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PubMed2006

Direct detection and kinetic analysis of covalent intermediate formation in the 4-amino-4-deoxychorismate synthase catalyzed reaction.

Chorismate-utilizing enzymes catalyze diverse reactions, providing critical physiological functions unique to plants, bacteria, fungi, and some parasites. Their absence in animals makes them excellent targets for antimicrobials and herbicides. 4-Amino-4-deoxychorismate synthase (ADCS) catalyzes the first step in folate biosynthsis and shares a common core mechanism with isochorismate synthase (IS) and anthranilate synthase (AS), in which nucleophile addition at C2 initiates these reactions. Evidence was presented previously [He, Z., Stigers Lavoie, K. D., Bartlett, P. A., and Toney, M. D. (2004) J. Am. Chem. Soc. 126, 2378-2385] that K274 is the nucleophile in ADCS, implying formation of a covalent intermediate. Herein, we report the direct detection of this covalent intermediate formed in ADCS-catalyzed reactions by ESI-MS. Difference spectra show the covalent intermediate has an absorption maximum at 310 nm. This was used to study the pre-steady-state kinetics of covalent intermediate formation under various conditions. Additionally, E258 in ADCS was shown to be critical to formation of the covalent intermediate by acting as a general acid catalyst for loss of the C4 hydroxyl group. The E258A/D mutants both exhibit very low activity. Acetate is a poor chemical rescue agent for E258D but an excellent one for E258A, with a 20000-fold and 3000-fold rate increase for Gln-dependent and NH(4)(+)-dependent activities, respectively. Lastly, A213 in IS (structurally homologous to K274 in ADCS) was changed to lysine in an attempt to convert IS to an ADCS-like enzyme. HPLC studies support the formation of a covalent intermediate with this mutant.

Carbon-Nitrogen Ligases↗
PubMed2006

Direct detection of bacterial biofilms on the middle-ear mucosa of children with chronic otitis media.

CONTEXT: Chronic otitis media (OM) is a common pediatric infectious disease. Previous studies demonstrating that metabolically active bacteria exist in culture-negative pediatric middle-ear effusions and that experimental infection with Haemophilus influenzae in the chinchilla model of otitis media results in the formation of adherent mucosal biofilms suggest that chronic OM may result from a mucosal biofilm infection. OBJECTIVE: To test the hypothesis that chronic OM in humans is biofilm-related. DESIGN, SETTING, AND PATIENTS: Middle-ear mucosa (MEM) biopsy specimens were obtained from 26 children (mean age, 2.5 [range, 0.5-14] years) undergoing tympanostomy tube placement for treatment of otitis media with effusion (OME) and recurrent OM and were analyzed using microbiological culture, polymerase chain reaction (PCR)-based diagnostics, direct microscopic examination, fluorescence in situ hybridization, and immunostaining. Uninfected (control) MEM specimens were obtained from 3 children and 5 adults undergoing cochlear implantation. Patients were enrolled between February 2004 and April 2005 from a single US tertiary referral otolaryngology practice. MAIN OUTCOME MEASURES: Confocal laser scanning microscopic (CLSM) images were obtained from MEM biopsy specimens and were evaluated for biofilm morphology using generic stains and species-specific probes for H influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis. Effusions, when present, were evaluated by PCR and culture for evidence of pathogen-specific nucleic acid sequences and bacterial growth, respectively. RESULTS: Of the 26 children undergoing tympanostomy tube placement, 13 (50%) had OME, 20 (77%) had recurrent OM, and 7 (27%) had both diagnoses; 27 of 52 (52%) of the ears had effusions, 24 of 24 effusions were PCR-positive for at least 1 OM pathogen, and 6 (22%) of 27 effusions were culture-positive for any pathogen. Mucosal biofilms were visualized by CLSM on 46 (92%) of 50 MEM specimens from children with OME and recurrent OM using generic and pathogen-specific probes. Biofilms were not observed on 8 control MEM specimens obtained from the patients undergoing cochlear implantation. CONCLUSION: Direct detection of biofilms on MEM biopsy specimens from children with OME and recurrent OM supports the hypothesis that these chronic middle-ear disorders are biofilm-related.

Adolescent↗
PubMed2005

Direct detection and identification of Mycobacterium tuberculosis and Mycobacterium bovis in bovine samples by a novel nested PCR assay: correlation with conventional techniques.

Mycobacterium tuberculosis and M. bovis infect animals and humans. Their epidemiology in developed and developing countries differs, owing to differences in the implementation of preventive measures (World Health Organization, 1999). Identification and differentiation of these closely related mycobacterial species would help to determine the source, reservoirs of infection, and disease burden due to diverse mycobacterial pathogens. The utility of the hupB gene (Rv2986c in M. tuberculosis, or Mb3010c in M. bovis) to differentiate M. tuberculosis and M. bovis was evaluated by a PCR-restriction fragment length polymorphism (RFLP) assay with 56 characterized bovine isolates. The degree of concordance between the PCR-RFLP assay and the microbiological characterization was 99.0% (P < 0.001). A nested PCR (N-PCR) assay was developed, replacing the PCR-RFLP assay for direct detection of M. tuberculosis and M. bovis in bovine samples. The N-PCR products of M. tuberculosis and M. bovis corresponded to 116 and 89 bp, respectively. The detection limit of mycobacterial DNA by N-PCR was 50 fg, equivalent to five tubercle bacilli. M. tuberculosis and/or M. bovis was detected in 55.5% (105/189) of the samples by N-PCR, compared to 9.4% (18/189) by culture. The sensitivities of N-PCR and culture were 97.3 and 29.7, respectively, and their specificities were 22.2 and 77.7%, respectively. The percentages of animals or samples identified as infected with M. tuberculosis or M. bovis by N-PCR and culture reflected the clinical categorizations of the cattle (P of <0.05 to <0.01). Mixed infection by N-PCR was detected in 22 animals, whereas by culture mixed infection was detected in 1 animal.

Animals↗
PubMed1996

Direct detection of Brucella spp. in raw milk by PCR and reverse hybridization with 16S-23S rRNA spacer probes.

The 16S-23S rRNA spacer regions of Brucella abortus, B. melitensis, and B. suis were cloned and subcloned after PCR amplification. Sequence analysis of the inserts revealed a spacer of about 800 bp with very high ( > 99%) homology among the three species examined. Two genus-specific primer pairs, BRU-P5-BRU-P8 and BRU-P6-BRU-P7, that could be used in a nested PCR format and three genus-specific DNA probes, BRU-ICG2, BRU-ICG3, and BRU-ICG4, were deduced from this spacer. The specificity and sensitivity of both primer sets and probes were examined by testing them against a collection of 18 Brucella strains and 56 strains from other relevant taxa by using PCR and the Line Probe Assay (LiPA), respectively. A method for direct detection of Brucella spp. in 1 ml of raw milk was developed on the basis of enzymatic treatment of the milk components and subsequent PCR and LiPA hybridization. After a single PCR, sensitivities of 2.8 x 10(5) and 2.8 x 10(4) CFU/ml were obtained for detection by agarose gel electrophoresis and LiPA, respectively. Nested PCR yielded a sensitivity of 2.8 x 10(2) CFU/ml for both methods.

Animals↗
PubMed1998

Simple and direct detection of Staphylococcus aureus in milk by a tube coagulase test.

A tube coagulase test (TCT) is described as a simple and non-expensive system for detection of Staphylococcus aureus directly in milk. The procedure is characterized by mixing milk samples with rabbit citrate plasma followed by incubation at 37 degrees C for clot formation. The tube coagulase test demonstrated 91.5% accuracy, 88.5% sensitivity and 100% specificity for the direct recognition of Staph. aureus in milk samples from quarters with subclinical mastitis, when compared with plating of milk on blood agar. The TCT has the potential to detect other coagulase positive staphylococci in milk. It is concluded that TCT may be of use to veterinary practitioners with limited laboratory facilities, or to dairy farmers as a simple diagnostic test on site.

Animals↗
PubMed1997

Direct detection of potato leafroll virus in potato tubers by immunocapture and the isothermal nucleic acid amplification method NASBA.

NASBA, an isothermal amplification method for nucleic acids, was applied to the detection of RNA of potato leafroll virus (PLRV) in a single enzymatic reaction at 41 degrees C. A set of primers was selected from the coat protein open reading frame sequence of PLRV to allow amplification of viral RNA. The NASBA reaction products were visualized after electrophoresis by ethidium bromide or acridine orange staining. The specificity of the amplification products was validated by Northern blot analysis with a PLRV-specific 32P-labelled oligonucleotide probe. The procedure was coupled to immunocapture of PLRV virions from tuber extracts by immobilized antibodies in microtubes. It was possible to discriminate readily by this method between uninfected and primarily PLRV-infected potato tubers. NASBA is suitable for the direct detection of PLRV in potato tubers from primarily infected plants, offering the potential to considerably simplify the inspection of seed-potatoes for virus infection.

Animals↗
PubMed1995

Direct detection of ascorbyl radical in experimental brain injury: microdialysis and an electron spin resonance spectroscopic study.

To examine the role played by free radicals in brain injury, we performed experiments to detect radicals in the frontal cortex of rats, using electron spin resonance (ESR) and microdialysis. A dialysis probe was inserted into the frontal cortex, and spin adducts in perfusates were immediately detected by ESR. We obtained a relatively stable doublet signal, with parameters of g = 2.0057 and aH = 0.17 mT. This signal corresponded with that of the ascorbyl radical. Ascorbyl radical in the perfusate collected from the frontal cortex was augmented by microinjection of H2O2 and FeCl2 adjacent to the dialysis probe. When the rats were challenged with cold-induced brain injury, ascorbyl radical and lactate dehydrogenase (LDH) level in the perfusate increased significantly. Pretreatment with superoxide dismutase and catalase attenuated the increase in ascorbyl radical and LDH level induced by the cold injury. Infusion of FeCl2 dissolved in perfusate caused a pronounced increase in ascorbyl radical and LDH level after the cold injury. We conclude that the direct detection of free radical formation further supports the hypothesis that free radicals play an important role in traumatic brain injury. Our findings also indicate that combined microdialysis with ESR spectroscopy is a useful in vivo method for monitoring free radical production in the brain.

Animals↗
PubMed2000

Frequent contribution of T cell clonotypes with public TCR features to the chronic response against a dominant EBV-derived epitope: application to direct detection of their molecular imprint on the human peripheral T cell repertoire.

In an attempt to provide a global picture of the TCR repertoire diversity of a chronic T cell response against a common Ag, we performed an extensive TCR analysis of cells reactive against a dominant HLA-A2-restricted EBV epitope (hereafter referred to as GLC/A2), obtained after sorting PBL or synovial fluid lymphocytes from EBV-seropositive individuals using MHC/peptide multimers. Although TCR beta-chain diversity of GLC/A2+ T cells was extensive and varied greatly from one donor to another, we identified in most cell lines several recurrent Vbeta subsets (Vbeta2, Vbeta4, and Vbeta16 positive) with highly conserved TCRbeta complementarity-determining region 3 (CDR3) length and junctional motifs, which represented from 11 to 98% (mean, 50%) of GLC/A2-reactive cells. While TCR beta-chains expressed by these subsets showed limited CDR1, CDR2, and CDR3 homology among themselves, their TCR alpha-chains comprised the same TCRAV region, thus suggesting hierarchical contribution of TCR alpha-chain vs TCR beta-chain CDR to recognition of this particular MHC/peptide complex. The common occurrence of T cell clonotypes with public TCR features within GLC/A2-specific T cells allowed their direct detection within unsorted PBL using ad hoc clonotypic primers. These results, which suggest an unexpectedly high contribution of public clonotypes to the TCR repertoire against a dominant epitope, have several implications for the follow-up and modulation of T cell-mediated immunity.

Amino Acid Motifs↗
PubMed2003

Laboratory-based diagnosis of brucellosis--a review of the literature. Part I: Techniques for direct detection and identification of Brucella spp.

Brucellosis is a world-wide re-emerging zoonosis and the most frequent laboratory-acquired bacterial infection, causing severe disease in humans with unspecific clinical signs affecting numerous organs. Contact with infected animals, ingestion of contaminated animal products and handling of Brucella isolates in laboratories are risk factors. Various other febrile illnesses, e.g. malaria, tuberculosis, typhoid fever and tularemia may present with the same symptoms. Therefore, clinical diagnosis is difficult to establish but effective therapy requires an early diagnosis. Vaccines for humans are still not commercially available. Blood culturing of Brucella is time-consuming and not reliable. Thus diagnosis is usually based on indirect serological tests, i.e. serum agglutination test, complement fixation or the Coombs test. However, these 'conventional' serological tests lack sensitivity and specificity. Hence, a combination of various tests is mandatory for a definite diagnosis. Enzyme-linked immunosorbent assays can be used for screening and confirmation of brucellosis in one step. Molecular techniques like the polymerase chain reaction and restriction fragment length polymorphism are needed to differentiate species and strains within the genus Brucella. This review will summarize advantages and disadvantages of the techniques used in clinical laboratories for direct detection and identification of Brucella spp.

Animals↗
PubMed2000

Direct detection and magnetic isolation of Chlamydia trachomatis major outer membrane protein-specific CD8+ CTLs with HLA class I tetramers.

We recently identified HLA class I-presented epitopes in the major outer membrane protein (MOMP) of Chlamydia trachomatis that elicit CTL responses in human genital tract infections. T cells possessing cytolytic activities specific for these epitopes could be detected following in vitro stimulation of peripheral blood CD8(+) T cells with peptides. In the present study we used HLA-A2 tetramers for detailed characterization of MOMP-specific CTL responses. Ex vivo tetramer analysis detected MOMP-specific T cells in the peripheral blood of infected individuals at significant frequencies (0.01-0.20% of CD8(+) T cells). After in vitro stimulation with peptides, the frequencies of MOMP peptide-specific T cells increased up to 2.34% of CD8(+) T cells in bulk cultures. In contrast, HLA-A2/MOMP tetramer-binding T cells were virtually undetectable in the peripheral blood from uninfected individuals, either ex vivo or after 3 wk of in vitro peptide stimulation of their T cells. Magnetically sorted, tetramer-bound T cells specifically lysed peptide-pulsed targets as well as C. trachomatis-infected epithelial cells with nearly 50-fold greater per cell efficiency than that of unsorted populations. This study provides conclusive evidence of in vivo induction of HLA class I-restricted CD8(+) CTL responses to C. trachomatis MOMP. Direct detection of these cells with tetramers will allow their further characterization without prior manipulation and facilitate monitoring of CTL responses during infections and in immunization trials with MOMP-based vaccines.

Bacterial Outer Membrane Proteins↗
PubMed2007

Peptide-nucleic acid-modified ion-sensitive field-effect transistor-based biosensor for direct detection of DNA hybridization.

Here, we report the development of a peptide-nucleic acid (PNA)-modified ion-sensitive field-effect transistor (IS-FET)-based biosensor that takes advantage of the change in the surface potential upon hybridization of a negatively charged DNA. PNA was immobilized on a silicon nitride gate insulator by an addition reaction between a maleimide group introduced on the gate surface, the succinimide group of N-(6-maleimidocaproyloxy) succinimide, and the thiol group of the terminal cysteine in PNA. The surface was characterized after each step of the reaction by X-ray photoelectron spectroscopy analysis, and the kinetic analysis of the hybridization events was assessed by surface plasmon resonance. In addition, we measured the -potential before and after PNA-DNA hybridization in the presence of counterions to investigate the change in surface charge density at the surface-solution interface within the order of the Debye length. On the basis of the zeta-potential, the surface charge density, DeltaQ, calculated using the Grahame equation was approximately 4.0 x 10(-3) C/m2 and the estimated number of hybridized molecules was at least 1.7 x 10(11)/cm2. The I-V characteristics revealed that the PNA-DNA duplexes induce a positive shift in the threshold voltage, VT, and a decrease in the saturated drain current, ID. These results demonstrate that direct detection of DNA hybridization should be possible using a PNA-modified IS-FET-based biosensor. PNA is particularly advantageous for this system because it enables highly specific and selective binding at low ionic strength.

Base Sequence↗
PubMedDate not supplied

Use of the polymerase chain reaction for the specific and direct detection of Clostridium difficile in human feces.

The polymerase chain reaction was used for the detection of Clostridium difficile, the etiologic agent of antibiotic-associated colitis. An upstream primer identical to a coding region (segment I) of the C. difficile 16S rRNA gene and a downstream primer complementary to a highly conserved region of eubacterial 16S rRNA served to amplify a targeted 270-base-pair fragment of genomic DNA. This technique allowed the detection of as few as 10 C. difficile organisms among 10(6) Escherichia coli bacteria. This level of sensitivity represents a 100-fold increase over that of conventional anaerobic culture. C. difficile was detected in DNA extracted directly from the stools of 23 patients with antibiotic-associated colitis and from those of four patients with diarrhea whose stools had been negative for C. difficile when assessed in a cytotoxicity assay. No amplification products were found in the stools of asymptomatic patients. When detected in stools of symptomatic patients, amplification products of C. difficile were confirmed by Southern blotting with a nonradioactive, horseradish peroxidase-catalyzed, chemiluminescent probing system in which biotin-labeled oligonucleotides were used. This system discriminates between C. difficile and similar organisms, such as Clostridium sordellii and Clostridium bifermentans. The combination of the polymerase chain reaction with enzyme-linked probing results in a faster and more sensitive assay for C. difficile than standard culture.

Base Sequence↗
PubMed2002

Evaluation of the BDProbeTec ET DTB assay(1) for direct detection of Mycobacterium tuberculosis complex from clinical samples.

The purpose of this study was to evaluate the ability of BDProbeTec ET DTB system to detect Mycobacterium tuberculosis complex directly from clinical specimens. A total of 628 specimens (553 respiratory and 75 non respiratory specimens) were collected from 478 patients. These samples were tested with the BDProbeTec ET DTB assay and results were compared with acid fast microscopy and culture. Sixty eight out of 77 culture positive M. tuberculosis complex samples were detected with overall sensitivity and specificity of 89.5% and 98.2% respectively. Overall sensitivity was 100% in smear positive samples and 79% in smear negative samples. After resolution of discrepant results, sensitivity and specificity for respiratory samples were 91.6% and 98.7% respectively. BDProbeTec ET DTB assay demonstrated to be a rapid, sensitive and specific method for detection of M. tuberculosis complex.

Bacteriological Techniques↗
PubMed1996

Direct detection of Mycobacterium tuberculosis in respiratory samples from patients in Scandinavia by polymerase chain reaction.

OBJECTIVE: To investigate the use of DNA amplification by the polymerase chain reaction (PCR) for the detection of Mycobacterium tuberculosis directly in human respiratory specimens. METHODS: The PCR assay employed was the Amplicor M. tuberculosis Test (Roche Diagnostics, Switzerland), which uses the 16S rDNA as the target template. Nine hundred and sixty samples from 741 patients in two clinical microbiology laboratories in Norway and Sweden were processed by routine culture analysis and PCR. RESULTS: Of the 56 specimens containing cultivatable M. tuberculosis, 49 (87.5%) were detected by PCR. Among the 904 culture-negative specimens, 897 samples were negative also by PCR and seven (0.8%) were positive by PCR. In comparison with culture, the sensitivity, specificity, and positive and negative predictive values of PCR were 91.7%, 99.6%, 94.2% and 99.4% for laboratory 1 and 80.0%, 98.7%, 76.2% and 99.0% for laboratory 2, respectively. For both laboratories combined the values were 87.5%, 99.2%, 87.5% and 99.2%. CONCLUSIONS: These results indicate that multiple (two or three) respiratory samples from each patients should be tested, to allow sufficient accuracy in detecting M. tuberculosis in the specimens. Still, the labor-intensive format of this test necessitates strong clinical indications and patient prioritization to provide a service feasible within the current limits of routine laboratories.

Journal Article↗
PubMed1994

Evaluation of an oligonucleotide probe and an immunological test for direct detection of toxigenic Clostridium difficile in stool samples.

A 33 basepair oligonucleotide probe, designed from the sequence of the Clostridium difficile toxin B gene, was evaluated for its ability to detect toxigenic Clostridium difficile directly in stool samples, without culture or DNA isolation. Two different labelling techniques were investigated: radiolabelling and digoxigenin-labelling. One hundred ninety-six stools were tested, with a good correlation (96%) obtained between the oligonucleotide probe and the gold standard, the cytotoxicity tissue culture assay. The sensitivity and specificity were 83% and 100%, respectively. In parallel, a new commercially available enzyme immunoassay for the detection of Clostridium difficile toxin A in stool specimens was investigated. In 162 samples tested, a sensitivity of 80% and a specificity of 98% were obtained.

Animals↗
PubMed1998

Comparative evaluation of two commercial assays for direct detection of Mycobacterium tuberculosis in respiratory specimens.

Two commercial systems for the amplification and detection of Mycobacterium tuberculosis directly from respiratory samples were compared. The Roche Cobas Amplicor MTB Test and the Roche manual Amplicor MTB Test (Roche Diagnostic Systems, USA) were applied to 755 decontaminated respiratory specimens collected from 470 patients. Results were compared with those of acid-fast staining and culture. A total of 251 specimens were collected from 156 patients diagnosed with pulmonary tuberculosis, including 28 specimens corresponding to 13 patients that were receiving antituberculous treatment. Given the overall positivity rate of 33.2% (251/755), the sensitivity, specificity, and positive and negative predictive values were 92.4, 100, 100, and 96.5%, respectively, for the Cobas Amplicor MTB Test and 90.8, 100, 100, and 95.8%, respectively, for the Amplicor MTB Test. For 204 (81.3%) smear positive specimens and 47 (19.7%) smear negative specimens, the sensitivity values were 100 and 59.6%, respectively, for the Cobas Amplicor MTB Test and 100 and 51%, respectively, for the Amplicor MTB Test. There were no statistically significant differences in sensitivity or specificity between the two assays and culture (p>0.05). The overall results of both assays were concordant for 99.5% of the samples. It is concluded that although both nucleic acid amplification methods are rapid and specific for the detection of Mycobacterium tuberculosis complex in respiratory specimens, the Cobas Amplicor MTB Test appears to be slightly more sensitive than the Amplicor MTB Test when smear negative specimens are investigated.

Evaluation Studies as Topic↗
PubMed1988

A new chromogenic assay for direct detection of staphylocoagulase.

Tube test for detection of staphylococcal coagulase, despite of many disadvantages, is commonly used in clinical microbiology for identification of Staphylococcus aureus. In this paper a new chromogenic method for detection of the coagulase directly in staphylococcal cultures is described and evaluated on the basis of a comparison with the standard tube assay. The chromogenic assay appeared to be as sensitive as the tube test but results of the former one can be read in a few hours without any apparatus.

Chromogenic Compounds↗
PubMed1998

Reverse transcription-polymerase chain reaction (RT-PCR) for direct detection of cucumber mosaic virus (CMV) in gladiolus.

A diagnostic method based on Reverse Transcription-Polymerase Chain Reaction (RT-PCR) was performed for detection of CMV genome directly in crude extracts of both healthy and infected gladiolus tissue using primers from the conserved sequences of CMV RNA-3. RT-PCR resulted in the amplification of 540 bp long fragment of CMV coat protein gene (CMV-CP), as expected in most of the plant parts of infected gladiolus samples. Positive signals in Southern hybridization of amplified fragments with cloned CMV-CP cDNA probe also confirmed the presence of CMV genome in gladiolus.

Animals↗