mastitis were examined for fimbriae production, for the presence of genes coding for enterotoxins (LT and ST1), verotoxins (VT), and for the production of cytotoxic necrotizing factors (CNF1 and CNF2). Fimbriae could be isolated from four strains. The N-terminal amino acid sequence of the fimbriae from two strains, was determined. The two sequences were almost identical and homologous to that of the major subunit of E. coli F17 fimbriae. A DNA probe was derived from this N-terminal sequence and used as probe in hybridization experiments with chromosomal DNA of the 20 strains. To test if the strains contained genes that code for the F17 adhesin and the F17 major subunit, a Polymerase Chain Reaction (PCR) assay was performed with primers based on the nucleotide sequence of the genes. Eleven of 20 strains contained sequences that were homologous with sequences for the F17 fimbrial subunit and the F17 adhesin. Strains were tested directly for toxin production on Hela cells and by PCR for the presence of toxin genes. One of the twenty strains, produced a CNF toxin. No strains reacted positive in the PCR for LT, ST1 and verotoxin genes.

Use of random amplified polymorphic DNA (RAPD) for generating specific DNA probes for microorganisms

We report the rapid generation of DNA probes for several Azospirillum strains. This method does not require any knowledge of the genetics and/or the molecular biology of the organism (genome) to be investigated. The procedure is based on the generation of random amplified polymorphic DNA (RAPD) fingerprints using primers with an embedded restriction site. The amplification product(s) peculiar to one strain or common to two or more strains can be purified, cloned, sequenced and used as molecular probes in hybridization experiments for the detection and identification of microorganisms. We have tested this methodology in the nitrogen-fixing bacterium Azospirillum by amplyfing the total DNA extracted from several Azospirillum strains. We have used amplification bands with different specificity as molecular probes in hybridization experiments performed on amplified DNA. Results obtained have demonstrated the usefulness of this methodology for Azospirillum. Its use in microbial ecology studies as a general strategy to generate specific DNA probes is also discussed.

DNA- and PCR-fingerprinting in fungi.

DNA-fingerprinting has been successfully used to detect hypervariable, repetitive DNA sequences (minisatellites and microsatellites) in fungi. Combined with methods used to identify random amplified polymorphic DNA (RAPD), conventional DNA-fingerprinting hybridization probes can also be used as single primers to detect DNA polymorphisms among fungal species and strains. The oligonucleotides (CA)8, (CT)8, (CAC)5, (GTG)5, (GACA)4 and (GATA)4, as well as the phage M13 and its core sequence, have been used as specific probes in hybridization experiments and as primers for PCR analysis. Both methods have enabled the differentiation of all the fungal species and strains that were examined, including species of Penicillium, Trichoderma, Leptosphaeria, Saccharomyces, Candida and Cryptococcus. These methods have been used 1) to clarify the taxonomic relationships among relevant species of the Trichoderma aggregate, 2) to discriminate between aggressive and non-aggressive isolates of the rape seed phytopathogen, Leptosphaeria maculans, and 3) to identify strains of the pathogenic yeasts, Cryptococcus neoformans and Candida albicans. PCR-fingerprinting allowed serotypes of C. neoformans to be distinguished. The application of DNA- and PCR-fingerprinting to fungal DNA should aid in clarification of their taxonomy and improved diagnosis of mycotic disease.

A procedure for repeated usage of 33P-labeled DNA probes in hybridization experiments

We describe a technique for repeated use of 33P-labeled DNA probes in Southern hybridization experiments. A nick-translated 33P-labeled DNA probe in a volume of 0.5–1.0 ml of hybridization mixture (final concentration, 10–100 ng/ml) is used to wet a sheet of filter paper (approx 10 μl/cm 2), which covers a nylon membrane with DNA transferred by Southern blotting, and both are set between two washed X-ray films. The “sandwich” is placed in a plastic bag for hybridization for 16–24 h at 42°C. This very simple procedure using 33P-labeled DNA probes has a number of advantages over the standard method using 32P-labeled probes: (a) a significantly lower biohazard (body/arms exposure); (b) a very small volume of hybridization mixture in contact with a DNA-containing membrane and the higher probe concentrations attainable, causing some increase in sensitivity, and, finally, (c) repeated use of the probe-containing filter (over approx 3 days for unique sequences and up to 2 weeks for reiterated sequences) due to a relatively long 33P half-life (25.3 days).

The difference in the IcrV sequences between Y. pestis and Y. pseudotuberculosis and its application for characterization of Y. pseudotuberculosis strains

We have sequenced the IcrGVH operon from Y. pseudotuberculosis plasmid pYV995 and compared its sequence with that of Y. pestis. The sequences were highly homological, however, six base pair substitutions were found in one short 14 bp region termed variable sequence. Two oligonucleotides corresponding to variable sequence of Y. pestis ( pes-V) or Y. pseudotuberculosis ( ptb-V) were synthesized and were used as molecular probes in hybridization experiments with sets of Y. pestis and Y. pseudotuberculosis strains. All 17 Y. pestis strains tested were positive only with the pes-V probe, 18 of 21 Y. pseudotuberculosis strains were positive with the ptb-V probe, while three Y. pseudotuberculosis strains reacted with the pes-V probe but not the ptb-V probe. The 200 bp fragment including variable sequence was sequenced in seven Y. pseudotuberculosis strains. The Y. pseudotuberculosis strains which were positive with the pes-V probe possessed the 200 bp fragment sequence almost identical with that from Y. pestis. No correlation between the Y. pestis-like IcrV sequence and virulence was found for these strains. Moreover, the Y. pseudotuberculosis strains with Y. pestis-like sequences in contrast to Y. pestis possessed unaltered yadA gene. However, we have found the yadA frameshift mutation characteristic for Y. pestis in one Y. pseudotuberculosis strain 312.

The use of genomic DMA fingerprinting in studies of the epidemiology of bacteria in periodontitis

Recent studies of microbial epidemiology emphasizing the genetic organization and distribution of organisms associated with orofacial infections have led to new insights into the possible origins of pathogenicity. Studies into genetic heterogeneity, acquisition and transmission of these organisms have been markedly advanced by the utilization of the powerful technique of genomic DNA fingerprinting. Characteristic fingerprints for each bacterial isolate can be produced by cleavage of high molecular weight genomic DNA by restriction endonucleases. It is assumed that each DNA fingerprint represents a clonal type. In this report, we review and analyze studies of the epidemiology of bacteria associated with orofacial infections with an emphasis on periodontal disease. Studies of nontypable (NT) Haemophilus influenzae associated with recurrent otitis media illustrate the utility of this technique. DNA fingerprinting clearly demonstrates genetic heterogeneity of NT H. influenzae isolates, and clonality of infection of any individual. Furthermore, DNA fingerprinting has shown that the same clonal type is seen in siblings concurrently suffering from otitis media, suggesting horizontal transmission within the family. Studies of mutans Streptococci also show extensive genetic heterogeneity and show vertical transmission of a predominant clonal type only from mother to infant, but not from father to infant. Studies of Actinobacillus actinomycetemcomitans show considerable genetic heterogeneity among monkey isolates. Thus far, three clonal types have been reported with DNA fingerprinting among isolates from periodontal patients, but additional genetic heterogeneity can be found using specific DNA fragments as probes in hybridization experiments. Intrafamilial transmission of A. actinomycetemcomitans has been demonstrated. Porphyromonas (Bacteroides) gingivalis shows extensive genetic heterogeneity and case reports suggest clonal infection of any one individual. In contrast, results with DNA fingerprinting of Eikenella corrodens, Fusobacterium nucleatum, and Bacteroides intermedius show that individuals may be infected with 2 or more clonal types. These studies point to the great potential of DNA fingerprinting for investigating the epidemiology of putative orofacial pathogens. Such studies with periodontal microorganisms will likely reveal steps in the acquisition, intraoral and person-to-person transmission, which then could possibly be inhibited or interfered with to prevent periodontal disease or its recurrence.

Evidence for salt-associated restriction pattern modifications in the archaeobacterium Haloferax mediterranei

DNA restriction pattern modifications were detected when Haloferax mediterranei was grown in low (10%) salt concentrations. After cells were grown again in optimal (25%) salt concentrations, the original pattern was recovered. These salt-associated DNA modifications were revealed with 5% of the 160 DNA fragments cloned and used as probes in hybridization experiments. Patterns obtained when genomic DNA was digested with different restriction enzymes showed that these modifications are related not to insertions or deletions in genome but to modifications of some specific sequences.

Physical mapping, amplification, and overexpression of the mouse mdr gene family in multidrug-resistant cells.

The mouse mdr gene family consists of three distinct genes (mdr1, mdr2, and mdr3), for which we have isolated full-length cDNA clones. cDNA subfragments corresponding to discrete regions showing little sequence conservation among the three mdr genes were used as gene-specific DNA probes in hybridization experiments. Long-range mapping by pulse-field gel electrophoresis indicated that the three mdr genes are closely linked on a genomic DNA segment of approximately 625 kilobases. The gene order and direction of transcription of the three genes were determined and indicate the arrangement (5') mdr3 (3')-(5') mdr1 (3')-(3') mdr2 (5'). Southern blotting analyses of genomic DNA from a panel of independently derived multidrug-resistant cell lines identified mdr gene amplification in 10 of 12 cell lines studied. In individual cell lines showing gene amplification, the copy number of each of the three mdr genes was identical, suggesting that the three mdr genes became amplified as part of a single amplicon in these cells. Although increased expression of all three mdr genes was detected in 2 of 12 cell lines tested, multidrug resistance was associated in 10 of 12 lines with the independent overexpression of either mdr1 (7 of 12) or mdr3 (3 of 12) but not mdr2. mdr1 overexpression was consistently associated with gene amplification, while increased mdr3 expression was detected in certain cell lines that did not show gene amplification. Increased levels of mdr1 mRNA were linked to the overexpression of a P glycoprotein of apparent molecular weight 180,000 to 200,000, whereas increased mdr3 expression resulted in increased expression of a P glycoprotein of molecular weight 160,000 to 180,000. Our results suggest that at least two members of the mouse mdr gene family, mdr1 and mdr3, can independently confer multidrug resistance in the cell lines examined.

Physical Mapping, Amplification, and Overexpression of the Mouse mdr Gene Family in Multidrug-Resistant Cells

The mouse mdr gene family consists of three distinct genes (mdr1, mdr2, and mdr3), for which we have isolated full-length cDNA clones. cDNA subfragments corresponding to discrete regions showing little sequence conservation among the three mdr genes were used as gene-specific DNA probes in hybridization experiments. Long-range mapping by pulse-field gel electrophoresis indicated that the three mdr genes are closely linked on a genomic DNA segment of approximately 625 kilobases. The gene order and direction of transcription of the three genes were determined and indicate the arrangement (5') mdr3 (3')-(5') mdr1 (3')-(3') mdr2 (5'). Southern blotting analyses of genomic DNA from a panel of independently derived multidrug-resistant cell lines identified mdr gene amplification in 10 of 12 cell lines studied. In individual cell lines showing gene amplification, the copy number of each of the three mdr genes was identical, suggesting that the three mdr genes became amplified as part of a single amplicon in these cells. Although increased expression of all three mdr genes was detected in 2 of 12 cell lines tested, multidrug resistance was associated in 10 of 12 lines with the independent overexpression of either mdr1 (7 of 12) or mdr3 (3 of 12) but not mdr2. mdr1 overexpression was consistently associated with gene amplification, while increased mdr3 expression was detected in certain cell lines that did not show gene amplification. Increased levels of mdr1 mRNA were linked to the overexpression of a P glycoprotein of apparent molecular weight 180,000 to 200,000, whereas increased mdr3 expression resulted in increased expression of a P glycoprotein of molecular weight 160,000 to 180,000. Our results suggest that at least two members of the mouse mdr gene family, mdr1 and mdr3, can independently confer multidrug resistance in the cell lines examined.

Duplication of the tuf gene: a new insight into the phylogeny of eubacteria

The conservation and duplication of the tuf gene encoding the elongation factor EF-Tu were used to define phylogenetic relationships among eubacteria. When the tufA gene of Escherichia coli was used as a probe in hybridization experiments, duplicate tuf genes were found in gram-negative bacteria from three major phyla: purple bacteria, bacteroides, and cyanobacteria. Only a single copy of tuf was found in gram-positive bacteria, including mycobacteria and mycoplasmas. Gram-positive clostridia were found to carry two copies of tuf.

Characterization of glucosyltransferase expressed from a Streptococcus sobrinus gene cloned in Escherichia coli.

The gene encoding a glucosyltransferase which synthesized water-insoluble glucan, gtfI, previously cloned from Streptococcus sobrinus strain MFe28 (mutans serotype h) into a bacteriophage lambda vector, was subcloned into the plasmid pBR322. The recombinant plasmid was stable in Escherichia coli and gtfI was efficiently expressed. The GTF-I expressed in E. coli was compared to the corresponding enzymes in S. sobrinus strains MFe28 (serotype h), B13 (serotype d) and 6715 (serotype g) and shown to resemble them closely in molecular mass and isoelectric point. The insoluble glucan produced by GTF-I from recombinant E. coli consisted of 1,3-alpha-D-glycosyl residues (approximately 90%). An internal fragment of the gtfI gene was used as a probe in hybridization experiments to demonstrate the presence of homologous sequences in chromosomal DNA of other streptococci of the mutans group.

Isolation of a cDNA clone for the liver cell adhesion molecule (L-CAM).

Liver cell adhesion molecule (L-CAM) is a calcium-dependent cell adhesion molecule found in very early vertebrate embryos and on liver and other epithelial cells in adults. To describe the genes coding for the molecule and study its synthesis, we have cloned cDNA from poly(A)+ RNA of 10-day embryonic chicken liver using the delta gt11 expression vector. One clone, lambda L301, has been characterized and used in analyses of L-CAM mRNA and genomic DNA. Clone lambda L301 produced a fusion protein that reacted strongly with polyclonal antibodies that recognize L-CAM (Mr 124,000) and its Mr 81,000 NH2-terminal fragment, Ft1, released from liver membranes by trypsin. This result indicates that lambda L301 contains a cDNA insert complementary to protein coding sequence within the two-thirds of the mRNA coding region beginning at the 5' end. The 220-base-pair cDNA insert was isolated and used as a probe in hybridization experiments. RNA transfer blot analysis of poly(A)+ RNA showed a single 4-kilobase mRNA; Southern blot analysis showed multiple components consistent with the presence of one to three L-CAM genes. To test whether different tissues express different forms of L-CAM message, poly(A)+ RNA from eight embryonic organs was analyzed. Only organs that expressed L-CAM protein contained poly(A)+ RNA that hybridized to the lambda L301 probe; in all cases a single band, with the same mobility as that in liver, was observed. The L-CAM mRNA in each tissue was present in proportions similar to those detected previously for the L-CAM protein in these tissues. The combined results suggest that any possible heterogeneity in the L-CAM genes is not reflected in the size of either the mRNA or protein.

A complex of single-strand binding protein and M13 DNA as hybridization probe

Single-stranded DNA was complexed to the single-strand binding protein (SSB) of Escherichia coli in a mass ratio of 30:1. The protein moiety of this complex can be labelled by a number of methods of which we have chosen radio-iodination and biotinylation as examples. The SSB-M13 DNA complexes, labelled to high specific activities, were used as probes in hybridization experiments in which 1.6 X 10(-18) moles of immobilized target DNA were detected. The stability of the hybrids was not severely decreased by the binding of SSB. Analysis of hybrids by electron microscopy showed that complexing of DNA with SSB could be used to allow its subsequent identification in the hybrids.

Assessment of sequence relatedness of double-stranded RNA genes by RNA-RNA blot hybridization

Three well-characterized reovirus serotypes were used to investigate the usefulness of RNA-RNA blot hybridization as a means to assess the genetic relatedness of double-stranded RNA (dsRNA) viruses. [5'- 32P]pCp-labeled genomic dsRNAs from reovirus 1, 2 and 3 were used as probes in hybridization experiments in which segments of the three serotypes were separated in 10% polyacrylamide gels and transferred electrophoretically to membranes. Nine of the 10 reovirus genes cross-hybridized between the serotypes. The S1 gene was serotype specific. The L2 gene of reovirus 2 showed a lower level of cross-hybridization with types 1 and 3 when compared to the hybridization signal observed for L2 when types 1 and 3 were hybridized to each other. The data were consistent with previous studies on the relatedness of the three virus serotypes. Since RNA-RNA blot hybridization allows the number and identity of conserved genes to be determined, this approach may prove useful for assessing the genetic relatedness among other viruses in the family Reoviridae.