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PubMed1988

Comparison of DNA probe and cytogenetic methods for identifying field collected Anopheles gambiae complex mosquitoes.

A recently developed DNA probe method was compared with the standard cytogenetic method for identifying the species of individual mosquitoes in the Anopheles gambiae complex. The complex consists of 6 morphologically indistinguishable sibling species that include the major African malaria vectors. Half-gravid, field collected mosquitoes were split into 2 portions: the abdomen was preserved for ovarian nurse cell cytotaxonomy and the head/thorax portion was desiccated for DNA extraction. Cytogenetic examination of the Kenya specimens showed 88 An. gambiae and 108 An. arabiensis. The Zimbabwe specimens consisted of 6 An. gambiae and 55 An. Quadriannulatus. All samples of the 3 species were polymorphic for the major chromosomal inversions previously recorded in field specimens from eastern and southern Africa, indicating that the collections reflected natural levels of intraspecific variation in the field populations sampled. Approximately 97% of the cytologically identified mosquitoes were also identified to species by the DNA probe method, and in every case the DNA probe and cytogenetic methods of species identification produced concordant results.

Animals↗

PubMed1989

Demand for DNA probe testing in three genetic centres in Britain (August 1986 to July 1987).

We report a preliminary analysis of the data collected during the first year of the evaluation of clinical genetics in the context of DNA probes in three genetic centres, to show the pattern of the demand for genetic services in the three centres and the services used in meeting that demand. The analysis includes information on 10,185 persons from 2852 families. The results are presented according to mode of inheritance and according to the most common disorders for which DNA probes have been used in the three centres. The results indicate that the use of DNA probes is now a major element of activity in genetic departments, and that as long as indirect DNA probe testing is the predominant manner of using recombinant technology, the clinical input will be an important element of the costs, probably more so than that of the DNA laboratories, as a large number of family members needs to be tested. In most cases centres have concentrated activity on DNA testing for common and severe genetic disorders. However, there are disorders, such as familial hypercholesterolaemia, which have not been part of the established pattern of services. Conversely, a relatively high number of families have been studied for some disorders of very low incidence. This suggests that the number of DNA laboratories should be limited. The precise arrangements will need to be established. With such services the distribution of DNA testing facilities for different disorders can be controlled to limit duplication. The model followed in Scotland based on collaboration between centres is worth considering. We have detected very large differences in take up rate of services within and between regions. Although many factors may contribute to these differences, ease of access and lay and professional awareness are probably the most important. This is supported by the fact that more patients from the same or neighbouring DHAs attend the genetic centre than from those further away. We also concluded that published guidelines for clinicians in general on the uses of DNA probes, the type of families that could benefit, and the centres to which referrals should be sent would be very useful in increasing coverage and maximising the effectiveness of the services. Since this may increase demand, this educative tool should be coordinated and agreed by the Departments of Health with all the genetic departments and centres in the country.

DNA Probes↗

PubMed1988

Mapping of porcine parvovirus DNA and development of a diagnostic DNA probe.

Dimeric and monomeric replicative forms of DNA of porcine parvovirus (PPV) strain NADL-2 were isolated and examined by restriction enzyme analysis and reciprocal Southern blot hybridization during development of a DNA probe for PPV. Genomic single stranded PPV DNA was 5.0 kb long, and results substantiated the rolling-hairpin model of parvovirus DNA replication with the primer sequence located in the 3' terminal hairpin loop. An additional finding was the generation of a 4.7 kb species of viral DNA which was considered to be a 0.3 kb deletion variant of genomic PPV DNA. A 3.0 kb DNA fragment obtained by Pst I/Hind III digestion of monomer replicative form DNA was cloned into a plasmid vector, pUC 19. The cloned fragment, recovered from transformed Escherichia coli strain TB1 and labelled with [32P] dCTP, was evaluated by dot hybridization as a probe for PPV in infected cell cultures. The probe was specific for PPV infected cells, and was 100 times more sensitive than the standard hemagglutination test.

Animals↗

PubMed1994

Specific DNA probes to detect Escherichia coli strains producing cytotoxic necrotising factor type 1 or type 2.

Cytotoxic necrotising factors type 1 (CNF1) and type 2 (CNF2) are produced by many Escherichia coli strains isolated from man and animals with intestinal or extra-intestinal colibacillosis. In most laboratories, CNF-producing strains are detected by a cell cytotoxicity assay and confirmed with a neutralisation assay or a mouse footpad assay. In this study, we sought to determine whether DNA probes could detect clinical isolates of E. coli producing CNF2 or CNF1, or both, without the need for cell cultures or animal assays. Two internal fragments of the gene encoding CNF2 were used as DNA probes: a 875-bp XhoI-PstI DNA fragment and an adjacent 335-bp PstI-ClaI fragment. A positive response with both DNA probes was associated with CNF2-producing strains, whereas a positive response with only the 335-bp probe was associated with CNF1-producing strains. Results of colony hybridisation experiments with 185 clinical isolates of E. coli demonstrated that these DNA probes detected CNF2-producing strains with a sensitivity and specificity of 100% and CNF1-producing strains with a sensitivity and specificity of 99%. These two DNA probes should greatly facilitate epidemiological studies to assess the importance of CNF-producing strains as agents of diarrhoea and septicaemia.

Animals↗

PubMed1993

Evaluation of non-radioactive trivalent DNA probe (LT, ST1a, ST1b) for detecting enterotoxigenic Escherichia coli.

AIMS: To evaluate a digoxigenin-labelled trivalent DNA probe (LT, ST1a, ST1b) for detecting enterotoxigenic Escherichia coli (ETEC), by comparison with a cell culture assay for detecting LT, individual DNA probes for LT, ST1a and ST1b, and an enzyme immunoassay for detecting ST1. METHODS: A 1268 base pair DNA fragment, containing parts of the genes for E coli heat labile enterotoxin (LT) and heat stable enterotoxins (ST1a and ST1b), was random prime labelled with digoxigenin-dUTP. The labelled DNA was used as a probe in colony hybridisation reactions to examine 180 E coli strains of which 92 had previously been shown by a cell culture assay to produce LT. Six LT negative ST1 positive E coli, 34 Verotoxin producing E coli (VTEC), and 84 organisms from other genera were also examined. All organisms other than VTEC were isolated from travellers returning from abroad with diarrhoea. All E coli strains were retested by cell culture for LT, and were tested by enzyme immunoassay (EIA) for ST1, and by the trivalent and individual DNA probes. RESULTS: All 81 isolates, that on retesting by cell culture were positive for LT, also hybridised with the trivalent and LT probes; 27 of these were also enzyme immunoassay (EIA) positive for ST1 of which 24 hybridised with the ST1b probe and three with the ST1a probe. Of 99 isolates, that on retesting by cell culture were negative for LT, all were negative by LT probe and only three were EIA positive for ST1; these three were positive by both trivalent and ST1b probes. Four isolates were positive by the trivalent probe but negative by cell culture and EIA; all four were positive by ST1b probe. Compared with the cell culture assay for LT, the probe had a sensitivity and specificity both of 100%; compared with the EIA for ST1, the probe had a sensitivity of 100% and specificity of 88%. CONCLUSIONS: The trivalent DNA probe is a sensitive, specific, and reliable method for detecting ETEC that should be considered for use by diagnostic microbiology laboratories.

Bacterial Toxins↗

PubMed1999

Polymerase chain reaction and DNA probe hybridization to assess the efficacy of diminazene treatment in Trypanosoma brucei-infected cattle.

Four of eight Ankole longhorn cattle experimentally infected with Trypanosoma brucei were treated with 7 mg/kg diminazene aceturate (Berenil, Hoechst AG, Germany) at day 71 postinfection. The trypanocidal activity was monitored using polymerase chain reaction (PCR) and DNA probe hybridization. When extracted parasite DNA (without host DNA) was used, as little as 1 fg per reaction, which is equivalent to about 1-10% of the DNA in a single trypanosome, produced a specific product that was visible as a 177-bp band in an agarose gel. In infected cattle, specific PCR products could be amplified at as early as 1 day postinfection. PCR signals remained positive during infection, except in one sample, although aparasitemic phases occurred. In cases where treatment resulted in a significant clinical improvement, PCR signals disappeared at 3-4 days after the administration of the drug. By contrast, in cattle that showed clinical signs of CNS involvement after treatment, although aparasitemic, and died before the termination of the experiment, specific products could be amplified on several occasions following treatment. The PCR signals generated after treatment could be further enhanced by subsequent slot-blot hybridization with a T. brucei-specific DNA probe. We conclude that PCR coupled with DNA probe hybridization provides a highly sensitive tool for the assessment of therapeutic efficiency and disease progression in trypanosome infections, especially in chronic infections when the level of parasitemia is low or when trypanosomes are sequestered at cryptic sites.

Animals↗

PubMed2003

A new method for rapid screening of bacterial species- or subspecies-specific DNA probes.

A simple assay for the rapid screening of bacterial species- or subspecies-specific DNA probes for the random cloning method is presented, involving the use of genomic DNAs as probes and recombinant plasmid DNAs containing genomic DNA digested with HindIII as targets. The optimal amount of target DNAs and the concentration of digoxigenin-labeled genomic DNA probes were 20 ng and 100 ng ml(-1) (or 10 ng and 200 ng ml(-1)), respectively. The method was applied to the development of Fusobacterium nucleatum subspecies-specific probes. Our results showed that four out of 96 probes were F. nucleatum subspecies-specific, which was confirmed by Southern blot analysis. Our results indicate that the new method can be used for the rapid screening of species- or subspecies-specific probes.

Bacterial Typing Techniques↗

PubMed1988

A comparative field study of radiolabeled and enzyme-conjugated synthetic DNA probes for the diagnosis of falciparum malaria.

Synthetic, 21-base, DNA probes to the genome of Plasmodium falciparum were either 32P-labeled or enzyme-conjugated for comparative field studies. The sensitivity of both probes was compared with microscopy in the examination of blood samples from 97 Thai villagers, 47 Thai Rangers, and 19 malaria-free Bangkok residents. The probes were also used to monitor the therapeutic response of 18 of the Rangers during 7 days of treatment. The probes proved highly specific. Both probes had lower limits of detection of about 100 parasites per microliter blood. Thus, the low parasite densities in partially immune villagers from an endemic area were often missed, while higher parasite densities in the nonimmune Rangers were usually detected. As monitors of response to treatment, the probes paralleled microscopy in identifying reversion from positive to negative parasitemia. The enzymelabeled DNA probe as shown to perform similarly to the radiolabeled probe in populations with different malarial immune status and during curative treatment.

Alkaline Phosphatase↗

PubMed2003

Species-specific DNA probe for the detection of Porphyromonas gingivalis from adult Chinese periodontal patients and healthy subjects.

BACKGROUND: It has been reported that Porphyromonas gingivalis is closely associated with chronic periodontitis and its detection has been recommended as a routine marker for periodontal diagnosis. The purpose of this study was to evaluate the sensitivity and specificity of a DNA probe to detect P. gingivalis in adult Chinese periodontitis patients as well as to find a rapid and convenient method to detect P. gingivalis in clinical practice. METHODS: A total of 26 bacterial strains (20 reference strains and 6 clinical isolates) were collected, of which 5 were P. gingivalis and 21 were heterologous species. A DNA fragment of 542 bp, which encodes the fimbriae subunit protein (fimA) of P. gingivalis, was obtained by polymerase chain reaction (PCR) and molecular cloning techniques and used to construct the DNA probe, labeled with 32P or with digoxigenin. The constructed DNA probe was used to detect P. gingivalis in specimens collected from the periodontal pockets of 100 patients clinically confirmed with chronic periodontitis. One hundred periodontally healthy persons served as a control group. RESULTS: Positive reactions were seen in all 5 strains of P. gingivalis while no visible reaction was found in other species. The DNA probe was capable of detecting as few as 100 P. gingivalis cells in samples. A significant difference in the positive rates of P. gingivalis between the periodontitis patients and the control group was found (P<0.01). In addition, the amount of detected P. gingivalis was positively correlated with the extent of tooth mobility, depth of periodontal pockets, and patient age (P<0.01). CONCLUSION: The DNA probe is specific and sensitive for the detection of P. gingivalis in chronic periodontitis specimens and may be a suitable method for the clinical diagnosis of chronic periodontitis.

Adult↗

PubMed1998

Comparison of HCV RNA levels by branched DNA probe assay and by competitive polymerase chain reaction to predict effectiveness of interferon treatment for patients with chronic hepatitis C virus.

To compare hepatitis C virus (HCV) RNA levels determined by branched DNA probe assay and by competitive polymerase chain reaction (PCR) as predictive markers of the response to interferon for treatment of patients with chronic HCV infection, we studied data on 140 patients treated for six months with natural interferon-alpha. Serum samples were tested for HCV RNA by PCR. HCV RNA was grouped into four genotypes by PCR with type-specific primers, and HCV RNA level was measured by branched DNA probe assay and by competitive PCR. HCV RNA was detected in all patients prior to initiation of the treatment. A complete response, sustained elimination of HCV RNA, occurred in 51 patients (36.4%). With multiple logistic regression analysis assessment, when using competitive PCR, a low level of HCV RNA (P < 0.0001), younger age (P = 0.0054) and genotype 2a and 2b (P < 0.0158) were significant predictive markers for a complete response to interferon treatment. When using branched DNA probe assay, a low level of HCV RNA (P < 0.0001) and age (P = 0.0089) were predictive markers, but genotype was not. The branched DNA probe assay had a narrower linear range for quantitation of HCV RNA level than competitive PCR. In conclusion, HCV RNA level determined by branched DNA probe assay proved to be useful for prediction of effects of interferon and it is cost effective as a marker of complete response to interferon treatment for patients with chronic HCV infection.

DNA Probes↗

PubMed1992

Use of DNA probes to monitor nutritional effects on ruminal prokaryotes and Fibrobacter succinogenes S85.

We used DNA probes to study dietary effects on the prokaryotic population in the rumen. Procedures used to isolate and quantify prokaryotic 16S ribosomal RNA (rRNA) from the rumen using universal and species-specific DNA probes were evaluated. In this experiment, three ruminally fistulated steers were fed orchard-grass hay, and ruminal digesta were collected at 0, 3, and 9 h after offering hay (0800). Samples of ruminal digesta were taken from the interior portion of the digesta mat and from the fluid below the mat in the dorsal rumen. Freezing (-65 degrees C) and blending samples both increased (P less than .07) the yield of 16S rRNA from ruminal digesta. Extraction of prokaryotic rRNA was greater (P less than .04) when phenol buffered with sodium acetate was used than when it was buffered with hydroxymethyl-amino-methane. Prokaryotic 16S rRNA concentration of the fluid phase was similar (P greater than .10) at 0, 3, and 9 h after offering hay. Prokaryotic 16S rRNA concentration of the mat phase increased up to the 9 h after feeding. The proportion of Fibrobacter succinogenes remained constant in both digesta phases at all times measured. From these data we concluded that DNA probes can be used to monitor bacterial population shifts in the rumen.

Animals↗

PubMed1988

Identification of a Yersinia pestis-specific DNA probe with potential for use in plague surveillance.

A 900-base-pair DNA fragment derived from a 9.5-kilobase plasmid in Yersinia pestis hybridized specifically with Y. pestis DNA. We demonstrated the feasibility of using this DNA fragment to detect plague bacilli directly in fleas, suggesting that this Y. pestis-specific DNA probe may be used for plague surveillance in the field. Additional applications for this DNA probe may include plague diagnosis and pathogenesis research.

Animals↗

PubMed1989

Rapid fluorescence detection of in situ hybridization with biotinylated bovine herpesvirus-1 DNA probes.

The use of biotinylated DNA hybridization probes for clinical detection of bovine herpesvirus-1 was investigated. Biotinylated DNA hybridization probes were prepared from bovine herpesvirus-1 DNA purified from infected cell cultures. The viral DNA was nick translated in the presence of biotin-dUTP with DNA polymerase to incorporate biotin into the newly synthesized strand. The probe was tested for specificity in in situ hybridization assays with bovine herpesvirus-1 DNA. Hybridization was detected using avidin-fluorescein single sandwich systems and an avidin-globulin with anti-globulin-fluorescein double sandwich system. Hybridization was detected by specific fluorescence of infected cells. Fluorescence was present only in bovine herpesvirus-1-infected cell culture and not in noninfected cell culture or cell cultures infected with several other viruses. The assay was performed in 6 hr.

Animals↗

PubMed1991

Using the polymerase chain reaction to maintain DNA probe inventories in clinical and diagnostic laboratories.

Clinical and diagnostic DNA laboratories must maintain a large inventory of DNA probes for use in hybridization studies. The preparation of plasmid DNA and isolation of DNA fragments for use as probes in both expensive and time consuming. We present here a rapid and relatively inexpensive method of producing large amounts of DNA fragments from stocks, using the polymerase chain reaction (PCR). Our experience over the past year using this technique has been very positive and we believe many laboratories could benefit by employing such a labor-saving approach to maintaining DNA probes. The technique uses the bacteriophage M13 DNA sequencing primers to amplify cloned inserts contained in commonly used plasmid vectors. As examples, we illustrate the use of DNA produced in this manner as probes for linkage analysis of the fragile X syndrome and for detection of deletions in the Duchenne muscular dystrophy gene. We have also found that at least two probes can be amplified in the same PCR reaction, allowing the detection of two different restriction fragment length polymorphisms (RFLP) simultaneously. It should be possible for laboratories to devise strategies particular to their individual needs using more than one DNA probe produced in the same PCR reaction to detect RFLP's. Such strategies would need only to consider that the predicted alleles of the multiple polymorphisms do not migrate to the same position during electrophoresis. Stocks of single or multiple probes produced by the PCR could then be maintained for more rapid Southern analyses.

Bacteriophages↗

PubMedDate not supplied

Sex determination of blood stains with a recombinant DNA probe: comparison with radioactive and non-radioactive labeling methods.

A recombinant DNA probe hybridizing specifically to human repeat DNA sequence (pHY10) of which about 3000 copies are present on the Y chromosome was used for sex determination of degraded DNA samples of blood stains. Human blood stains of male and female origin were readily differentiated with the pHY10 DNA probe. This radioactive technique enabled reliable and sensitive sex determination from blood or dried blood stains greater than 20 years old. Less than 1 microliter of blood or 1 piece of 0.5 cm length thread of blood stain from cotton fabric was sufficient for the test using dot blot hybridization. Compared with the radioactive labeling method, the photobiotin labeling method showed one thirtieth to one fiftieth lower sensitivity and presented some problems which are expected to be resolvable.

Blood Stains↗

PubMed1995

Multiple trypanosome infections in wild tsetse in Côte d'Ivoire detected by PCR analysis and DNA probes.

Trypanosomes were isolated from the midguts of Glossina palpalis palpalis, G. pallicera pallicera and G. nigrofusca nigrofusca captured around the village of Guediboua, South West of Daloa in Côte d'Ivoire. Seventy of the 124 isolates, obtained from 688 flies, were examined for four different kinds of trypanosome using the Polymerase Chain Reaction (PCR). Prevalences were: Trypanozoon 46%, riverine-forest T. congolense 86% and savannah T. congolense 54%. Only 29 samples were examined for T. simiae but it was not detected. Just 30% of the infections involved a single kind of trypanosome; the remainder were mixtures either of two (37%) or all three (27%) of the target organisms. 30 of the 70 isolates examined by PCR were successfully amplified to provide material for DNA probe hybridization. To a large extent, DNA probes confirmed the PCR results; all (28/28) of the riverine-forest and 82% (18/22) of the savannah T. congolense infections were identified. However, only 8% (1/13) of the PCR positives for Trypanozoon hybridized with the appropriate DNA probe. No T. simiae or T. godfreyi infections were identified using DNA probes but a large proportion (97%) (29/30) of the probed midguts were shown to contain Kilifi T. congolense. Four isolates out of 70 could not be identified by any method. There was no obvious association between the different species of flies and the infecting trypanosomes.

Animals↗

PubMedDate not supplied

A simplified combination of DNA probe preparation and fluorescence in situ hybridization.

Fluorescence in situ hybridization (FISH) has found widespread applications in cytogenetics. So far the standard protocols for probe amplification (and simultaneous labeling) by PCR, nick translation and in situ hybridization involve different buffer systems leading to a number of time consuming washing steps even before hybridization. In this manuscript we show a fast technique of a close combination of DNA probe preparation and in situ hybridization (ISH). This method was applied to metaphase chromosomes from human lymphocytes fixed on slides. Two specific repetitive DNA probes, the pUC 1.77 DNA probe and the DYZ1 repetitive DNA fraction were used, amplified and labeled in different ways. Additional experiments with total genomic male human DNA as the DNA probe suggest that this method may be extended to a large variety of other probes. Moreover the ISH technique described does not require toxic denaturing agents, such as formamide.

Chromosomes, Human↗

PubMed1987

A DNA probe to distinguish the species Anopheles quadriannulatus from other species of the Anopheles gambiae complex.

DNA probes used previously to distinguish the species Anopheles gambiae sensu stricto, An.arabiensis, An.melas and An.merus were tested against An.quadriannulatus. Using these DNA probes, An.gambiae s.s. and An.quadriannulatus were indistinguishable. A genomic library was constructed for An.quadriannulatus. Differential screening of this genomic library with An.gambiae s.s. and An.quadriannulatus genomic DNAs identified a species-specific, repeated DNA sequence. When used as a hybridization probe, this DNA sequence clearly distinguished An.gambiae s.s. from An.quadriannulatus. A simplified protocol for the use of DNA probes is described which may be used to identify material squashed directly on to nitrocellulose filter paper.

Animals↗