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PubMed1996

Molecular test for the detection of tumor cells in blood and sentinel nodes of melanoma patients.

Lymph node metastasis dramatically decreases the 5-year survival of melanoma patients. The so-called sentinel node surgery offers a therapeutic approach to resect the first draining lymph node. This technique enables accurate staging of melanoma patients in an early stage of the disease. Detection of a sentinel node metastasis is a strong argument for local lymphadenectomy. To improve the detection of micrometastasis in sentinel nodes of melanoma patients, molecular biological techniques were used. The exclusively melanocyte-specific tyrosinase transcript was amplified by reverse transcription followed by polymerase chain reaction (RT-PCR). In sentinel node examination, the detection of tyrosinase-positive cells by RT-PCR was compared with routine immunohistochemistry. From 16 patients, a total of 28 lymph nodes were tested. The lymph nodes were derived after lymphadenectomy (4 patients) and after sentinel node resection (12 patients with melanoma stage I). By using RT-PCR we could detect 100 tumor cells in a background of 10(8) peripheral blood mononuclear cells. The negative controls were all negative for tyrosinase. Cryostat sections of lymph nodes for mRNA isolation were alternated with sections for immunohistochemistry. By using tyrosinase RT-PCR, we detected 6 additional positive sentinel nodes in patients with melanoma stage I. Furthermore, the tyrosinase RT-PCR enabled us to design a blood test for circulating melanoma cells. Therefore, mRNA was directly isolated from whole blood of 23 blood samples, of which 3 samples were positive for tyrosinase. The present study demonstrates the possibility of a simple and rapid blood test for melanoma patients that has not been available until now. Furthermore, the detection of micrometastasis in sentinel nodes by tyrosinase RT-PCR dramatically increases the accuracy of melanoma staging.

Base Sequence↗
PubMed1997

Nosocomial enterococcal blood stream infections in the SCOPE Program: antimicrobial resistance, species occurrence, molecular testing results, and laboratory testing accuracy. SCOPE Hospital Study Group.

Characteristics of nosocomial enterococcal blood stream infection (NEBSI) isolates obtained from patients at 41 U.S. hospitals participating in the SCOPE Program were studied. Isolates from 480 episodes of NEBSI were characterized according to species and antimicrobial susceptibility profile. Selected isolates were also identified to species and vancomycin resistance genotype using polymerase chain reaction based methods. Polymerase chain reaction genotyping and ribotyping were used as genetic markers for molecular epidemiologic typing. Enterococci were the third most common cause of nosocomial blood stream infection in this study, accounting for 11.7% of all isolates reported. Enterococcus faecalis was the most common species (59.6%), followed by E. faecium (19.4%). Species identification errors involving E. faecium, E. durans, E. avium, and E. raffinosus were observed. Vancomycin resistance was observed in 36.4% of all participating medical centers and varied from 11.1% of medical centers in the Northwest to 60.9% of medical centers in the Southwest. Vancomycin-resistant enterococci accounted for 20.6% of NEBSI in the Northeast, 11.4% in the Southeast, 11.1% in the Southwest, and 9.5% in the Northwest regions. VanA genotypes predominated in the Northeast and Southwest, whereas vanA and vanB genotypes were equally prevalent in the Northwest and Southeast. Molecular typing studies identified strains that were unique to individual hospitals as well as strains that were prevalent in several different hospitals. NEBSI with vancomycin-resistant enterococci continues to escalate among hospitalized patients in all geographic areas of the USA.

Anti-Bacterial Agents↗
PubMed2005

Molecular testing of multiple HIV-1 transmissions in a criminal case.

OBJECTIVE: To test the a priori hypothesis of HIV-1 transmission from one suspect to six recipients in a criminal case. METHODS: Partial pol and/or env sequences were obtained for at least two samples of the suspect and the victims. Appropriate local controls were sampled based on epidemiological and subtype criteria. Phylogenetic testing was performed using different reconstruction methods. RESULTS: Phylogenetic analyses consistently inferred a monophyletic cluster for the suspect and victim samples in both genome regions. This was highly supported by parametric and non-parametric bootstrapping techniques. Moreover, the controls most closely related to the suspect-victim cluster had a similar geographical origin to the suspect. CONCLUSIONS: Taking into account the limitations on the conclusions that can be drawn from molecular investigations we could infer that our molecular data is consistent with a scenario of multiple HIV transmission between suspect and victims.

Bayes Theorem↗
PubMed2006

Method for efficient storage and transportation of sputum specimens for molecular testing of tuberculosis.

SETTING: The polymerase chain reaction (PCR) is a highly sensitive method for the detection of Mycobacterium tuberculosis and is available in most countries, though to a lesser extent in rural areas. OBJECTIVE: To amplify M. tuberculosis DNA sequences of sputum spotted on FTA cards and compare them with the results of microscopic examination among culture-positive samples. DESIGN: A total of 102 sputum specimens of TB patients in treatment were spotted on FTA cards and stored at room temperature until DNA analysis. We assessed the IS6110 region of M. tuberculosis. The efficacy of the PCR assay for the direct detection of M. tuberculosis was evaluated and compared with the results of cultures (Middlebrook 7H9 broth) and smears of fresh sputum specimens. RESULTS: We were able to detect 10 fg/microl of mycobacterial DNA even after 6 months in storage. The PCR sensitivity and specificity using the FTA card system were 82% and 96%, while microscopic examination showed 41% and 95%, respectively. CONCLUSION: The FTA card system for the storage of bacterial DNA from sputum samples should be considered for the molecular diagnosis of tuberculosis. Samples can easily be obtained from geographically isolated populations and shipped by mail for accurate molecular diagnosis.

Bacteriological Techniques↗
PubMed2004

A molecular test of alternative hypotheses of tetraodontiform (Acanthomorpha: Tetraodontiformes) sister group relationships using data from the RAG1 gene.

Two primary competing hypotheses regarding the identity of the sister group of the order Tetraodontiformes exist. The first hypothesis holds that some or all acanthuroid fishes represent the sister of Tetraodontiformes. The second, proposed in 1984 by Rosen, holds that the order Zeiformes is sister to Tetraodontiformes and that the family Caproidae is sister to this Zeiformes + Tetraodontiformes clade. These two hypotheses were tested using data from the single-copy nuclear gene RAG1. Representatives of most major orders of acanthomorph fishes were included to provide an appropriate context in which to place Tetraodontiformes and its hypothesized sister groups. The results of an unweighted parsimony analysis indicate that Zeiformes is not the sister group of Tetraodontiformes. In addition, Caproidae appears unrelated to Zeiformes. A monophyletic Tetraodontiformes was recovered as the sister group of the clade Ephippidae + Drepanidae and was more distantly related to the included zeiform and caproid representatives.

Animals↗
PubMed1997

Limits of commercial molecular tests for diagnosis of pulmonary tuberculosis.

Several studies report high specificity, but variable sensitivity, of Amplified Mycobacterium tuberculosis Direct Test (AMTDT, Gen-Probe) based on ribosomal ribonucleic acid (rRNA) amplification and Amplicor Mycobacterium tuberculosis test (Amplicor, Roche) based on deoxyribonucleic acid (DNA) amplification for diagnosis of pulmonary tuberculosis. We have retrospectively evaluated these assays on selected acid-fast bacilli (AFB)-positive and -negative smear specimens and compared the results obtained from nucleic acid amplification with those of AFB staining of semi-quantitative cultures as determined by radiometric Bactec and Löwenstein-Jensen cultures. In comparison to cultures, Amplicor and AMTDT assays exhibited identical overall sensitivities of 80%, while the staining had a lower sensitivity of 62%. The sensitivities of Amplicor and AMTDT were 98% and 100%, respectively, for the AFB-positive specimens, and 50 and 46%, respectively for the AFB-negative specimens in comparison to cultures. The sensitivities of both assays appeared similar, and were directly related to the number of bacilli in the specimens studied. The low sensitivity (50%) for smear-negative specimens showed that current amplification assays may be unsuitable to replace cultures for diagnosis of tuberculosis. The decision to perform these molecular techniques should result from close co-operation between clinicians and microbiologists, taking into account the sensitivity results reported here, as well as the expense of the assays.

DNA↗
PubMed1999

[A new method of molecular testing in the differential diagnosis of hereditary hemochromatosis].

Hereditary hemochromatosis is an autosomal, recessive disorder of the iron metabolism. The hemochromatosis gene (HFE) was previously located on chromosome 6 and recently identified by positional cloning. A point mutation, C282Y, was found to be present in the HFE gene in homozygous form in 64 to 100% of patients with established hemochromatosis. The relationship of a second polymorphic variant of the HFE gene, H63D to the formation of iron overload is debated. Although hemochromatosis is one of the most common inherited disorders among Caucasians, in the absence of specific signs it is rarely diagnosed. In order to obtain comparable epidemiological data for Hungary, we tested 1271 and 277 randomly selected, unrelated, healthy subjects for C282Y and H63D respectively. In addition C282Y testing was carried out in 58 patients suffering from liver cirrhosis, and in 191 individuals with suspected hemochromatosis. For C282Y and H63D mutation analyses polymerase chain reaction technique followed by Rsa I and Bcl I restriction enzyme digestion was used. We developed an alternative method for the detection of C282Y based on an amplification-generated Kpn I restriction site. The allele frequencies were 3.8% and 12.3% for C282Y and H63D respectively in the normal Hungarian population. There was no significant difference in C282Y allele frequencies between liver disease patients (1.7%) and the normal population. We identified 15 homozygous and 25 heterozygous individuals among 191 individuals with suspected hemochromatosis. The C282Y and the H63D allele frequencies in the normal Hungarian population were found to be similar to the allele frequencies observed in other European populations, indicating that there is a large number of individuals susceptible for iron overload in Hungary (1:700). Mutation analysis is a novel, non-invasive method in the diagnostics of hereditary hemochromatosis, which increasingly becomes part of the routine clinical work.

Alleles↗
PubMed2001

RNA virus error catastrophe: direct molecular test by using ribavirin.

RNA viruses evolve rapidly. One source of this ability to rapidly change is the apparently high mutation frequency in RNA virus populations. A high mutation frequency is a central tenet of the quasispecies theory. A corollary of the quasispecies theory postulates that, given their high mutation frequency, animal RNA viruses may be susceptible to error catastrophe, where they undergo a sharp drop in viability after a modest increase in mutation frequency. We recently showed that the important broad-spectrum antiviral drug ribavirin (currently used to treat hepatitis C virus infections, among others) is an RNA virus mutagen, and we proposed that ribavirin's antiviral effect is by forcing RNA viruses into error catastrophe. However, a direct demonstration of error catastrophe has not been made for ribavirin or any RNA virus mutagen. Here we describe a direct demonstration of error catastrophe by using ribavirin as the mutagen and poliovirus as a model RNA virus. We demonstrate that ribavirin's antiviral activity is exerted directly through lethal mutagenesis of the viral genetic material. A 99.3% loss in viral genome infectivity is observed after a single round of virus infection in ribavirin concentrations sufficient to cause a 9.7-fold increase in mutagenesis. Compiling data on both the mutation levels and the specific infectivities of poliovirus genomes produced in the presence of ribavirin, we have constructed a graph of error catastrophe showing that normal poliovirus indeed exists at the edge of viability. These data suggest that RNA virus mutagens may represent a promising new class of antiviral drugs.

Antiviral Agents↗
PubMed2004

Molecular testing for detection of in vitro infectivity of plasma pools contaminated with B19 virus.

B19 virus can be transmitted by contaminated blood or blood products. Recent observations, in healthy volunteers, suggest that active B19 infection can follow the administration of plasma pools with a concentration > or =10(7) genome equivalents/ml (geq/ml) of B19 DNA. However, patients receiving batches with levels of virus DNA lower than 10(4) geq/ml do not show any evidence of transmission of the virus. The aim of the study was to show, by in vitro assays, a threshold of viral load in B19 contaminated plasma pools over which the infection can be transmitted. Twenty plasma pools, each containing 960 single donations, were tested to correlate the viral load and the level of antibodies anti-B19 with the in vitro infectivity and expression of B19 virus. All the plasma pools, titrated for B19 viral load by competitive PCR, were inoculated into KU812Ep6 erythroid human cell line. Five of the nine contaminated plasma pools, with a B19 DNA concentration > or =3.60 x 10(6) geq/ml, were able to infect KU812Ep6 cells. In vitro infectivity was shown in KU812Ep6 cells at 24 h post-infection by in situ hybridisation and amplification assays for viral DNA and RNAs. Plasma pools with a viral load in the range of 6.00 x 10(3)-8.96 x 10(4) geq/ml did not show infectivity when inoculated into KU812Ep6 cells. Medium-high titres of IgG antibodies anti-B19 were detectable in all the plasma pools and the neutralising activity associated with specific IgG anti-B19 may explain the lack of infectivity of plasma pools contaminated with a low viral load. In conclusion, in situ hybridisation and amplification assays for viral DNA and RNAs in KU812Ep6 cells inoculated with plasma pools can be valid assays to test for the presence of infectious virus in the production of B19-safe material.

Antibodies, Viral↗
PubMedDate not supplied

Schistocephalus solidus: a molecular test of premature gamete exchange for fertilization in the intermediate host Gasterosteus aculeatus.

We tested the hypothesis that the cestode Schistocephalus solidus is capable of premature gamete exchange as a plerocercoid in the last intermediate stickleback host. The existence of such a reproductive mode is suggested by the highly advanced gonadal development in the plerocercoid and the large fitness gain of outcrossing. In addition, eggs from selfing cestodes have a higher hatching rate when the cestode originated from a doubly infected stickleback than when it came from a singly infected fish. We hatched eggs from 10 singly breeding cestodes that originated from doubly infected sticklebacks with the prediction that some should be outcrossed and share alleles with both the breeding cestode and the second cestode in the coinfection if the hypothesis is correct. However, all of the 430 tested larvae matched only the alleles of the breeding cestode. It is therefore very unlikely that S. solidus engaged in gamete exchange in its fish host. We suggest an alternative hypothesis to explain the higher hatching rate of eggs produced by cestodes from doubly infected fish as compared to those from single infections.

Animals↗
PubMed2004

Experimental resolution of early steps in protein folding: testing molecular dynamics simulations.

Time-resolved Tyr fluorescence spectroscopy coupled with a laser-induced temperature-jump (T-jump) was employed to follow the folding relaxation dynamics of the B-domain of Staphylococcal protein A. The single Tyr is located in helix 1 (H1) and is a sensitive probe of the structure of this helix and the overall helical bundle structure. The results from this study were compared to those from a complementary infrared T-jump study on this protein [Vu, D. M.; Myers, J. K.; Oas, T. G.; Dyer, R. B. Biochemistry 2004, 43, 3582]. Both methods detect a microsecond process that follows the cooperative relaxation of the helical bundle core. However, a fast process (10-7 s) that follows the relaxation of the individual helices was observed only with the infrared probe. Thus, fast formation of H1 is not observed, but rather H1 forms in the microsecond phase, concomitantly with the docking to (and stabilization by) the other two helices to form the helical bundle structure. This observation validates the results of several previous molecular dynamics simulations that predict H1 formation only in the final assembly of the helix bundle.

Computer Simulation↗
PubMed2005

Molecular tests can allow confirmation of invasive meningococcal disease when isolates yield atypical maltose, glucose or gamma-glutamyl peptidase test results.

Analysis of atypical meningococci from invasive disease that either (i) did not produce acid from maltose and glucose or (ii) were gamma-glutamyl peptidase test negative for porA and porB DNA variable region (VR) type, multilocus sequence type, and for presence of capsule transport gene ctrA, conclusively demonstrated that these are Neisseria meningitidis.

DNA, Bacterial↗