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Testing environment for single-gene disorders in U.S. reference laboratories.

Molecular diagnosis is the detection of pathogenic mutations in DNA and RNA samples prepared from at-risk patients. Principles underlying DNA-based diagnosis originate from localization and identification of genes responsible for human disease and the characterization of pathogenic mutations; new diagnostic tests are in constant development. Indications for testing include diagnosis, carrier risk revision, prenatal diagnosis, presymptomatic diagnosis, and population screening. The majority of DNA diagnoses are performed in a reference laboratory in which the referring physician, rather that the patient, is the client of the laboratory. Thus, the role of the genetic counselor in a reference laboratory is quite different from traditional clinical practice. As with all clinical laboratory tests, molecular diagnostics are interpreted within the context of the patient's overall clinical presentation and are overlaid with regulatory programs of quality assurance, quality improvement, and quality control. The greatest challenges facing the clinical laboratory are genetic heterogeneity, cost control, regulatory and patent compliance, technology transfer, and the genetic education of the referring physician.

Genetic Counseling↗

BAC array CGH reveals genomic aberrations in idiopathic mental retardation.

Array using 2,173 BAC clones covering the whole human genome has been constructed. All clones spotted were confirmed to show a unique signal at the predicted chromosomal location by FISH analysis in our laboratory. A total of 30 individuals with idiopathic mental retardation (MR) were analyzed by comparative genomic hybridization using this array. Three deletions, one duplication, and one unbalanced translocation could be detected in five patients, which are likely to contribute to MR. The constructed array was shown to be an efficient tool for the detection of pathogenic genomic rearrangements in MR patients as well as copy number polymorphisms (CPNs).

Chromosome Aberrations↗

Composite surface for blocking bacterial adsorption on protein biochips.

The design and fabrication of protein biochips requires characterization of blocking agents that minimize nonspecific binding of proteins or organisms. Nonspecific adsorption of Escherichia coli, Listeria innocua, and Listeria monocytogenes is prevented by bovine serum albumin (BSA) or biotinylated BSA adsorbed on SiO(2) surfaces of a biochip that had been modified with a C(18) coating. Biotinylated BSA forms a protein-based surface that in turn binds streptavidin. Because streptavidin has multiple binding sites for biotin, it in turn anchors other biotinylated proteins, including antibodies. Hence, biotinylated BSA simultaneously serves as a blocking agent and a foundation for binding an interfacing protein, avidin or streptavidin, which in turns anchors biotinylated antibody. In our case, the antibody is C11E9, an IgG-type antibody that binds Listeria spp. Nonspecific adsorption of another bacterium, Escherichia coli, is also minimized due to the blocking action of the BSA. The blocking characteristics of BSA adsorbed on C(18)-derivatized SiO(2) surfaces for construction of a protein biochip for electronic detection of pathogenic organisms is investigated.

Adsorption↗

Proteome analysis of human macrophages reveals the upregulation of manganese-containing superoxide dismutase after toll-like receptor activation.

Macrophages are essential for the development of innate immune responses against a variety of infectious factors. They detect invading pathogens via their pattern recognition receptors such as toll-like receptors (TLRs). TLR7/8 recognizes ssRNA from various viruses. In the present study, we have used 2-DE gel-based proteomics to find novel TLR7/8 target proteins in human monocyte-derived macrophages in order to improve our understanding of the virus recognition by this TLR. A total of 27 protein spots were found to be reproducibly differentially expressed between control and TLR7/8 activated 2-DE gel pairs, 18 spots being more than two-fold upregulated and nine spots being at least two-fold downregulated. Several proteins involved in defense against toxic superoxide (O2-) and other reactive oxygen species, such as manganese-containing superoxide dismutase (SOD2), glutathione peroxidase, and peroxiredoxins 1 and 6 were highly upregulated after TLR7/8 activation. Western blot analysis showed that activation of macrophages with TLR2, TLR3, TLR4, and TLR7/8 ligands also strongly upregulated SOD2 protein expression. In conclusion, our results show that the activation of pattern recognition receptors of the innate immune system results in strong upregulation of SOD2 gene expression suggesting that SOD2 protects macrophages from oxidative stress during microbial infection.

Cells, Cultured↗

The effect of humidity on germination and infection of termites by the hyphomycete, Metarhizium anisopliae.

The effect of relative humidities (r.h.) from 90 to 100% on germination of a termite-active isolate of Metarhizium anisopliae (isolate FI25 and FI610) was studied using a liquid germinating medium to which the appropriate amount of glycerol had been added. Germination was increasingly delayed at water activities equivalent to 99, 98, and 96% r.h. and completely inhibited at 94, 92, and 90%. Twenty-one isolates were then screened for germination at 96 and 100% r.h. All isolates showed delayed germination at 96% r.h. but most isolates eventually gave a high final percentage germination at this humidity. Two isolates, FI527 and FI638, were markedly slower to germinate at both humidities. The susceptibility of two species of termites, Nasutitermes exitiosus and Coptotermes acinaciformis, to FI610 was tested at r.h. down to 86%-the lowest humidity at which the insects would survive. No consistent effect of humidity on pathogenicity was detected. Mortality occurred over the range range of humidities tested; sporulation from the disease-killed termites, however, occurred only at r.h. above 93%. It is concluded that the microclimate around living termites is usually sufficiently humid to ensure infection under most field conditions and that humidity is unlikely to limit the efficacy of the fungus in controlling termites.

Animals↗

Rapid identification of Renibacterium salmoninarum using an oligonucleotide probe complementary to 16S rRNA.

Bacterial kidney disease in salmonid fish is caused by the slow-growing Gram-positive rod, Renibacterium salmoninarum. The partial sequence of 16S rRNA from R. salmoninarum was determined and compared with published bacterial 16S rRNA sequences. From this sequence information, a 30-bases-long oligonucleotide was designed and used as a specific probe for identification of R. salmoninarum in filter hybridization experiments. Strong specific hybridization signals were observed for all strains of R. salmoninarum tested. Furthermore, no cross-hybridization could be seen against 22 other bacterial species, among them other salmonid fish pathogens. The detection limit for the probe in direct filter hybridization by the dot-blot technique was 2.5 x 10(4) bacteria. It was also possible to detect R. salmoninarum in clinical samples by direct filter hybridization.

Animals↗

The polymerase chain reaction: an improved method for the analysis of nucleic acids.

The polymerase chain reaction (PCR) is a method for the selective amplification of DNA or RNA segments of up to 2 kilobase-pairs (kb) or more in length. Synthetic oligonucleotides flanking sequences of interest are used in repeated cycles of enzymatic primer extension in opposite and overlapping directions. The essential steps in each cycle are thermal denaturation of double-stranded target molecules, primer annealing to both strands and enzymatic synthesis of DNA. The use of the heat-stable DNA polymerase from the archebacterium Thermus aquaticus (Taq polymerase) makes the reaction amenable to automation. Since both strands of a given DNA segment are used as templates, the number of target sequences increases exponentially. The reaction is simple, fast and extremely sensitive. The DNA or RNA content of a single cell is sufficient to detect a specific sequence. This method greatly facilitates the diagnosis of mutations or sequence polymorphisms of various types in human genetics, and the detection of pathogenic components and conditions in the context of clinical research and diagnostics; it is also useful in simplifying complex analytical or synthetic protocols in basic molecular biology. This article describes the principles of the reaction and discusses the applications in different areas of biomedical research.

Base Sequence↗

[Technic of nucleic acid hybridization and its significance for diagnostic problems].

Nucleic acid hybridization techniques (e.g., Southern blotting and in situ hybridization) gain increasing importance in laboratory medicine, as demonstrated by examples in this paper. The molecular basis of this approach to detect nucleic acids homologous to known DNA probes is explained. It is concluded that this technique has advantages in the detection of pathogens compared to other methods used in laboratory medicine.

Clinical Laboratory Techniques↗

Evaluation of the new improved BHI-lysis blood culture medium for the BCB Roche system.

The new BHI-lysis blood culture medium for the BCB system (BCB release, Hoffmann-La Roche), which lyses blood cells, was compared with the BHI-S broth of the same BCB system and the Signal system (Oxoid). A total of 2394 sets consisting of three bottles were each inoculated with 7 ml of blood at the bedside. In the laboratory agar-coated paddles were attached to the BHI-lysis and the BHI-S bottles, and the Signal device was mounted onto the Oxoid bottle. All systems were incubated at 35 degrees C for seven days. Of the 309 (13%) positive sets, 73 (3%) were contaminated and in 242 (10%) sets a total of 250 pathogenic microorganisms were isolated. These could be grown significantly more often from the BHI-lysis bottle (n = 213) than from either the BHI-S (n = 189) or Signal bottle (n = 176). No significant differences in the time needed to achieve a positive result was noted between the BHI-lysis and BHI-S bottles, but comparison of the BHI-lysis and Signal bottles revealed that overall pathogens were detected earlier significantly more often with the BHI-lysis bottle. In view of the good performance of blood culture broths containing lysing agents, their wider use is warranted in future.

Adult↗

Comparison of nasopharyngeal aspirates and throat swab specimens in a polymerase chain reaction-based test for Mycoplasma pneumoniae.

Nasopharyngeal aspirates and throat swab specimens were compared in a polymerase chain reaction (PCR)-based test for Mycoplasma pneumoniae. The pathogen was detected in 50% and 45% of throat swab specimens and aspirates, respectively. However, in specimens negative for Mycoplasma pneumoniae by PCR, amplification inhibitors were detected in 0% and 36% of throat specimens and aspirates, respectively. Further investigations confirmed that no throat specimens, but one-quarter of aspirates, are likely to be rejected for containing inadequate respiratory material or excess amplification inhibitors. Because rejection of most of the unsuitable specimens is possible only after PCR, the use of aspirates is less cost-effective. This, and the reluctance to subject patients to aspiration, make the aspirate an inferior specimen for detection of Mycoplasma pneumoniae by PCR.

Adult↗

DNA chip technology ante portas.

The recent popularity of DNA chip technology has been fostered by the increasing demand for new diagnostic tools which allow the simultaneous analysis of large numbers of nucleic acid hybridization experiments in a timely fashion. The development of DNA chip-based assays has been strongly driven by modern approaches aiming at the comprehensive analysis of multiple gene mutations and expressed sequences. The broad range of current DNA chip applications include the detection of pathogens, the measurement of differences in the expression of genes between different cell populations, and the analysis of genomic alterations such as sequence and copy number alterations in disease-related genes and single nucleotide polymorphisms. We present an overview of the impact of DNA chip technology on the field of molecular medicine and discuss developments that can be expected in the near future.

Animals↗

Eosinophilic alveolitis in BAL after lung transplantation.

Lung transplantation has become a therapeutic option for patients with end stage lung disease. However, outcome after transplantation is complicated by episodes of rejection and infections. Bronchoalveolar lavage is a valuable tool in monitoring patients after transplantation, since it allows the detection of pathogens. A marker specifically indicating rejection from changes in BAL fluid has not been found yet. Especially changes in differential cell count, like lymphocytosis or an increase in polymorphnuclear granulocytes, are unspecific. The role of high eosinophil levels in BAL has not been elucidated yet. We analyzed 25 BAL samples and clinical data of 4 patients who underwent lung transplantation and presented with recurrent episodes of eosinophilic alveolitis in BAL. All patients demonstrated a deterioration of clinical condition, lung function, and blood gas analysis during times of eosinophilia in BAL, compared to previous examinations. In all cases, eosinophilia in BAL was accompanied by rejection. All patients were finally treated with high doses of steroids, resulting in improvement of all parameters. Eosinophilia was not associated with significant changes in the IL-5 concentration in BAL or the pattern of IL-5 expression in BAL cells. In conclusion, eosinophilic alveolitis may indicate acute rejection in patients after lung transplantation, if other causes of eosinophilia are excluded.

Bronchoalveolar Lavage Fluid↗

Prevalence of germline mutations of hMLH1, hMSH2, hPMS1, hPMS2, and hMSH6 genes in 75 French kindreds with nonpolyposis colorectal cancer.

Hereditary nonpolyposis colorectal cancer (HNPCC) is a syndrome characterized by familial predisposition to colorectal carcinoma and extracolonic cancers of the gastrointestinal, urological, and female reproductive tracts. This dominant disorder is caused by germline defects in one of at least five DNA mismatch repair (MMR) genes: hMLH1, hMSH2, hPMS1, hPMS2, and hMSH6 (GTBP). Germline mutations of hMSH2 and hMLH1 are also frequently identified in families not fulfilling all the Amsterdam criteria, thereby demonstrating that the involvement of these genes is not confined to typical HNPCC. To evaluate the respective involvement of the various MMR genes in typical and incomplete HNPCC syndromes, we have performed an analysis of the hMLH1, hMSH2, hPMS1, hPMS2, and hMSH6 genes in a large series of French kindreds (n=75) with colorectal tumors and/or aggregation of extracolonic cancers belonging to the HNPCC spectrum. Mutational analysis has been performed in all families, without preselection for the tumor phenotype. We have detected 26 pathogenic germline mutations of the hMLH1 and hMSH2 genes and several novel variants of the hPMS1, hPMS2, and hMSH6 genes. Our data confirm that, regardless of the type of families and the tumor phenotype, hPMS1, hPMS2, and hMSH6 germline mutations are rare in familial aggregation of colorectal cancers. Furthermore, they suggest that the presence of multiple primary malignancies in a single individual and the observation of extracolonic tumors in relatives of a colorectal cancer patient should be included among the guidelines for referring patients for genetic testing.

Adaptor Proteins, Signal Transducing↗

Vaccines against traveler's diarrhoea and rotavirus disease - a review.

Diarrheal diseases constitute one of the most important health problems worldwide, preferentially in developing countries with a morbidity of estimated 5 billion and a mortality of 5 million cases per year. Children less than 5 years are particularly in danger with respect to the incidence and severity of the gastrointestinal symptoms. Travelers to developing countries are also at risk to develop diarrheal disorders; around 30-50% of them acquire so called "travelers's diarrhea" caused by bacteria, viruses or protozoa. It has been estimated that approximately 30-70% of diarrhea are due to bacteria, of which the most frequently detected enteric pathogens are non-invasive, enterotoxigenic Escherichia coli (ETEC). Their exotoxins, the heat stabile (ST) and the heat labile (LT) toxins are in large part responsible for the pathogenicity of the bacteria. About 20% of cases of traveler's diarrhea are caused by LT producing ETEC. This heat labile toxin exhibits a 80% sequence homology with cholera toxin. The presently available vaccine against cholera (Dukoral) contains inactivated Vibrio cholerae bacteria and the recombinant non-toxic B subunit of cholera toxin. Consequently, this vaccine displays also some efficacy against traveler's diarrhoea with up to 25% of travelers being protected against this disease. Rotaviruses are the leading recognized cause of diarrhoea-related illness and deaths among infants worldwide in developing and industrialized countries. Based on the high incidence of this disease two oral vaccines have been developed and will be available in Europe in 2006. Due to the impact of rotavirus diseases also in Austria vaccination against this disease has been already suggested in the Austrian vaccination schedules for infants from 6-24 weeks of age. One of the two vaccines, Rotarix, is an attenuated monovalent vaccine with a broad cross-reactivity against the most frequent serotypes. The second one, RotaTeq, is a pentavalent attenuated vaccine containing 5 human-bovine reassortants. Both vaccines display 85-98% efficacy against severe rotavirus disease and an excellent tolerability with no difference in side reactions to the placebo controls, particularly with respect to intussusceptions. With respect to increasing travel habits with infants and small children, particularly when visiting friends and relatives, vaccination against rotavirus infections will also be important in international travel.

Adult↗

Oxyleghemoglobin scavenges nitrogen monoxide and peroxynitrite: a possible role in functioning nodules?

It has been demonstrated that the NO* produced by nitric oxide synthase or by the reduction of nitrite by nitrate reductase plays an important role in plants' defense against microbial pathogens. The detection of nitrosyl Lb in nodules strongly suggests that NO* is also formed in functional nodules. Moreover, NO* may react with superoxide (which has been shown to be produced in nodules by various processes), leading to the formation of peroxynitrite. We have determined the second-order rate constants of the reactions of soybean oxyleghemoglobin with nitrogen monoxide and peroxynitrite. At pH 7.3 and 20 degrees C, the values are on the order of 10(8) and 10(4) M-1 s-1, respectively. In the presence of physiological amounts of CO2 (1.2 mM), the second-order rate constant of the reaction of oxyleghemoglobin peroxynitrite is even larger (10(5) M-1 s-1). The results presented here clearly show that oxyleghemoglobin is able to scavenge any NO* and peroxynitrite formed in functional nodules. This may help to stop NO* triggering a plant defense reaction.

Free Radical Scavengers↗

Respiratory pathogens in dental plaque of hospitalized patients with chronic lung diseases.

Bacterial cultivation studies have shown that dental plaque is a reservoir for respiratory pathogens in intensive care unit patients and in elderly who are debilitated, hospitalized or in a nursing home, placing them at risk of bacterial pneumonia. No information is available, however, concerning dental plaque as a reservoir of putative respiratory pathogens in hospitalized patients with chronic lung diseases. Supragingival plaque colonization of 34 hospitalized chronic lung-diseased Romanian citizens, excluding those with tuberculosis and less than 20 teeth, was therefore assessed by checkerboard DNA-DNA hybridization using a selected panel of whole genomic DNA probes produced from eight respiratory pathogens and eight oral pathogens. Thirty-one lung-healthy dental outpatients served as reference population. Respiratory pathogens were detected in plaque from 29 of the 34 (85.3%) hospitalized patients and 12 of the 31 (38.7%) reference population subjects. Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, and Enterobacter cloacae occurred significantly (p<0.05) more frequent among the hospitalized patients. Hospitalized chronic lung-diseased patients harbored in their supragingival plaque samples bacteria known to cause nosocomial pneumonia significantly (p<0.001) more frequent than lung-healthy dental outpatients. Our results indicate that dental plaque in patients with chronic lung diseases often serves as a reservoir of bacteria known to cause nosocomial pneumonia in susceptible individuals.

Adult↗

A case of lung transplantation following Mycoplasma pneumoniae infection.

Reported here is a case of severe necrotizing pneumonia following Mycoplasma pneumoniae infection that occurred in a 55-year-old man. The histological changes of lung parenchyma included granulomas and bronchiolitis obliterans. Mycoplasma infection was diagnosed by repeated antibody determination (complement fixation test) and confirmed using the polymerase chain reaction to detect the pathogen from a tracheal aspirate. Prior to this episode of pneumonia, the patient had been healthy, except for Reiter's disease that had been diagnosed 18 years previously. In addition to severe pulmonary involvement, the patient developed rhabdomyolysis with subsequent acute renal failure, Stevens-Johnson syndrome, biochemical pancreatitis, severe anemia, and an effusion of the right knee. Contrary to the symptoms of pulmonary disease, all of the extrapulmonary manifestations except anemia were transient. Due to persistent respiratory insufficiency and long-term failure to wean the patient from a respirator, a lung transplantation was performed. Five weeks after transplantation the patient died as a result of intrapulmonary hemorrhage. To the best of our knowledge, this is the first report of pneumonia due to Mycoplasma pneumoniae leading to lung transplantation. Furthermore, the multiple extrapulmonary manifestations in this case make it exceptional.

Anti-Bacterial Agents↗

Aetiology and clinical presentation of mild community-acquired bacterial pneumonia.

A prospective study was initiated to analyse the bacterial aetiology and clinical picture of mild community-acquired pneumonia in Slovenia using the previously described Pneumonia Severity Index. Radiographically confirmed cases of pneumonia in patients treated with oral antibiotics in seven study centres were included. An aetiological diagnosis was attempted using culture of blood and sputum, urinary antigen testing for Streptococcus pneumoniae and Legionella pneumophila, and antibody testing for Mycoplasma pneumoniae, Chlamydia pneumoniae, and Legionella pneumophila in paired serum samples. One hundred thirteen patients were evaluable for clinical presentation and 109 for aetiological diagnosis. At least one pathogen was detected in 62.4% patients. The most common causative agents were Mycoplasma pneumoniae in 24.8%, Chlamydia pneumoniae in 21.1%, and Streptococcus pneumoniae in 13.8% of patients. Dual infection was detected in 8.3% of patients. Most patients suffered from cough, fatigue, and fever. Patients with atypical aetiology of pneumonia differed from those with typical bacterial pneumonia or pneumonia of unknown aetiology in age, presence of dyspnea, and bronchial breathing on lung auscultation. Patients with pneumococcal, chlamydial, and mycoplasmal infections differed in age, risk class, presence of dyspnea, bronchial breathing, and proteinuria. There was an overlap of other clinical symptoms, underlying conditions, and laboratory and radiographic findings among the groups of patients classified by aetiology. Since patients with mild community-acquired pneumonia exhibit similar clinical characteristics and, moreover, since a substantial proportion of cases are attributable to atypical bacteria, broad-spectrum antibiotic treatment seems to be recommended.

Adult↗